Publications HAL du labo/EPI 37751;1002097 de la collection INRAE

2025

Journal articles

titre
A deletion in a photosynthesis-related gene (PpPSAK) determines the anthocyanin accumulation in the mesocarp of French blood-flesh peaches
auteur
Laure Heurtevin, Carole Confolent, Patrick Lambert, Sylvie Bureau, Thierry Pascal, Zhijun Shen, Bénédicte Quilot-Turion
article
Plant Science, 2025, 359, pp.112572. ⟨10.1016/j.plantsci.2025.112572⟩
resume
Accumulation of anthocyanin pigments is a primary determinant of fruit quality in peach (Prunus persica L. Batsch). The recessive blood-flesh trait (bf), identified in French cultivars was first mapped on chromosome 4. However, the underlying gene is yet to be identified. In this study, the genetic, molecular and transcriptional bases of the bf trait were investigated. Blood-flesh cultivars showed high levels of cyanidin-3-glucoside and cyanidin-3-rutinoside in the fruit mesocarp about 45-60 days after anthesis. Fine mapping coupled to a positional cloning strategy mapped the bf locus to an 80-kb interval on peach linkage group 4. The sequence polymorphism analysis of genes present in this interval allowed the identification of only one candidate gene for bf a deletion of 21-bp in exon 3 of a PSAK-like gene (PSAK:photosystem I subunit K). A specific marker for the deletion was developed and validated in different genetic backgrounds. An expression study of PpPSAK as well as analysis of structural, regulatory and photosynthesis related genes was performed to compare cultivars with blood-flesh (Montarsa) and without blood-flesh (S11332) during fruit development from 60 days after blooming until fruit maturity. Differently expressed of PpPSAK in the flesh of bf fruit was correlated with expression of anthocyanin biosynthesis structural genes. A protein-protein interaction study was performed and is presented with an open discussion on functional pathways in peach.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-05108290/file/Heurtevin%20etal_PlantScience_2025.pdf BibTex
titre
Multi-environment GWAS uncovers markers associated to biotic stress response and genotype-by-environment interactions in stone fruit trees
auteur
Marie Serrie, Vincent Segura, Alain Blanc, Laurent Brun, Frédéric Gilles, Laure Heurtevin, Mathilde Le Pans, Véronique Signoret, Sabrina Viret, Jean-Marc Audergon, Bénédicte Quilot-Turion, Morgane Roth, Naïma Dlalah
article
Horticulture research, 2025, 12 (7), ⟨10.1093/hr/uhaf088⟩
resume
While breeding for improved immunity is essential to achieve sustainable fruit production, it also requires to account for genotype-by-environment interactions (G × E), which still represent a major challenge. To tackle this issue, we conducted a comprehensive study to identify genetic markers with main and environment-specific effects on pest and disease response in peach (Prunus persica) and apricot (Prunus armeniaca). Leveraging multienvironment trials (MET), we assessed the genetic architecture of resistance and tolerance to seven major pests and diseases through visual scoring of symptoms in naturally infected core collections, repeated within and between years and sites. We applied a series of genome-wide association models (GWAS) to both maximum of symptom severity and kinetic disease progression. These analyses lead to the identification of environment-shared quantitative trait loci (QTLs), environment-specific QTLs, and interactive QTLs with antagonist or differential effects across environments. We mapped 60 high-confidence QTLs encompassing a total of 87 candidate genes involved in both basal and host-specific responses, mostly consisting of the Leucine-Rich Repeat Containing Receptors (LRR-CRs) gene family. The most promising disease resistance candidate genes were found for peach leaf curl on LG4 and for apricot and peach rust on LG2 and LG4. These findings underscore the critical role of G × E in shaping the phenotypic response to biotic pressure, especially for blossom blight. Last, models including dominance effects revealed 123 specific QTLs, emphasizing the significance of non-additive genetic effects, therefore warranting further investigation. These insights will support the development of marker-assisted selection to improve the immunity of Prunus varieties in diverse environmental conditions.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genomic prediction in Persian walnut: Optimization levers according to genetic architecture of complex traits
auteur
Anthony Bernard, Juliette Bénéjam, Morgane Roth, Fabrice Lheureux, Elisabeth Dirlewanger
article
Plant Genome, 2025, 18 (2), pp.e70047. ⟨10.1002/tpg2.70047⟩
resume

Persian walnut (Juglans regia L.) is a widespread cultivated nut tree species in temperate regions. Advances in genomic tools, such as the high-density Axiom J. regia 700K single nucleotide polymorphism (SNP) genotyping array, enable the exploration of genomic prediction (GP) for this crop. This study is the first to evaluate GP accuracy and several influencing factors in walnut for traits related to phenology and nut quality. A core-collection of 170 accessions was phenotyped for 25 traits over 1 or 2 years. Highly heritable traits, such as budbreak date and female flowering date, were predicted with high accuracy (∼0.75) using ridge regression best linear unbiased prediction (rrBLUP). Three key factors influencing GP performance were examined: marker density, prediction model, and training set size. Selecting the top 1% of 364,275 SNPs based on their variance (∼3600 SNPs) was sufficient to achieve accurate predictions. Bayesian models slightly improved prediction accuracy for some traits when using this reduced SNP set, but rrBLUP provided robust results, balancing accuracy, simplicity, and computational efficiency. Training population size also influenced accuracy, with a subset comprising 50% of the population still yielding reliable predictions. Optimization of training set was assessed using coefficient of determination mean, prediction error variance mean, and mean relatedness (MeanRel) parameters, with MeanRel performing best for shell traits. However, incorporating SNPs identified in genome-wide association study into the prediction models did not enhance accuracy. In summary, this study demonstrates the feasibility and potential of GPs for walnut breeding programs using a core-collection, offering valuable insights for optimizing GP approaches in this crop.

typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-05068423/file/The%20Plant%20Genome%20-%202025%20-%20Bernard%20-%20Genomic%20prediction%20in%20Persian%20walnut%20Optimization%20levers%20according%20to%20genetic.pdf BibTex
titre
Genome-wide association studies to assess genetic factors controlling cucumber resistance to CABYV and CMV in crop fields and the attractiveness for their Aphis gossypii vector
auteur
Séverine Monnot, Anaïs Ravineau, Eva Coindre, Pascale Mistral, Karine Leyre, Joel Chadœuf, Melissa Cantet, Nathalie Boissot
article
Horticulture research, 2025, 12 (5), ⟨10.1093/hr/uhaf016⟩
resume
Cucumber crops face high pressure from pathogens, including various viral species. Mapping quantitative trait loci (QTL) for vegetable resistance to viruses has primarily been conducted after mechanical inoculation in controlled environments, but not in crop field conditions. Moreover, viruses that cannot be mechanically inoculated, e.g. the cucurbit aphid-borne yellows virus (CABYV), have been overlooked in resistance studies. Here, we aimed to identify QTLs reducing epidemics of two prevalent cucumber viruses: CABYV and the cucumber mosaic virus (CMV). We evaluated the resistance of 256 elite cucumber lines and landraces in crop field conditions by screening for the presence of both viruses six-times during the season. We mapped twelve QTLs reducing CABYV epidemics and seven QTLs reducing CMV epidemics by combining multiloci genome-wide association studies and local score approach analyses. We also examined the attractiveness of this cucumber panel for Aphis gossypii, a major cucumber virus vector. We identified five QTLs that reduced the attractiveness, including one co-localizing with a QTL reducing CABYV epidemics. Interestingly, some accessions deemed CMV-resistant after mechanical inoculation in controlled environments showed high infection rates in crop field conditions. Only one QTL for CMV resistance was detected in both conditions, indicating that these phenotypes are regulated by independent QTLs. Local linkage disequilibrium study findings suggested that certain QTLs reducing epidemics were introduced early into elite lines through serendipity or selection. QTLs could be pyramided with other low-effect QTLs through genomic selection to obtain cucumber cultivars with enhanced field resistance to viruses.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-05038538/file/Monnot_horticultureResearch_2025.pdf BibTex
titre
Genetic diversity assessment towards core collection construction of Moroccan apricot (Prunus armeniaca L.) germplasm using genomic SSR markers
auteur
Jamal Ayour, Imane Elateri, Mohammed Alami, Hasnaâ Harrak, Mohamed Alfeddy, Jean-Marc Audergon, Catherine M.G.C. Renard, Mohamed Benichou
article
South African Journal of Botany, 2025, 180, pp.21-34. ⟨10.1016/j.sajb.2025.02.038⟩
resume
Strengthening the study of genetic diversity and population structure is crucial for the conservation and sustainable use of plant genetic resources. This study evaluated the genetic diversity and population structure of Moroccan apricot germplasm based on the geographical origins of 92 accessions and their agroecosystem conditions using 21 microsatellite markers. The analysis revealed high genetic diversity within each geographical origin (94%) and lower diversity between the 10 studied regions (6%). A total of 120 alleles were identified, averaging 5.71 alleles per locus, with BPPCT038 and BPPCT001 being, respectively, the most informative (11 alleles) and the least informative (2 alleles) primers. The genetic structure analysis divided the germplasm into two main populations: a predominant group linked to the Delpatriarca variety and a smaller and less diverse group associated with the Canino variety. Low genetic differentiation and significant gene flow between these populations, influenced by pollen dispersal, overlapping geographical origins, and human intervention, contributed to the observed structure of two gene pools. These findings simplify the management of Moroccan apricot genetic resources and highlight a population structure that could serve as a core collection summarising the diversity of Moroccan apricot germplasm.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Molecular polymorphisms of the nuclear and chloroplast genomes among African melon germplasms reveal abundant and unique genetic diversity, especially in Sudan
auteur
Odirichi Nnennaya Imoh, Gentaro Shigita, Mitsuhiro Sugiyama, Tran Phuong Dung, Katsunori Tanaka, Mami Takahashi, Kazusa Nishimura, Yuki Monden, Hidetaka Nishida, Mashaer Goda, Michel Pitrat, Kenji Kato
article
Annals of Botany, 2025, XX:, pp.1-15. ⟨10.1093/aob/mcaf028⟩
resume
Background and Aims Africa is rich in wild species of Cucumis and is considered one of the places of origin of melon. However, our knowledge of African melon is limited, and genetic studies using melon germplasms with wide geographical coverage are required. Here, we analysed the genetic structure of African melons, with emphasis on Sudan. Methods Ninety-seven accessions of African melon were examined along with 77 reference accessions representing Asian melon and major horticultural groups. Molecular polymorphisms in the nuclear and chloroplast genomes were investigated using 12 RAPD, 7 SSR and 3 SNP markers. Horticultural traits, including seed size, were measured for 46 accessions, mainly from Sudan. Key Results African melons were divided into large and small seed-types based on seed length: large seed-type from Northern Africa and small seed-type from Western and Southern Africa. Both seed types are common in Sudan. Molecular genetic diversity in these geographical populations was as high as in India, the Asian centre of melon domestication. Large seed-types from Northern Africa were assigned to Pop4 by structure analysis and had Ib cytoplasm in common with Cantalupensis, Inodorus and Flexuosus. Small seed-types were highly diversified and geographically differentiated; specifically, Pop1 with Ia cytoplasm in Southern Africa and South Asia, Pop2 with Ia in East Asia, including Conomon and Makuwa, and Pop3 with Ia or Ic in Africa. Sudanese small seed-types were grouped in Pop3, while their cytoplasm type was a mixture of Ia and Ic. Sudanese Tibish had Ic cytoplasm, which was unique in Africa, common in Western Africa and Sudan, and also found in wild or feral types. Conclusions Melon of Ic lineage, including Tibish, originated from wild melon in the ‘western Sudan region’, and independently of melon with Ia or Ib cytoplasm, which originated in Asia. This clearly indicates the polyphyletic origin of melon.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-05080109/file/Nnennaya%20Imoh_annalsofbotany_2025.pdf BibTex
titre
New QTLs involved in the control of stigma position in tomato
auteur
Alessandro Riccini, Fabrizio Olivieri, Barbara Farinon, Frédérique Bitton, Isidore Diouf, Yolande Carretero, Salvador Soler, Maria del Rosario Figàs, Jaime Prohens, Antonio Jose Monforte, Antonio Granell, Mathilde Causse, Andrea Mazzucato
article
BMC Plant Biology, 2025, 25 (1), pp.423. ⟨10.1186/s12870-025-06449-2⟩
resume
Background: Tomato mating systems were strongly affected by domestication events. Mutations disrupting self-incompatibility paralleled by changes retracting the stigma position (SP) within the staminal cone conferred strict autogamy and self-fertility to the cultivated forms. Although major genes affecting these changes have been identified, SP control in domesticated forms that retain a constitutive or heat-inducible noninserted SP needs elucidation. To widen the possibility of identifying SP genetic determinants, we analyzed the trait in four populations (two germplasm collections, a multiparental recombinant inbred and a biparental progeny) under different environmental conditions (normal and heat stressed). Results: Overall, 37 markers significantly associated with the trait were identified. Several colocalizations were found, both among regions first reported in this work and among them and previously reported positions. This finding supported the reliability of the analysis. Three such regions, in the long arms of chromosomes 1, 8 and 11, were validated in an independent segregating population, and candidate genes in confidence intervals were identified among transcription factors and hormone-, stress- and cell wall-related genes. Conclusion: Overall, this work supported the hypothesis that the SP phenotype is controlled by different key genes in tomato, paving the way for the identification of novel players and novel mechanisms involved in the regulation of herkogamy.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-05042790/file/riccini_bmcplantBiology.pdf BibTex
titre
Organization of plant Biological Resource Centers for research in France: History, evolution and current status
auteur
Valerie Bergheaud, Jean-Marc Audergon, Arnaud Bellec, Anne Delaunay, Jérôme Duminil, Stéphane Dussert, Florence Esnault, Emmanuel Geoffriau, Brigitte Gouesnard, Christophe Jenny, Alain Label, Philippe Lashermes, Najate Maghnaoui, Cécile Marchal, Franciane Nuissier, Nilda Paulo-De-La-Réberdiere, Aurélia Priet, Valérie Riecau, Paule Térès, Anne-Françoise Adam-Blondon
article
Genetic Resources, 2025, Plant Genetic Resources. Ex situ conservation in Europe (S2), pp.78-90. ⟨10.46265/genresj.aszo2413⟩
resume
Since their inception, the French academic organizations dedicated to agricultural research have developed plant collections in genebanks, often within a public-private framework, to support the study of plant traits and the development of new improved varieties. In addition, since the 2000s, a centre for genomic resources has also been established in France. Over the last 20 years, this decentralized system, consisting of the academic genebanks and the centre for genomic resources, has been supported by a national coordination structure. The objectives were to align the network activities with the framework proposed by the Organisation for Economic Co-operation and Development (OECD) for Biological Resource Centres and to foster collaboration with other national stakeholders involved in the conservation and characterization of plant genetic resources (PGR). In 2015, the network was named BRC4Plants and become part of the French National Research Infrastructure RARe (www.agrobrc-rare.org), supported by the French Ministry of Research. This paper describes BRC4Plants, its users, services and cross-cutting activities. We also highlight its relations with its national and international stakeholders involved in the conservation and characterization of PGRs. BRC4Plants aims to be a key player in addressing societal and research challenges regarding agroecology, climate change mitigation and healthy food systems.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04991099/file/Organization_of_plant_Biological_Resource_Centers_.pdf BibTex
titre
Identification and expression of the peach TNL RMia genes for the resistance to the root-knot nematode Meloidogyne incognita
auteur
Henri Duval, Laure Heurtevin, Naïma Dlalah, Claire Caravel, Caroline Callot, Cyril van Ghelder
article
Scientia Horticulturae, 2025, 343, pp.114081. ⟨10.1016/j.scienta.2025.114081⟩
resume
Root-Knot Nematodes (RKN) are major pests for world agriculture. As RKN are polyphagous endoparasites, present in various climates and able to multiply rapidly, the quest to discover new natural resistances in plants is essential. In Prunus species, several major resistance genes to RKN that belong to the NLR family, have been detected in recent years. In Peach, the RMia gene, which confers resistance to the RKN Meloidogyne incognita, M. arenaria, and M. ethiopica, was localized on the chromosome 2. In this study, we used short-and long-read sequencing technologies to identify the RMia gene in two independent RKN-resistant peach varieties. We characterized three candidate genes and studied their expression profile upon RKN infection. Our study identified and characterized these candidates that are most likely involved in the RKN resistance. Ultimately, we developed new molecular markers associated to this resistance that can be used in breeding programs.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-05036400/file/duval_scientiaeHorticultarae_2025.pdf BibTex
titre
Nanopore adaptive sampling to identify the NLR gene family in melon (Cucumis melo L.)
auteur
Javier Belinchon-Moreno, Aurélie Berard, Aurélie Canaguier, Véronique Chovelon, Corinne Cruaud, Stéfan Engelen, Rafael Feriche-Linares, Isabelle Le-Clainche, William Marande, Vincent Rittener-Ruff, Jacques Lagnel, Damien Hinsinger, Nathalie Boissot, Patricia Faivre-Rampant
article
BMC Genomics, 2025, 26, ⟨10.1186/s12864-025-11295-5⟩
resume
Background Nanopore adaptive sampling (NAS) offers a promising approach for assessing genetic diversity in targeted genomic regions. Here we designed and validated an experiment to enrich a set of resistance genes in several melon cultivars as a proof of concept.
Results

Using the same reference to guide read acceptance or rejection with NAS, we successfully and accurately reconstructed the 15 regions in two newly assembled ssp. melo genomes and in a third ssp. agrestis cultivar. We obtained fourfold enrichment regardless of the tested samples, but with some variations according to the enriched regions. The accuracy of our assembly was further confirmed by PCR in the agrestis cultivar. We discussed parameters that could influence the enrichment and accuracy of NAS generated assemblies.

Conclusions Overall, we demonstrated that NAS is a simple and efficient approach for exploring complex genomic regions, such as clusters of Nucleotide-binding site leucine-rich repeat (NLR) resistance genes. These regions are characterized by containing a high number of copy number variations, presence-absence polymorphisms and repetitive elements. These features make accurate assembly challenging but are crucial to study due to their central role in plant immunity and disease resistance. This approach facilitates resistance gene characterization in a large number of individuals, as required when breeding new cultivars suitable for the agroecological transition.

typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04957046/file/2025_Belinchon-Moreno_BMC-Genomics.pdf BibTex
titre
Publisher Correction: Crop traits and production under drought
auteur
Vincent Vadez, Alexandre Grondin, Karine Chenu, Amelia Henry, Laurent Laplaze, Emilie J. Millet, Andrea Carminati
article
Nature Reviews Earth & Environment, 2025, ⟨10.1038/s43017-024-00636-9⟩
resume
In the version of this article initially published, the name of Di He was misspelled in the peer reviewer acknowledgements section, which is now amended in the HTML and PDF versions of the article.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Assessing inter-individual genetic variability in peach sugar metabolism through reliable parameter estimation of a kinetic model
auteur
Hussein Kanso, Valentina Baldazzi, Bénédicte Quilot, Charlotte Baey, Mohamed-Mahmoud Memah
article
European Journal of Agronomy, 2025, 168, pp.127641. ⟨10.1016/j.eja.2025.127641⟩
resume
Integrating genetic information into dynamical models is crucial for understanding genotype variation and improving crop performance in the face of current agronomic and ecological constraints. Calibration over a large number of genotypes is a key step in building gene-to-phenotype models but remains challenging. We compared two strategies for calibrating an Ordinary Differential Equations (ODE) kinetic model simulating sugar accumulation during peach fruit development. In the first strategy, a Genotype-Based (GB) approach, the model was calibrated independently for each genotype, using either a Single-Objective Optimization (GBS) or a Multi-Objective Optimization (GBM) formulation. In the second strategy, a Population-Based (PB) approach, the model was calibrated for all genotypes simultaneously. The two strategies were applied to simulated data and to a real dataset from 106 peach genotypes. Results showed that the GB strategy allowed for a high goodness of fit for most genotypes, especially in the GBS formulation. However, the estimated parameters suffered from a lack of practical identifiability as independent repetitions of the estimation algorithm did not always converge to the same value for most genotypes. The PB calibration strategy overcame this issue showing a good identifiability of the population parameter values, a goodness of fit comparable to the one obtained with the GB strategy, and a good characterization of parameter variations within the progeny, which is key to assess the inter-individual genetic variability. This study demonstrates the value of the PB calibration strategy in capturing interindividual genetic variability, a critical step toward developing robust gene-to-phenotype models.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-05036459/file/Hussein%20et%20al%202025.pdf BibTex

2024

Journal articles

titre
Interdependence of plasma membrane nanoscale dynamics of a kinase and its cognate substrate underlies Arabidopsis response to viral infection
auteur
Marie-Dominique Jolivet, Anne-Flore Deroubaix, Marie Boudsocq, Nikolaj B Abel, Marion Rocher, Terezinha Robbe, Valérie Wattelet-Boyer, Jennifer Huard, Dorian Lefebvre, Yi-Ju Lu, Brad Day, Grégoire Saias, Jahed Ahmed, Valérie Cotelle, Nathalie Giovinazzo, Jean-Luc Gallois, Yasuyuki Yamaji, Sylvie German-Retana, Julien Gronnier, Thomas Ott, Sébastien Mongrand, Véronique Germain
article
eLife, 2024, 12, pp.RP90309. ⟨10.7554/eLife.90309.2⟩
resume
Plant viruses represent a risk to agricultural production and as only a few treatments exist, it is urgent to identify resistance mechanisms and factors. In plant immunity, plasma membrane (PM)-localized proteins play an essential role in sensing the extracellular threat presented by bacteria, fungi or herbivores. Viruses are intracellular pathogens and as such the role of the plant PM in detection and resistance against viruses is often overlooked. We investigated the role of the partially PM-bound Calcium-dependent protein kinase 3 (CPK3) in viral infection and we discovered that it displayed a specific ability to hamper viral propagation over CPK isoforms that are involved in immune response to extracellular pathogens. More and more evidence support that the lateral organization of PM proteins and lipids underlies signal transduction in plants. We showed here that CPK3 diffusion in the PM is reduced upon activation as well as upon viral infection and that such immobilization depended on its substrate, Remorin (REM1.2), a scaffold protein. Furthermore, we discovered that the viral infection induced a CPK3-dependent increase of REM1.2 PM diffusion. Such interdependence was also observable regarding viral propagation. This study unveils a complex relationship between a kinase and its substrate that contrasts with the commonly described co-stabilisation upon activation while it proposes a PM-based mechanism involved in decreased sensitivity to viral infection in plants.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04873172/file/CPK3_Rem_virus_nanodomain_eLife24.pdf BibTex
titre
Diversity analysis of the INRAE and IRTA almond collections from the Axiom 60K SNP almond chip
auteur
Henri Duval, F. Pérez de los Cobos, Eva Coindre, Naïma Dlalah, Ignasi Batlle, Iban Eduardo Muñoz, Pere Arús
article
Acta Horticulturae, 2024, 1406, pp.43-46. ⟨10.17660/ActaHortic.2024.1406.6⟩
resume
Following the works of the “almond genome” consortium, and the publication of the almond genome reference ‘Texas’, we developed a 60K SNPs axiom almond array as tools for almond breeders and genetic studies. From a pool of 80 resequenced varieties, a set of 60581 SNPs markers was filtered for the development of the array. These SNP were well distributed along the eight chromosomes. With this array, we genotyped 219 almond accessions available in the two collections of INRAE in Avignon and IRTA in Reus. We excluded from our statistical analysis wild and hybrid accessions and SNPs with more than 10% of missing data. At the end of the process, we had an initial matrix with 152 individuals and 54K SNPs. Analysis with the SNMF R package showed that two models with five or seven ancestral groups were most probable. The model with five groups contained 21, 14, 19, 14, 12 varieties, and the first three groups included mainly Spanish, Italian and Chinese varieties respectively, while the two other groups and the admixture group contained different origins. The kinship analysis highlighted the relationships between the varieties and we observed that the identified clusters corresponded well with origin of the countries; most notably with Italian, Chinese, Californian and Spanish varieties. The French varieties were more scattered. Our analysis showed that data provided by the axiom almond array were of good quality and could be used for genome-wide association studies (GWASs)
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Volatile emissions from almond trees and response of the almond wasp (Eurytoma amygdali) to these volatiles
auteur
Henri Duval, Anjélica Leconte, Adrien Le Navenant, Philippe Lucas, Eugénie Coutagne, Michael Staudt
article
Acta Horticulturae, 2024, 1406, pp.353-358. ⟨10.17660/ActaHortic.2024.1406.50⟩
resume
Eurytoma amygdali Enderlein, the almond wasp, is an important pest in almond orchards in southeastern France. To develop a biocontrol strategy against wasp infestations, we studied the emission of volatiles emitted by almond trees and their detection by adult almond wasps. Our approach consists in identifying and quantifying volatile organic compounds (VOCs) released by almond trees at different phenological stages using headspace technique combined with GC-MS (Gas chromatography - mass spectrometry) and PTR-ToF-MS (proton transfer reaction - time of flight - mass spectrometry). These VOCs are then tested by electroantennography (EAG) to measure their detection by the female antennae. The attractiveness for females of the best detected VOCs, tested first alone and then in simple mixtures, is currently evaluated in linear olfactometers to develop a kairomone trap.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The French project LEVEAB: remove the barriers to growing almonds in organic farming
auteur
Henri Duval, J.M. Montagnon, Philippe Lucas, J.P. Rouvier, J. Planche, Adrien Le Navenant, M. Alix, M. Berud, F. Warlop, M. Jacquot, W. Chambeyron, C. Calcet, B. Chauvin Buthaud, J.M. Thevier, F. Fraisse
article
Acta Horticulturae, 2024, 1406, pp.391-394. ⟨10.17660/ActaHortic.2024.1406.55⟩
resume
Despite strong demand, organic almond production in France is limited by pest pressure. The lack of sustainable solutions to control pests and diseases (Eurytoma, Fusicoccum, etc.) is holding back the development of the organic sector and limiting the scope for agroecological progress in conventional production. In 2021, we started the LEVEAB project, whose objectives are to propose biocontrol methods and new active ingredients, and to evaluate their impacts and limits for the cultivation of almond trees in organic orchards. The project includes 4 research pillars. The first one is to study the possibility of a mass trapping method with kairomones for the almond wasp (Eurytoma amygdali). The second pillar consists of testing the effectiveness of new molecules against almond diseases and pests in producer’s fields. The third pillar consists of evaluating certain cover crops for the management of pests and beneficial insects in almond orchards. The objectives of the last pillar are to identify the environmental factors that favor the development of the almond wasp. In the last year of the project, it is planned to transfer and communicate the innovative strategies resulting from the project to almond growers. The first results show that it would be possible to limit the pressure from almond pest and disease and to produce almond in organic orchards, in France.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Unveiling pepper immunity’s robustness to temperature shifts: insights for empowering future crops
auteur
William Billaud, Judith Hirsch, Valentin Ribaut, Lucie Tamisier, Anne Massire, Marion Szadkowski, Félicie Lopez-Lauri, Benoît Moury, Véronique Lefebvre
article
Horticulture research, 2024, 11 (11), pp.uhae239. ⟨10.1093/hr/uhae239⟩
resume
Boosting plant immunity is an effective alternative to pesticides. However, environmental variations, accentuated by climate change, can compromise immunity. The robustness of a trait corresponds to the absence (or low level) of variation in that trait in the face of an environmental change. Here, we examined two types of robustness, robustness of immunity mean and robustness of immunity variation, and proposed nine quantitative robustness estimators. We characterized the immunity of a set of accessions representative of the natural diversity of pepper (Capsicum annuum L.), to two major pathogens: the oomycete Phytophthora capsici Leon. and potato virus Y. For each pathogen, we measured the immunity of accessions in two contrasting environments in terms of temperature. For each type of robustness and each pathogen, the impact of temperature change on immunity varied between accessions. The robustness estimators proved to be complementary and differed in terms of heritability and ability to discriminate between accessions. A positive and significant correlation was observed between immunity and robustness. There was no significant relationship between the robustness of immunity to the two pathogens, but some accessions showed high immunity and robustness against both pathogens. These results justify the need to consider both immunity and robustness to environmental variations in order to select varieties adapted to current and future climate conditions. Phenotypic robustness should also be considered when assessing the “value of sustainable cultivation and use” (VSCU) of future plant varieties, particularly during the application process for protection rights granted from the European Community Plant Variety Office (CPVO).
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04676704/file/2024_Billaud_HorticultureResearch.pdf BibTex
titre
Characterisation of a major QTL for sodium accumulation in tomato grown in high salinity
auteur
Alexandre Hereil, M. Guillaume, Renaud Duboscq, Yolande Carretero, Esther Pelpoir, Frédérique Bitton, C. Giraud, R. Karlova, C. Testerink, Rebecca Stevens, Mathilde Causse
article
Plant, Cell and Environment, 2024, ⟨10.1111/pce.15082⟩
resume
Soil salinity is a serious concern for tomato culture, affecting both yield and quality parameters. Although some genes involved in tomato salt tolerance have been identified, their genetic diversity has been rarely studied. In the present study, we assessed salt tolerance‐related traits at juvenile and adult stages in a large core collection and identified salt tolerance quantitative trait loci (QTLs) by genome‐wide association study (GWAS). The results suggested that a major QTL is involved in leaf sodium accumulation at both physiological stages. We were able to identify the underlying candidate gene, coding for a well‐known sodium transporter, called SlHKT1.2 . We showed that an eQTL for the expression of this gene in roots colocalized with the above ground sodium content QTL. A polymorphism putatively responsible for its variation was identified in the gene promoter. Finally, to extend the applicability of these results, we carried out the same analysis on a test‐cross panel composed of the core collection crossed with a distant line. The results indicated that the identified QTL retained its functional impact even in a hybrid genetic context: this paves the way for its use in breeding programs aimed at improving salinity tolerance in tomato cultivars.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Within-plant genetic drift to control virus adaptation to host-resistance genes
auteur
Lucie Tamisier, Frédéric Fabre, Marion Szadkowski, Lola Chateau, Ghislaine Nemouchi, Grégory Girardot, Pauline Millot, Alain Palloix, Benoît Moury
article
PLoS Pathogens, 2024, 20 (8), pp.e1012424. ⟨10.1371/journal.ppat.1012424⟩
resume
Manipulating evolutionary forces imposed by hosts on pathogens like genetic drift and selection could avoid the emergence of virulent pathogens. For instance, increasing genetic drift could decrease the risk of pathogen adaptation through the random fixation of deleterious mutations or the elimination of favorable ones in the pathogen population. However, no experimental proof of this approach is available for a plant-pathogen system. We studied the impact of pepper ( Capsicum annuum ) lines carrying the same major resistance gene but contrasted genetic backgrounds on the evolution of Potato virus Y (PVY). The pepper lines were chosen for the contrasted levels of genetic drift (inversely related to N e , the effective population size) they exert on PVY populations, as well as for their contrasted resistance efficiency (inversely related to the initial replicative fitness, W i , of PVY in these lines). Experimental evolution was performed by serially passaging 64 PVY populations every month on six contrasted pepper lines during seven months. These lines exhibited highly divergent evolutionary trajectories, ranging from viral extinctions to replicative fitness gains. The sequencing of the PVY VPg cistron, where adaptive mutations are likely to occur, allowed linking these replicative fitness gains to parallel adaptive nonsynonymous mutations. Evolutionary trajectories were well explained by the genetic drift imposed by the host. More specifically, N e , W i and their synergistic interaction played a major role in the fate of PVY populations. When N e was low ( i . e . strong genetic drift), the final PVY replicative fitness remained close to the initial replicative fitness, whereas when N e was high ( i . e . low genetic drift), the final PVY replicative fitness was high independently of the replicative fitness of the initially inoculated virus. We show that combining a high resistance efficiency (low W i ) and a strong genetic drift (low N e ) is the best solution to increase resistance durability, that is, to avoid virus adaptation on the long term.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04670293/file/2024_Tamisier_PlosPathogens.pdf BibTex
titre
Phenotyping floral attractiveness to pollinators using volatilomics, 3D imaging, and insect monitoring
auteur
Filip Slavković, Adnane Boualem, Catherine Dogimont, Abdelhafid Bendahmane
article
Molecular Plant, 2024, 17 (8), pp.1164-1166. ⟨10.1016/j.molp.2024.06.011⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Efficacy of 2 botanical aphicides, chicoric and 3,5-dicaffeoylquinic acids, on aphids susceptible and resistant to synthetic insecticides
auteur
Myriam Siegwart, Bertrand Gauffre, Elodie Lecerf, Jean-Luc Poëssel
article
Journal of Economic Entomology, 2024, 117 (4), pp.1347-1355. ⟨10.1093/jee/toae069⟩
resume
Dicaffeoyltartaric acid (diCT) and 3,5-dicaffeoylquinic acid (3,5-diCQ) are described for their aphicidal properties on several aphid species. Intending to valorize diCT and 3,5-diCQ as biocontrol products and because of the high adaptive capacities of aphids to xenobiotics, we sought to determine the existence of adaptation first in Myzus persicae (Sulzer) (Hemiptera: Aphididae) and then other aphids. Resistance of aphids to these biopesticides could be promoted by (i) the existence of resistance to synthetic insecticides that may confer cross-resistance and (ii) the presence of these compounds in wild plants likely which may have led to pre-existing adaptation in aphids. We assessed the resistance levels to diCT and 3,5-diCQ in 7 lab strains (including some resistant to synthetic aphicides) and 7 wild populations of M. persicae using biotests. The activities of detoxification enzymes contributing to insecticide resistance were also measured. Additionally, we followed the same method to characterize susceptibility to these caffeic derivatives in wild populations of Nasonovia ribisnigri (Mosley) (Hemiptera: Aphididae), Brevicoryne brassicae (Linnaeus) (Hemiptera: Aphididae) and, Aphis craccivora (Koch) (Hemiptera: Aphididae). Our results show variability in susceptibility to diCT between populations of M. persicae, but resistance ratios (RR) were low (RR = 3.59). We found no cross-resistance between synthetic insecticides and diCT. Carboxylesterase and glutathione-S-transferase did not seem to be involved in its detoxification. A clone of A. craccivora collected from peanut, a species rich in diCT, was not susceptible to either diCT or 3,5-diCQ, suggesting a common molecular target for these 2 molecules and the existence of a high-effect resistance mechanism. These active botanical substances remain good candidates for M. persicae biocontrol in agriculture.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04661222/file/Siegwart_JEE_2024.pdf BibTex
titre
Reshaping the Primary Cell Wall: Dual Effects on Plant Resistance to Ralstonia solanacearum and Heat Stress Response
auteur
Henri Desaint, Alessandro Gigli, Adrien Belny, Hua Cassan-Wang, Yves Martinez, Fabienne Vailleau, Fabien Mounet, Samantha Vernhettes, Richard Berthomé, Marta Marchetti
article
Molecular Plant-Microbe Interactions, 2024, 37 (8), pp.619-634. ⟨10.1094/MPMI-05-24-0059-R⟩
resume
Temperature elevation drastically affects plant defense responses to Ralstonia solanacearum and inhibits the major source of resistance in Arabidopsis thaliana, which is mediated by the receptor pair RRS1-R/RPS4. In this study, we refined a previous genome-wide association (GWA) mapping analysis by using a local score approach and detected the primary cell wall CESA3 gene as a major gene involved in plant response to R. solanacearum at both 27°C and an elevated temperature, 30°C.We functionally validated CESA3 as a susceptibility gene involved in resistance to R. solanacearum at both 27 and 30°C through a reverse genetic approach. We provide evidence that the cesa3mre1 mutant enhances resistance to bacterial disease and that resistance is associated with an alteration of root cell morphology conserved at elevated temperatures. However, even by forcing the entry of the bacterium to bypass the primary cell wall barrier, the cesa3mre1 mutant still showed enhanced resistance to R. solanacearum with delayed onset of bacterial wilt symptoms.We demonstrated that the cesa3mre1 mutant had con stitutive expression of the defense-related gene VSP1, which is upregulated at elevated temperatures, and that during infection, its expression level is maintained higher than in the wild-type Col-0. In conclusion, this study reveals that alterationof the primary cell wall by mutating the cellulose synthase subunit CESA3 contributes to enhanced resistance to R. solanacearum, remaining effective under heat stress.We expect that these results will help to identify robust genetic sources of resistance to R. solanacearum in the context of global warming.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04719242/file/Desaint%20et%20al%202024.pdf BibTex
titre
Integration of QTL and transcriptome approaches for the identification of genes involved in tomato response to nitrogen deficiency
auteur
Henri Desaint, Alexandre Héreil, Javier Belinchon-Moreno, Yolande Carretero, Esther Pelpoir, Michel Pascal, Marie Brault, Doriane Dumont, François Lecompte, Patricia Laugier, Renaud Duboscq, Frederique Bitton, Mara Grumic, Christophe Giraud, Paola Ferrante, Giovanni Giuliano, Francesco Sunseri, Mathilde Causse
article
Journal of Experimental Botany, 2024, 75 (18), pp.5880-5896. ⟨10.1093/jxb/erae265⟩
resume
Optimizing plant nitrogen (N) usage and inhibiting N leaching loss in the soil–crop system is crucial to maintaining crop yield and reducing environmental pollution. This study aimed at identifying quantitative trait loci (QTLs) and differentially expressed genes (DEGs) between two N treatments in order to list candidate genes related to nitrogen-related contrasting traits in tomato varieties. We characterized a genetic diversity core-collection (CC) and a multi-parental advanced generation intercross (MAGIC) tomato population grown in a greenhouse under two nitrogen levels and assessed several N-related traits and mapped QTLs. Transcriptome response under the two N conditions was also investigated through RNA sequencing of fruit and leaves in four parents of the MAGIC population. Significant differences in response to N input reduction were observed at the phenotypic level for biomass and N-related traits. Twenty-seven QTLs were detected for three target traits (leaf N content, leaf nitrogen balance index, and petiole NO3− content), 10 and six in the low and high N condition, respectively, while 19 QTLs were identified for plasticity traits. At the transcriptome level, 4752 and 2405 DEGs were detected between the two N conditions in leaves and fruits, respectively, among which 3628 (50.6%) in leaves and 1717 (71.4%) in fruit were genotype specific. When considering all the genotypes, 1677 DEGs were shared between organs or tissues. Finally, we integrated DEG and QTL analyses to identify the most promising candidate genes. The results highlighted a complex genetic architecture of N homeostasis in tomato and novel putative genes useful for breeding tomato varieties requiring less N input.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04664082/file/2024_Desaint_JExpBot_Postprint.pdf BibTex
titre
Harbinger transposon insertion in ethylene signaling gene leads to emergence of new sexual forms in cucurbits
auteur
Hsin-Ya Huang, Siqi Zhang, Fadi Abou Choucha, Marion Verdenaud, Feng-Quan Tan, Clement Pichot, Hadi Shirazi Parsa, Filip Slavkovic, Qinghe Chen, Christelle Troadec, Fabien Marcel, Catherine Dogimont, Leandro Quadrana, Adnane Boualem, Abdelhafid Bendahmane
article
Nature Communications, 2024, 15 (1), pp.4877. ⟨10.1038/s41467-024-49250-9⟩
resume
In flowering plants, the predominant sexual morph is hermaphroditism, and the emergence of unisexuality is poorly understood. Using Cucumis melo (melon) as a model system, we explore the mechanisms driving sexual forms. We identify a spontaneous mutant exhibiting a transition from bisexual to unisexual male flower, and identify the causal mutation as a Harbinger transposon impairing the expression of Ethylene Insensitive 2 ( CmEIN2 ) gene. Genetics and transcriptomic analysis reveal a dual role of CmEIN2 in both sex determination and fruit shape formation. Upon expression of CmACS11 , EIN2 is recruited to repress the expression of the carpel inhibitor, CmWIP1 . Subsequently, EIN2 is recruited to mediate stamina inhibition. Following the sex determination phase, EIN2 promotes fruit shape elongation. Genome-wide analysis reveals that Harbinger transposon mobilization is triggered by environmental cues, and integrates preferentially in active chromatin, particularly within promoter regions. Characterization of a large collection of melon germplasm points to active transpositions in the wild, compared to cultivated accessions. Our study underscores the association between chromatin dynamics and the temporal aspects of mobile genetic element insertions, providing valuable insights into plant adaptation and crop genome evolution.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04661928/file/Ya%20Huang_natureCommunication_2024.pdf BibTex
titre
Environmental conditions associated with initial northern expansion of anatomically modern humans
auteur
Frédérik Saltré, Joël Chadoeuf, Thomas Higham, Monty Ochocki, Sebastián Block, Ellyse Bunney, Bastien Llamas, Corey Bradshaw
article
Nature Communications, 2024, 15 (1), pp.4364. ⟨10.1038/s41467-024-48762-8⟩
resume
The ability of our ancestors to switch food sources and to migrate to more favourable environments enabled the rapid global expansion of anatomically modern humans beyond Africa as early as 120,000 years ago. Whether this versatility was largely the result of environmentally determined processes or was instead dominated by cultural drivers, social structures, and interactions among different groups, is unclear. We develop a statistical approach that combines both archaeological and genetic data to infer the more-likely initial expansion routes in northern Eurasia and the Americas. We then quantify the main differences in past environmental conditions between the more-likely routes and other potential (less-likely) routes of expansion. We establish that, even though cultural drivers remain plausible at finer scales, the emergent migration corridors were predominantly constrained by a combination of regional environmental conditions, including the presence of a forest-grassland ecotone, changes in temperature and precipitation, and proximity to rivers.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04589046/file/saltre_naturecommunication_2024.pdf BibTex
titre
AtHVA22a , a plant‐specific homologue of Reep/ DP1 /Yop1 family proteins is involved in turnip mosaic virus propagation
auteur
Mingshuo Xue, Luc Sofer, Vincent Simon, Nathalie Marissal-Arvy, Mamoudou Diop, Roxane Lion, Guillaume Beucher, Amandine Bordat, Jens Tilsner, Jean‐luc Gallois, Sylvie German‐retana
article
Molecular Plant Pathology, 2024, 25, pp.e13466. ⟨10.1111/mpp.13466⟩
resume
The movement of potyviruses, the largest genus of single‐stranded, positive‐sense RNA viruses responsible for serious diseases in crops, is very complex. As potyviruses developed strategies to hijack the host secretory pathway and plasmodesmata (PD) for their transport, the goal of this study was to identify membrane and/or PD‐proteins that interact with the 6K2 protein, a potyviral protein involved in replication and cell‐to‐cell movement of turnip mosaic virus (TuMV). Using split‐ubiquitin membrane yeast two‐hybrid assays, we screened an Arabidopsis cDNA library for interactors of TuMV 6K2. We isolated AtHVA22a ( Hordeum vulgare abscisic acid responsive gene 22 ), which belongs to a multigenic family of transmembrane proteins, homologous to Receptor expression‐enhancing protein (Reep)/Deleted in polyposis (DP1)/Yop1 family proteins in animal and yeast. HVA22/DP1/Yop1 family genes are widely distributed in eukaryotes, but the role of HVA22 proteins in plants is still not well known, although proteomics analysis of PD fractions purified from Arabidopsis suspension cells showed that AtHVA22a is highly enriched in a PD proteome. We confirmed the interaction between TuMV 6K2 and AtHVA22a in yeast, as well as in planta by using bimolecular fluorescence complementation and showed that TuMV 6K2/AtHVA22a interaction occurs at the level of the viral replication compartment during TuMV infection. Finally, we showed that the propagation of TuMV is increased when AtHVA22a is overexpressed in planta but slowed down upon mutagenesis of AtHVA22a by CRISPR‐Cas9. Altogether, our results indicate that AtHVA22a plays an agonistic effect on TuMV propagation and that the C‐terminal tail of the protein is important in this process.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04617334/file/xue_molecularPlantPathologie_2024.pdf BibTex
titre
Dare to be resilient: the key to future pesticide-free orchards?
auteur
Marie Serrie, Fabienne Ribeyre, Laurent Brun, Jean-Marc Audergon, Bénédicte Quilot, Morgane Roth
article
Journal of Experimental Botany, 2024, erae150, ⟨10.1093/jxb/erae150⟩
resume
Considering the urgent need for more sustainable fruit tree production, it is high time to fnd durable alternatives to the systematic use of phytosanitary products in orchards. To this end, resilience can deliver a number of benefts. Relying on a combination of tolerance, resistance, and recovery traits, disease resilience appears as a cornerstone to cope with the multiple pest and disease challenges over an orchard’s lifetime. Here, we describe resilience as the capacity of a tree to be minimally affected by external disturbances or to rapidly bounce back to normal functioning after being exposed to these disturbances. Based on a literature survey largely inspired from research on livestock, we highlight different approaches for dissecting phenotypic and genotypic components of resilience. In particular, multisite experimental designs and longitudinal measures of so-called ‘resilience biomarkers’ are required. We identified a list of promising biomarkers relying on ecophysiological and digital measurements. Recent advances in high-throughput phenotyping and genomics tools will likely facilitate fne scale temporal monitoring of tree health, allowing identifcation of resilient genotypes with the calculation of specifc resilience indicators. Although resilience could be considered as a ‘black box’ trait, we demonstrate how it could become a realistic breeding goal.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04560076/file/Serrie_review_resilience_2024%20%281%29.pdf BibTex
titre
Joint effects of inter-specific and intra-specific diversity of tomato volatile profiles on antixenosis against Tuta absoluta
auteur
Komla Exonam Amegan, Yasmine Fourati, Sylvia Del-Valle, Sylvia Salgon, Paola Ferrante, Christophe Robin, Anne-Violette Lavoir, Bernard Caromel, Romain Larbat, Alan Kergunteuil
article
Entomologia Generalis, 2024, 44 (2), pp.325-337. ⟨10.1127/entomologia/2024/2399⟩
resume
Since volatile organic compounds (VOCs) shape plant defenses against pests, ecologists strive to understand their sources of variation. The worldwide distribution of tomato offers an ideal system to explore the ecological diversity of VOCs produced by plants supporting a large range of local adaptations. In this study, we analyzed the diversity of VOC profiles released by 29 accessions of tomato belonging to five species with different natural histories and including domesticated plants and wild relatives. In addition, olfactometer assays were performed on 10 accessions characterized by strong differences in VOC emissions to test the consequences on host-plant location by a major pest specialized on solanaceous plants, Tuta absoluta. Based on 77 VOCs detected, our results suggest that the large diversity of volatile profiles reflect different biogeographic areas. A phylogenetic tree was constructed to test phylogenetic drivers in VOC emissions. The richness of volatile profiles and sesquiterpenoid emissions were relatively high in ancestral branches and decreased exponentially with evolution according to early-burst patterns. In olfactometer assays, we identified four repellent accessions belonging to S. pennellii, S. habrochaites and S. cheesmaniae. This study points out the importance of inter- and intra-specific diversity of VOCs in antixenosis. Further, our results suggest that methyl salicylate, β-myrcene and sesquiterpenoids such as (3E,7E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene or α-curcumene could serve as repellents against T. absoluta. In a greenhouse, we confirmed the biological relevance of agroecological research interested in screening repellent plants. Bridging chemical ecology with phylogenetic approaches helps to better understand the evolution of mechanisms supporting anti-herbivore plant defenses.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.univ-lorraine.fr/hal-04557514/file/Exoman_entomolgiaGeneralis_2024.pdf BibTex
titre
Genetic Diversity of Eggplant (Solanum melongena L.) Accessions Based on Morpho-Physiological Characteristics and Root System Architecture Traits
auteur
F Yousefi, F Soltani, A. R. Lalehparvar, Rebecca Stevens
article
Journal of Agricultural Science and Technology (JAST), 2024, 26 (2), pp.387-401. ⟨10.22034/JAST.26.2.387⟩
resume
The presence of genetic diversity leads to better adaptation of plants to different environments and enables researchers to select superior genotypes adapted to given culture conditions. In order to estimate the genetic diversity of eggplant, 22 accessions were obtained from the INRAe vegetable germplasm center and the National Plant Gene Bank of Iran and were planted in horticultural science station of University of Tehran, Karaj, in a randomized complete block design with three replicates. The number of flowers per plant and number of fruits per plant were higher in the MM00007 and FLT02 accessions, respectively. The maximum leaf area (190 cm2 plant-1) was recorded for MM 01597. Accessions FLT46, MM 0064, MM 00108 bis MM 01597 and MM 01010 revealed high variations in root characters. Higher number of root tips and maximum number of roots were assigned for FLT46, and average root orientation and steep root angle frequency for MM 01597 and MM 01010. The correlation of root angles frequency and root number could possibly be exploited in selection programs as factors indirectly involved in increasing yield and the number of flowers per plant. Based on all evaluated traits, genotypes FLT10, MM 01597, MM 01010, FLT46, and FLTE9012 could be used as parents for future eggplant breeding programs due to their desirable agricultural traits.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04565597/file/Yousefi_jast_2024.pdf BibTex
titre
Perspective Can genome editing help transitioning to agroecology?
auteur
Fabien Nogué, Mathilde Causse, Philippe Debaeke, Annabelle Déjardin, Stéphane Lemarié, Guy Richard, Peter Rogowsky, Carole Caranta
article
iScience, 2024, 27 (3), pp.109159. ⟨10.1016/j.isci.2024.109159⟩
resume
Meeting the challenges of agroecological transition in a context of climate change requires the use of various strategies such as biological regulations, adapted animal and plant genotypes, diversified production systems, and digital technologies. Seeds and plants, through plant breeding, play a crucial role in driving these changes. The emergence of genome editing presents a new opportunity in plant breeding practices. However, like any technological revolution involving living organisms, it is essential to assess its potential contributions, limits, risks, socio-economic implications, and the associated controversies. This article aims to provide a comprehensive review of scientific knowledge on genome editing for agroecological transition, drawing on multidisciplinary approaches encompassing biological, agronomic, economic, and social sciences.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04508623/file/1-s2.0-S2589004224003808-main.pdf BibTex
titre
Correction: Haegeman et al. Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests. Plants 2023, 12, 2139
auteur
Annelies Haegeman, Yoika Foucart, Kris de Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Z A Gaafar, Oscar P Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovšek, Marie Lefebvre, Martha Malapi, Irena Mavrič Pleško, Serkan Önder, Jean-Sébastien Reynard, Ferran Salavert Pamblanco, Olivier Schumpp, Kristian Stevens, Chandan Pal, Lucie Tamisier, Çiğdem Ulubaş Serçe, Inge van Duivenbode, David W Waite, Xiaojun Hu, Heiko Ziebell, Sébastien Massart
article
Plants, 2024, 13 (5), pp.623. ⟨10.3390/plants13050623⟩
resume
IIn the original publication [ 1], there were two mistakes in Figure 3 as published. The legend showed the wrong descriptions with the colors, and the Y-axis scale was not correctly labeled. The corrected Figure 3 with an adjusted description appears below.Plants 2024, 13, x FOR PEER REVIEW 2 of 3 * Correspondence: annelies.haegeman@ilvo.vlaanderen.be (A.H.); sebastien.massart@uliege.be (S.M.)
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04617460/file/Haegeman_plants_2024.pdf BibTex
titre
Crop traits and production under drought
auteur
Vincent Vadez, Alexandre Grondin, Karine Chenu, Amelia Henry, Laurent Laplaze, Emilie Millet, Andrea Carminati
article
Nature Reviews Earth & Environment, 2024, ⟨10.1038/s43017-023-00514-w⟩
resume
Drought limits crop productivity and threatens global food security, with moderate drought stress — when crops grow at a reduced rate — commonly experienced. Increasing plant tolerance to moderate drought is a key target for adaptation and management, but efforts to understand and increase drought tolerance often focus on more extreme drought that causes complete crop failure and only consider crop genetics. In this Review, we discuss the influence of moderate drought on crop productivity and the role of physiological traits in drought tolerance and adaptation. Traits related to crop water use, water capture, water availability, transpiration efficiency and phenology impact drought adaptation, but their overall effect varies situationally. For example, early restrictions in transpiration, higher transpiration efficiency or altered tillering increase water availability during grain filling and can double yield in some drought scenarios. However, these same traits under less severe drought scenarios can also lead to yield penalties. To assess when and under what conditions traits will be beneficial, crop models are used to integrate the effects of genetics, the environment and management, estimating the expected yield responses under these combinations of scenarios and traits. More robust characterization of moderate drought tolerance and better integration between plant genetic information and modelling will enable the local selection of crop varieties suited to the expected drought scenarios.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Microbial diversity in four Mediterranean irciniid sponges
auteur
Katerina Skaraki, Christina Pavloudi, Thanos Dailianis, Jacques Lagnel, Adriani Pantazidou, Antonios Magoulas, Georgios Kotoulas
article
Biodiversity Data Journal, 2024, 12, pp.e114809. ⟨10.3897/bdj.12.e114809⟩
resume
This paper describes a dataset of microbial communities from four different sponge species: Ircinia oros (Schmidt, 1864), Ircinia variabilis (Schmidt, 1862), Sarcotragus spinosulus Schmidt, 1862 and Sarcotragus fasciculatus (Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04575995/file/BDJ_skaraki_2024.pdf BibTex
titre
A highly diversified NLR cluster in melon contains homologs that confer powdery mildew and aphid resistance
auteur
Nathalie Boissot, Véronique Chovelon, Vincent Rittener-Ruff, Nathalie Giovinazzo, Pascale Mistral, Michel Pitrat, Myriam Charpentier, Christelle Troadec, Abdelhafid Bendahmane, Catherine Dogimont
article
Horticulture Research, In press, ⟨10.1093/hr/uhad256⟩
resume
Podosphaera xanthii is the main causal agent of powdery mildew (PM) on Cucurbitaceae. In Cucumis melo, the Pm-w resistance gene, which confers resistance to P. xanthii, is located on chromosome 5 in a cluster of nucleotide-binding leucine-rich repeat receptors (NLRs). We used positional cloning and transgenesis, to isolate the Pm-wWMR 29 gene encoding a coiled-coil NLR (CC-NLR). Pm-wWMR 29 conferred high level of resistance to race 1 of PM and intermediate level of resistance to race 3 of PM. Pm-wWMR 29 turned out to be a homolog of the Aphis gossypii resistance gene Vat-1PI 161375. We confirmed that Pm-wWMR 29 did not confer resistance to aphids, while Vat-1PI 161375 did not confer resistance to PM. We showed that both homologs were included in a highly diversified cluster of NLRs, the Vat cluster. Specific Vat-1PI 161375 and Pm-wWMR 29 markers were present in 10 - 13% of 678 accessions representative of wild and cultivated melon types worldwide. Phylogenic reconstruction of 34 protein homologs of Vat-1PI 161375 and Pm-wWMR 29 identified in 24 melon accessions revealed an ancestor with four R65aa -a specific motif in the LRR domain, evolved towards aphid and virus resistance, while an ancestor with five R65aa evolved towards PM resistance. The complexity of the cluster comprising the Vat/Pm-w genes and its diversity in melon suggest that Vat-homologs may contribute to the recognition of a broad range of yet to be identified pests and pathogens.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04315083/file/Boissot_horticultureResearch_2024_uhad256.pdf BibTex

2023

Journal articles

titre
The tomato P69 subtilase family is involved in resistance to bacterial wilt
auteur
Weiqi Zhang, Marc Planas-Marquès, Marianne Mazier, Margarita Šimkovicová, Mercedes Rocafort, Melissa Mantz, Pitter Huesgen, Frank Takken, Annick Stintzi, Andreas Schaller, Nuria Coll, Marc Valls
article
The Plant Journal, 2023, ⟨10.1111/tpj.16613⟩
resume
The intercellular space or apoplast constitutes the main interface in plant–pathogen interactions. Apoplastic subtilisin‐like proteases—subtilases—may play an important role in defence and they have been identified as targets of pathogen‐secreted effector proteins. Here, we characterise the role of the Solanaceae‐specific P69 subtilase family in the interaction between tomato and the vascular bacterial wilt pathogen Ralstonia solanacearum . R. solanacearum infection post‐translationally activated several tomato P69s. Among them, P69D was exclusively activated in tomato plants resistant to R. solanacearum . In vitro experiments showed that P69D activation by prodomain removal occurred in an autocatalytic and intramolecular reaction that does not rely on the residue upstream of the processing site. Importantly P69D‐deficient tomato plants were more susceptible to bacterial wilt and transient expression of P69B , D and G in Nicotiana benthamiana limited proliferation of R. solanacearum . Our study demonstrates that P69s have conserved features but diverse functions in tomato and that P69D is involved in resistance to R. solanacearum but not to other vascular pathogens like Fusarium oxysporum .
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04398628/file/The%20Plant%20Journal%20-%202023%20-%20Zhang%20-.pdf BibTex
titre
Phytophthora capsici genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing
auteur
Emmanuel Szadkowski, Jacques Lagnel, Nasradin Touhami, Amalia Sayeh, Céline Lopez-Roques, Olivier Bouchez, Véronique Lefebvre
article
Microbiology Resource Announcements, 2023, 12 (12), ⟨10.1128/mra.00196-23⟩
resume
The oomycete Phytophthora capsici is a common pathogen of the Solanaceae and Cucurbitaceae families. An improved assembly for the reference isolate LT1534 was constructed using Oxford Nanopore Technologies and Illumina data. Additionally, an unpolished assembly was produced for the European isolate Pc285 collected on chili pepper using Oxford Nanopore reads.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04521837/file/szadkowski-microbiology_2023.pdf BibTex
titre
Aphid adaptation to cucurbits: sugars, cucurbitacin and phloem structure in resistant and susceptible melons
auteur
Pierre Sadon, Marie-Noëlle Corre, Raphael Lugan, Nathalie Boissot
article
BMC Plant Biology, 2023, 23 (1), pp.239. ⟨10.1186/s12870-023-04248-1⟩
resume
Background Aphis gossypii, a strictly phloemophagaous aphid , colonize hundreds of plant families, and a group of clones formed a cucurbit-specialised host-race. Cucurbits are unique in having evolved a specific extra-fascicular phloem (EFP), which carries defence-related metabolites such as cucurbitacin, whereas the fascicular phloem (FP) is common to all higher plants and carries primary metabolites, such as raffinose-family oligosaccharides (RFOs). Both cucurbitacins (in the EFP) and galactinol (in the FP) have been suggested to be toxic to aphids. We investigated these hypotheses in cucurbit-specialized A. gossypii fed on melon plants with or without aphid-resistance conferred by the NLR gene Vat . We selected a plant-aphid system with (i) Vat -mediated resistance not triggered, (ii) Vat -mediated resistance triggered by an aphid clone adapted to the presence of Vat resistant alleles and (iii) Vat -mediated resistance triggered by a non-adapted aphid clone. Results We quantified cucurbitacin B, its glycosylated derivative, and sugars, in melon plants and aphids that fed on. The level of cucurbitacin in plants was unrelated to both aphid infestation and aphid resistance. Galactinol was present at higher quantities in plants when Vat -mediated resistance was triggered, but its presence did not correlate with aphid performance. Finally, we showed that cucurbit-specialized A. gossypii fed from the FP but could also occasionally access the EFP without sustainably feeding from it. However, the clone not adapted to Vat -mediated resistance were less able to access the FP when the Vat resistance was triggered. Conclusion We concluded that galactinol accumulation in resistant plants does not affect aphids, but may play a role in aphid adaptation to fasting and that Cucurbitacin in planta is not a real threat to Aphis gossypii. Moreover, the specific phloem of Cucurbits is involved neither in A. gossypii cucurbit specialisation nor in adaptation to Vat -dependent resistance.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04101668/file/2023_bmc_Sadon.pdf BibTex
titre
Genetic Variability in Seed Longevity and Germination Traits in a Tomato MAGIC Population in Contrasting Environments
auteur
Elise Bizouerne, Joseph Ly Vu, Benoît Ly Vu, Isidore Diouf, F. Bitton, Mathilde Causse, Jérôme Verdier, Julia Buitink, Olivier Leprince
article
Plants, 2023, 12 (20), pp.3632. ⟨10.3390/plants12203632⟩
resume
The stable production of high vigorous seeds is pivotal to crop yield. Also, a high longevity is essential to avoid progressive loss of seed vigour during storage. Both seed traits are strongly influenced by the environment during seed development. Here, we investigated the impact of heat stress (HS) during fruit ripening on tomato seed lifespan during storage at moderate relative humidity, speed (t50) and homogeneity of germination, using a MAGIC population that was produced under optimal and HS conditions. A plasticity index was used to assess the extent of the impact of HS for each trait. HS reduced the average longevity and germination homogeneity by 50% within the parents and MAGIC population. However, there was a high genetic variability in the seed response to heat stress. A total of 39 QTLs were identified, including six longevity QTLs for seeds from control (3) and HS (3) conditions, and six plasticity QTLs for longevity, with only one overlapping with a longevity QTL under HS. Four out of the six longevity QTL co-located with t50 QTL, revealing hotspots for seed quality traits. Twenty-one QTLs with intervals below 3 cM were analyzed using previous transcriptome and gene network data to propose candidate genes for seed vigour and longevity traits.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://institut-agro-rennes-angers.hal.science/hal-04258504/file/Bizouerne%202023%20plants-12-03632-reprint.pdf BibTex
titre
Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time
auteur
Felipe Pérez de los Cobos, Eva Coindre, Naima Dlalah, Bénédicte Quilot-Turion, Ignasi Batlle, Pere Arús, Iban Eduardo, Henri Duval
article
Horticulture research, 2023, 10 (10), ⟨10.1093/hr/uhad193⟩
resume
Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype–phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04300870/file/perezdeloscobos_horticultureResarch_uhad193.pdf BibTex
titre
Blueprint for non-transgenic edited plants
auteur
Jean-Luc Gallois, Fabien Nogué
article
Nature Plants, 2023, 2 p. ⟨10.1038/s41477-023-01532-8⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Allele mining of eukaryotic translation initiation factor genes in Prunus for the identification of new sources of resistance to sharka
auteur
David Tricon, Julie Faivre D’arcier, Jean-Philippe Eyquard, Shuo Liu, Stéphane Decroocq, Aurélie Chague, Weisheng Liu, Gulnara Balakishiyeva, Alamdar Mammadov, Timur Turdiev, Tatiana Kostritsyna, Bayram M Asma, Zeynal Akparov, Véronique Decroocq
article
Scientific Reports, 2023, 13, ⟨10.1038/s41598-023-42215-w⟩
resume
Members of the eukaryotic translation initiation complex are co-opted in viral infection, leading to susceptibility in many crop species, including stone fruit trees (Prunus spp.). Therefore, modification of one of those eukaryotic translation initiation factors or changes in their gene expression may result in resistance. We searched the crop and wild Prunus germplasm from the Armeniaca and Amygdalus taxonomic sections for allelic variants in the eIF4E and eIFiso4E genes, to identify alleles potentially linked to resistance to Plum pox virus (PPV). Over one thousand stone fruit accessions (1397) were screened for variation in eIF4E and eIFiso4E transcript sequences which are in single copy within the diploid Prunus genome. We identified new alleles for both genes differing from haplotypes associated with PPV susceptible accessions. Overall, analyses showed that eIFiso4E is genetically more constrained since it displayed less polymorphism than eIF4E. We also demonstrated more variations at both loci in the related wild species than in crop species. As the eIFiso4E translation initiation factor was identified as indispensable for PPV infection, a selection of ten different eIFiso4E haplotypes along 13 accessions were tested by infection with PPV and eight of them displayed a range of reduced susceptibility to resistance, indicating new potential sources of resistance to sharka.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04302686/file/Tricon%20et%20al_final_s41598-023-42215-w.pdf BibTex
titre
Analysis of >3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration‐diversification routes
auteur
Lorenzo Barchi, Giuseppe Aprea, M. Timothy Rabanus-Wallace, Laura Toppino, David Alonso, Ezio Portis, Sergio Lanteri, Luciana Gaccione, Emmanuel Omondi, Maarten van Zonneveld, Roland Schafleitner, Paola Ferrante, Andreas Börner, Nils Stein, Maria José Díez, Véronique Lefebvre, Jérémy Salinier, Hatice Filiz Boyaci, Richard Finkers, Matthijs Brouwer, Arnaud Bovy, Giuseppe Leonardo Rotino, Jaime Prohens, Giovanni Giuliano
article
The Plant Journal, 2023, ⟨10.1111/tpj.16455⟩
resume
Eggplant ( Solanum melongena ) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild relatives, consisting of 3499 accessions from seven worldwide genebanks, originating from 105 countries in five continents. The combination of genotypic and passport data points to the existence of at least two main centers of domestication, in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The wild and weedy eggplant ancestor S. insanum shows admixture with domesticated S. melongena , similar to what was described for other fruit‐bearing Solanaceous crops such as tomato and pepper and their wild ancestors. After domestication, migration and admixture of eggplant populations from different regions have been less conspicuous with respect to tomato and pepper, thus better preserving ‘local’ phenotypic characteristics. The data allowed the identification of misclassified and putatively duplicated accessions, facilitating genebank management. All the genetic, phenotypic, and passport data have been deposited in the Open Access G2P‐SOL database, and constitute an invaluable resource for understanding the domestication, migration and diversification of this cosmopolitan vegetable.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04204752/file/The%20Plant%20Journal%20-%202023%20-%20Barchi.pdf BibTex
titre
Ethylene produced in carpel primordia controls CmHB40 expression to inhibit stamen development
auteur
Dali Rashid, Ravi Sureshbhai Devani, Natalia Yaneth Rodriguez-Granados, Fadi Abou-Choucha, Christelle Troadec, Halima Morin, Feng-Quan Tan, Fabien Marcel, Hsin-Ya Huang, Melissa Hanique, Siqi Zhang, Marion Verdenaud, Clement Pichot, Vincent Rittener, Ying Huang, Moussa Benhamed, Catherine Dogimont, Adnane Boualem, Abdelhafid Bendahmane
article
Nature Plants, 2023, ⟨10.1038/s41477-023-01511-z⟩
resume
Sex determination evolved to control the development of unisexual flowers. In agriculture, it conditions how plants are cultivated and bred. We investigated how female flowers develop in monoecious cucurbits. We discovered in melon, Cucumis melo, a mechanism in which ethylene produced in the carpel is perceived in the stamen primordia through spatially differentially expressed ethylene receptors. Subsequently, the CmEIN3/CmEIL1 ethylene signalling module, in stamen primordia, activates the expression of CmHB40, a transcription factor that downregulates genes required for stamen development and upregulates genes associated with organ senescence. Investigation of melon genetic biodiversity revealed a haplotype, originating in Africa, altered in EIN3/EIL1 binding to CmHB40 promoter and associated with bisexual flower development. In contrast to other bisexual mutants in cucurbits, CmHB40 mutations do not alter fruit shape. By disentangling fruit shape and sex-determination pathways, our work opens up new avenues in plant breeding.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Multi‐environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection
auteur
Louis McLeod, Lorenzo Barchi, Giorgio Tumino, Pasquale Tripodi, Jérémy Salinier, Christophe Gros, Hatice Filiz Boyaci, Ramazan Ozalp, Yelena Borovsky, Roland Schafleitner, Derek Barchenger, Richard Finkers, Matthijs Brouwer, Nils Stein, Mark Timothy Rabanus‐wallace, Giovanni Giuliano, Roeland Voorrips, Ilan Paran, Véronique Lefebvre
article
The Plant Journal, 2023, ⟨10.1111/tpj.16425⟩
resume
Investigating crop diversity through genome‐wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P‐SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype‐by‐environment (G × E) interactions, multi‐environment GWAS with a 10 195‐marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries. Environment‐specific and multi‐environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high‐confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker‐assisted selection. The G2P‐SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker‐assisted breeding efforts by the pepper community.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
How to improve the accuracy of height data from bird tracking devices? An assessment of high-frequency GPS tracking and barometric altimetry in field conditions
auteur
Tonio Schaub, Alexandre Millon, Caroline de Zutter, Ralph Buij, Joël Chadœuf, Simon Lee, Aymeric Mionnet, Raymond Hendrikus Gerardus Klaassen
article
Animal Biotelemetry, 2023, 11 (1), pp.31. ⟨10.1186/s40317-023-00342-1⟩
resume
In the context of rapid development of wind energy infrastructure, information on the flight height of birds is vital to assess their collision risk with wind turbines. GPS tags potentially represent a powerful tool to collect flight height data, yet GPS positions are associated with substantial vertical error. Here, we assessed to what extent high-frequency GPS tracking with fix intervals of 2–3 s (GPS remaining turned on between fixes), or barometric altimetry using air pressure loggers integrated in GPS tags, improved the accuracy of height data compared to standard low-frequency GPS tracking (fix interval ≥ 5 min; GPS turned off between fixes). Results Using data from 10 GPS tag models from three manufacturers in a field setting (194 tags deployed on free-living raptors), we estimated vertical accuracy based on periods when the birds were stationary on the ground (true height above ground was approximately zero), and the difference between GPS and barometric height in flight. In GPS height data, vertical accuracy was mainly driven by noise (little bias), while in barometric data, it was mostly affected by bias (little noise). In high-frequency GPS data, vertical accuracy was improved compared to low-frequency data in each tag model (mean absolute error (AE) reduced by 72% on average; range of mean AE 2–7 vs. 7–30 m). In barometric data, vertical accuracy did not differ between high- and low-frequency modes, with a bias of − 15 to − 5 m and mean AE of 7–15 m in stationary positions. However, the median difference between GPS and barometric data was smaller in flight positions than in stationary positions, suggesting that the bias in barometric height data was smaller in flight. Finally, simulations showed that the remaining vertical error in barometric and high-frequency GPS data had little effect on flight height distributions and the proportion of positions within the collision risk height range, as opposed to the extensive noise found in low-frequency GPS data in some tag models. Conclusions Barometric altimetry may provide more accurate height data than standard low-frequency GPS tracking, but it involves the risk of a systematic error. Currently, high-frequency GPS tracking provides highest vertical accuracy and may thus substantially advance the study of wind turbine collision risk in birds.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://amu.hal.science/hal-04447704/file/Schaub_animalBiotelemetry_2023.pdf BibTex
titre
Diversity and genetic architecture of agro-morphological traits in a core collection of European traditional tomato
auteur
Clara Pons, Joan Casals, Matthijs Brower, Adriana Sacco, Alessandro Riccini, Patrick Hendrickx, Maria del Rosario Figás, Josef Fisher, Silvana Grandillo, Andrea Mazzucato, Salvador Soler, Dani Zamir, Mathilde Causse, Maria José Díez, Richard Finkers, Jaime Prohens, Antonio Jose Monforte, Antonio Granell
article
Journal of Experimental Botany, 2023, ⟨10.1093/jxb/erad306⟩
resume
Abstract European traditional tomato varieties have been selected by farmers given their consistent performance and adaptation to local growing conditions. Here we developed a multipurpose core collection, comprising 226 accessions representative of the genotypic, phenotypic, and geographical diversity present in European traditional tomatoes, to investigate the basis of their phenotypic variation, gene×environment interactions, and stability for 33 agro-morphological traits. Comparison of the traditional varieties with a modern reference panel revealed that some traditional varieties displayed excellent agronomic performance and high trait stability, as good as or better than that of their modern counterparts. We conducted genome-wide association and genome-wide environment interaction studies and detected 141 quantitative trait loci (QTLs). Out of those, 47 QTLs were associated with the phenotype mean (meanQTLs), 41 with stability (stbQTLs), and 53 QTL-by-environment interactions (QTIs). Most QTLs displayed additive gene actions, with the exception of stbQTLs, which were mostly recessive and overdominant QTLs. Both common and specific loci controlled the phenotype mean and stability variation in traditional tomato; however, a larger proportion of specific QTLs was observed, indicating that the stability gene regulatory model is the predominant one. Developmental genes tended to map close to meanQTLs, while genes involved in stress response, hormone metabolism, and signalling were found within regions affecting stability. A total of 137 marker–trait associations for phenotypic means and stability were novel, and therefore our study enhances the understanding of the genetic basis of valuable agronomic traits and opens up a new avenue for an exploitation of the allelic diversity available within European traditional tomato germplasm.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04189756/file/JEB-Pons_2023.pdf BibTex
titre
eIF4E-mediated resistance to potyviruses in plants: from natural alleles to edited genes
auteur
Jean-Luc Gallois, Sylvie German-Retana
article
Virologie, 2023, 27 (4), pp.225-337. ⟨10.1684/vir.2023.1012⟩
resume
Resistance to viruses is an important aspect of plant breeding. One way to achieve it is to select genetic resistances based on the susceptibility factors hijacked by the virus to infect the plants. Here, we recount work done on genes encoding translation initiation factors eIF4E, some of the most successful targets for obtaining resistance to potyviruses, starting from their characterization 20 years ago. With examples from different plant species, pepper, tomato, tobacco and arabidopsis, we present the basis of this type of resistances and their characteristics, highlighting the role of gene redundancy among 4E factors, their specificity for the virus and the need for the plant of a trade-off between resistance and development. Finally, we show how the new genome editing techniques could be used in plant breeding to develop eIF4E-based resistances in crops, mimicking the functional alleles that have been selected during evolution in many crops.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Stone fruit phenolic and triterpenoid compounds more significantly modulate gene expression of Monilinia spp. than its characteristics during in vitro growth
auteur
Majid Hassan Mustafa, Marie-Noëlle Corre, Laure Heurtevin, Daniele Bassi, Marco Cirilli, Bénédicte Quilot-Turion
article
Fungal Biology, 2023, 127 (7-8), pp.1085-1097. ⟨10.1016/j.funbio.2023.06.004⟩
resume
Phenolic and triterpenoid compounds are essential components in stone fruit skin and flesh tissues. They are thought to possess general antimicrobial activity. However, regarding brown rot disease, investigations were only confined to a limited number of phenolics, especially chlorogenic acid. The activity of triterpenoids against Monilinia spp., as an essential part of the peach cuticular wax, has not been studied before. In this work, the anti-fungal effect of some phenolics, triterpenoids, and fruit surface compound (FSC) extracts of peach fruit were investigated at two developmental stages on Monilinia fructicola and Monilinia laxa characteristics during in vitro growth. A new procedure for assaying anti-fungal activity of triterpenoids, which are notoriously difficult to assess in vitro because of their hydrophobicity, has been developed. Measurements of colony diameter, sporulation, and germination of second-generation conidia were recorded. Furthermore, the expression of twelve genes of M. fructicola associated with germination and/or appressorium formation and virulence-related genes was studied relative to the presence of the compounds. The study revealed that certain phenolics and triterpenoids showed modest anti-fungal activity while dramatically modulating M. fructicola gene expression. MfRGAE1 gene was overexpressed by chlorogenic and ferulic acids and MfCUT1 by betulinic acid, at 4-and 7-days of mycelium incubation. The stage II FSC extract, corresponding to the period when the fruit is resistant to Monilinia spp., considerably up-regulated the MfLAE1 gene. These findings effectively contribute to the knowledge of biochemical compounds effects on fungi on in vitro conditions.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04132330/file/Stone%20fruit%20phenolic%20and%20triterpenoid%20compounds_revised_3.pdf BibTex
titre
Looking beyond virus detection in RNA sequencing data: Lessons learned from a community-based effort to detect cellular plant pathogens and pests
auteur
Annelies Haegeman, Yoika Foucart, Kris de Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Gaafar, Oscar Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovšek, Marie Lefebvre, Martha Malapi, Irena Mavrič Pleško, Serkan Önder, Jean-Sébastien Reynard, Ferran Salavert Pamblanco, Olivier Schumpp, Kristian Stevens, Chandan Pal, Lucie Tamisier, Çiğdem Ulubaş Serçe, Inge van Duivenbode, David Waite, Xiaojun Hu, Heiko Ziebell, Sébastien Massart
article
Plants, 2023, 12 (11), pp.2139. ⟨10.3390/plants12112139⟩
resume
High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04117624/file/2023_Haegeman_plants.pdf BibTex
titre
Influence of Fruit Wounding on Subsequent Monilinia laxa Infection of Nectarines
auteur
Maximiliano Dini, Maria Do Carmo Bassols Raseira, Marie-Noëlle Corre, Véronique Signoret, Bénédicte Quilot-Turion
article
Agronomy, 2023, 13 (5), pp.1235. ⟨10.3390/agronomy13051235⟩
resume
Despite the fact that brown rot is the most economically important disease in stone fruits, the relationship between mechanical stress and infection has never been explored. Thus, to explore this connection, we carried out four experiments linking nectarine wounding and M. laxa infection. First, we evaluated a possible systemic reaction of the fruit to wounding that could impact the M. laxa infection. Afterward, we study the impact of the fruit in the environment on M. laxa colonies grown in vitro. Subsequently, we tested the disease susceptibility of fruits inoculated with M. laxa placed in the same environment as wounded fruits. Finally, in the fourth experiment, the effect of wounding on the subsequent fruit infections was evaluated at three fruit stages. As a result, we observed that there was no evidence of a fruit systemic reaction to wounding and M. laxa infection. In the study related to the impact of the fruit in the environment of M. laxa, the findings suggest that M. laxa “perceived” the fruit’s presence, resulting in accelerated in vitro growth. Moreover, the presence of wounded fruits in the box increased the susceptibility to brown rot. Inoculated fruits showed a delayed and reduced infection 7 h after being wounded, during the second stage of fruit development (15–19 weeks after full bloom). Moreover, a red reaction associated with inoculation was detected immediately after the fruits were wounded. Nine phenolic compounds exclusively related to the red areas were extracted, while six other compounds were present in higher proportions. These compounds may be actively involved in plant–pathogen interactions and the activation of metabolic pathways involved in nectarine susceptibility/resistance to M. laxa.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04132333/file/agronomy-13-01235-v2.pdf BibTex
titre
An iterative gene-editing strategy broadens eIF4E1 genetic diversity in Solanum lycopersicum and generates resistance to multiple potyvirus isolates
auteur
Kyoka Kuroiwa, Benoit Danilo, Laura Perrot, Christina Thenault, Florian Veillet, Fabien Delacote, Philippe Duchateau, Fabien Nogué, Marianne Mazier, Jean-Luc Gallois
article
Plant Biotechnology Journal, 2023, 21 (5), pp.918-930. ⟨10.1111/pbi.14003⟩
resume
Resistance to potyviruses in plants has been largely provided by the selection of natural variant alleles of eukaryotic translation initiation factors (eIF) 4E in many crops. However, the sources of such variability for breeding can be limited for certain crop species, while new virus isolates continue to emerge. Different methods of mutagenesis have been applied to inactivate the eIF4E genes to generate virus resistance, but with limited success due to the physiological importance of translation factors and their redundancy. Here, we employed genome editing approaches at the base level to induce non-synonymous mutations in the eIF4E1 gene and create genetic diversity in cherry tomato (Solanum lycopersicum var. cerasiforme). We sequentially edited the genomic sequences coding for two regions of eIF4E1 protein, located around the cap-binding pocket and known to be important for susceptibility to potyviruses. We show that the editing of only one of the two regions, by gene knock-in and base editing, respectively, is not sufficient to provide resistance. However, combining amino acid mutations in both regions resulted in resistance to multiple potyviruses without affecting the functionality in translation initiation. Meanwhile, we report that extensive base editing in exonic region can alter RNA splicing pattern, resulting in gene knockout. Altogether our work demonstrates that precision editing allows to design plant factors based on the knowledge on evolutionarily selected alleles and enlarge the gene pool to potentially provide advantageous phenotypes such as pathogen resistance.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-03979930/file/Plant%20Biotechnology%20Journal%20-%202023%20-%20Kuroiwa%20-%20An%20iterative%20gene%E2%80%90editing%20strategy%20broadens%20eIF4E1%20genetic%20diversity%20in.pdf BibTex
titre
Protecting Apricot Orchards with Rain Shelters Reduces Twig Blight Damage Caused by Monilinia spp. and Makes It Possible to Reduce Fungicide Use
auteur
Laurent Brun, Freddy Combe, Christophe Gros, Pascal Walser, Marc Saudreau
article
Agronomy, 2023, 13 (5), pp.1338. ⟨10.3390/agronomy13051338⟩
resume
Blossom and twig blight, caused by Monilinia spp., is the main disease in apricot trees. In this study, we installed transparent rain shelters in apricot orchards to study their influence on the modification of the microclimate at the level of the tree canopy and on the reduction in moniliosis damage in twigs. Rain shelters significantly reduced the leaf wetness time measured within the foliage compared to the unsheltered trees (a reduction of between 43% and 67%). However, very few differences were observed in the daily averaged air temperature (up to 6%) and daily averaged air relative humidity (up to 1%). In the first experiment, on the apricot variety Bergarouge® (CEP Innovation, Lyon, France), moniliosis damage on twigs in the absence of phytosanitary protection was reduced by up to 62% for the trees provided with rain protection compared to the trees that did not receive rain shelters. A second experiment, involving five apricot tree varieties, made it possible to verify that fungicide protection could be reduced for the trees protected by rain covers, reducing moniliosis damage on twigs compared to full fungicide protection combined without rain protection. Finally, a third experiment comprising two apricot tree varieties has shown that in organic orchards, rain protection provides protection against moniliosis (twig blight) that is equivalent to an organic farming fungicide protection programme based on the use of copper sulphate and calcium polysulphide.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04106602/file/2023_Brun_Agronomy.pdf BibTex
titre
Crop domestication as a step towards reproductive isolation
auteur
M. I. Tenaillon, Ewen Burban, Stella Huynh, Arthur Wojcik, Anne-Céline Thuillet, Domenica Manicacci, Pierre R. Gérard, Karine Alix, Harry Belcram, A. Cornille, Marie Brault, Rebecca Stevens, Jacques Lagnel, Catherine Dogimont, Yves Vigouroux, S Glémin
article
American Journal of Botany, 2023, 110 (7), pp.e16173. ⟨10.1002/ajb2.16173⟩
resume
Speciation, Darwin’s mystery of mysteries, is a continuous process that results in genomic divergence accompanied by the gradual increment of reproductive barriers between lineages. Since the beginning of research on the genetics of speciation, several questions have emerged such as: What are the genetic bases of incompatibilities? How many loci are necessary to prevent hybridization and how are they distributed along genomes? Can speciation occur despite gene flow and how common is ecological speciation? Early stages of divergence are key to understand the ecology and genetics of speciation, and semi-isolated species where hybrids can still be produced are particularly relevant.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04088575/file/Tenaillon%20et%20al.%20-%202023%20-%20Crop%20domestication%20as%20a%20step%20towards%20reproductive%20.pdf BibTex
titre
Genotype-by-environment and QTL-by-environment interactions in sweet cherry (Prunus avium L.) for flowering date
auteur
Camille Branchereau, Craig Hardner, Elisabeth Dirlewanger, Bénédicte Wenden, Loïck Le Dantec, David Alletru, Julien Parmentier, Anton Ivančič, Daniela Giovannini, Federica Brandi, Gregorio Lopez-Ortega, Federico Garcia-Montiel, Bénédicte Quilot-Turion, José Quero-García
article
Frontiers in Plant Science, 2023, 14, ⟨10.3389/fpls.2023.1142974⟩
resume
In sweet cherry ( Prunus avium L.), flowering date is strongly dependent on the environment conditions and, therefore, is a trait of major interest for adaptation to climate change. Such trait can be influenced by genotype-by-environment interaction (G×E), that refers to differences in the response of genotypes to different environments. If not taken into account, G×E can reduce selection accuracy and overall genetic gain. However, little is known about G×E in fruit tree species. Flowering date is a highly heritable and polygenic trait for which many quantitative trait loci (QTLs) have been identified. As for the overall genetic performance, differential expression of QTLs in response to environment (QTL-by-environment interaction, QTL×E) can occur. The present study is based on the analysis of a multi-environment trial (MET) suitable for the study of G×E and QTL×E in sweet cherry. It consists of a sweet cherry F 1 full-sib family (n = 121) derived from the cross between cultivars ‘Regina’ and ‘Lapins’ and planted in two copies in five locations across four European countries (France, Italy, Slovenia and Spain) covering a large range of climatic conditions. The aim of this work was to study the effect of the environment on flowering date and estimate G×E, to carry QTL detection in different environments in order to study the QTL stability across environments and to estimate QTL×E. A strong effect of the environment on flowering date and its genetic control was highlighted. Two large-effect and environment-specific QTLs with significant QTL×E were identified on linkage groups (LGs) 1 and 4. This work gives new insights into the effect of the environment on a trait of main importance in one of the most economically important fruit crops in temperate regions. Moreover, molecular markers were developed for flowering date and a strategy consisting in using specific markers for warm or cold regions was proposed to optimize marker-assisted selection (MAS) in sweet cherry breeding programs.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04050266/file/2023-Branchereau-Frontiers_in_Plant_Science.pdf BibTex
titre
Genetic variability in the susceptibility of immature peach fruit to Monilinia laxa is associated with surface conductance but not stomatal density
auteur
Leandro de Oliveira Lino, Carole Confolent, Véronique Signoret, Michel Génard, Quilot-Turion Bénédicte
article
Journal of Plant Science and Phytopathology, 2023, 6 (3), pp.091-100. ⟨10.29328/journal.jpsp.1001081⟩
resume
Monilinia laxa is a fungus that causes brown rot in stone fruit. Immature green fruits in the first stage of fruit development (stage I) are generally susceptible. To investigate the relationship between the physical characteristics of immature fruit and susceptibility to M. laxa, we characterized the progeny, derived from a clone of wild peach (Prunus davidiana) crossed with two commercial nectarines (Prunus persica) varieties, through laboratory infection, transpiration monitoring and stomata counting. Two types of fruit infections were observed - ‘classic’ brown rot and ‘clear spot’ symptoms - which have not previously been described in the literature. The number and density of stomata did not explain the observed variability of infection in the progeny. However, surface conductance was positively correlated with infection level. This study provides experimental evidence partially linking physical fruit characteristics to brown rot infection at the immature fruit stage. The role of delayed cuticle deposition in susceptibility to brown rot of immature fruit is discussed.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03935451/file/Lino_etal_ImmatureFruitMoniliaConductanceStomata_JPSP_2022.pdf BibTex
titre
Exploration of high‐throughput data for heat tolerance selection in Capsicum annuum
auteur
Nathan Fumia, Michael Kantar, Ya‐ping Lin, Roland Schafleitner, Véronique Lefebvre, Ilan Paran, Andreas Börner, Maria José Diez, Jaime Prohens, Arnaud Bovy, Filiz Boyaci, Gancho Pasev, Pasquale Tripodi, Lorenzo Barchi, Giovanni Giuliano, Derek Barchenger
article
The Plant Phenome Journal, 2023, 6 (1), pp.e20071. ⟨10.1002/ppj2.20071⟩
resume
Recently, there has been a substantial increase in high-throughput technologies that generate highly complex large datasets for use in the sciences. Plant breeding and genetics have benefited from this data explosion where many public and private institutions now implement genomic and phenomic data to predict performance thus informing germplasm selection. However, the multitude of methodologies and data generates a situation of strategic uncertainty. We set out to compare different methods of genomic and phenomic selection in the Capsicum core collection, developed through the G2P-SOL project, producing a combination of unique and similar selected genotypes for heat tolerance. Combined, the methods tested identified a total of 33 genotypes that show tremendous promise for use as parents in heat tolerance breeding: with 13 of these being present in more than 1 selection method. Combining classical and multispectral phenotyping methods produced better selection results than either method alone. When each method was conducted without being informed by the other, similar results were obtained. Our weighted rank-sum selection index identified 10 entries across environments that show heat tolerance, 8 of which are also selected within heat environments. This suggests that different breeding programs can reach similar results despite having different logistical constraints. Our case study within pepper germplasm using phenomic and genomic data exhibits the potential to compensate for the dearth of germplasm knowledge with high-throughput data as well as the converse, to compensate for logistical or financial constraint to new technologies with breeder knowledge.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04176395/file/The%20Plant%20Phenome%20Journal%20-%202023%20-%20Fumia.pdf BibTex
titre
Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis)
auteur
Henri Duval, Eva Coindre, Sebastian E Ramos-Onsins, Konstantinos G Alexiou, Maria J Rubio-Cabetas, Pedro J Martínez-García, Michelle Wirthensohn, Amit Dhingra, Anna Samarina, Pere Arús
article
Plants, 2023, 12 (2), pp.242. ⟨10.3390/plants12020242⟩
resume
A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-03935771/file/2022-Duva-plants.pdf BibTex
titre
NLRs are highly relevant resistance genes for aphid pest
auteur
Nathalie Boissot
article
Current Opinion in Insect Science, In press, 56, pp.101008. ⟨10.1016/j.cois.2023.101008⟩
resume
Since the beginning of the 20th century, when plant resistance to aphids has been available, it has been widely used by farmers. This has boosted breeding programs for resistant cultivars. More recently, the inheritance of plant resistance has been understood for several crops. However, it is only when the plant-aphid relationship was compared to that of microbial pathogens, that aphid resistance has begun to be understood and integrated into the plant immune network. Until now, genes have only been identified for plant resistance in four crops and, for three of them (tomato, melon and wheat), these genes encode nucleotide-binding site LRR receptor (NLR) proteins responsible for aphid-effector triggered immunity. Aphids are vectors for many plant viruses, and aphid-effector triggering immunity when they pierce plant cells are expected to trigger resistance to the viruses that are transmit to the plant with effectors, as has been shown for aphid resistance in melon. This dual phenotype increases the interest of NLRs in the control of aphids. New NLRs and genes belonging to other families are also obviously involved in aphid resistance. Genome Wide Association Studies (GWAS) are promising strategies to identify these genes when high throughput phenotyping is available
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03972031/file/Resistance%20to%20aphids_version_auteur.pdf BibTex
titre
Adapting stone fruit trees to pesticide reduction: screening apricot and peach core collections for multi-pest resistance via integrative phenotyping under low pesticide management
auteur
Marie Serrie, A. Blanc, Laurent Brun, G. Clauzel, Freddy Combe, F. Gilles, G. Roch, V. Signoret, S. Viret, Jean-Marc Audergon, B. Quilot-Turion, M. Roth
article
Acta Horticulturae, 2023, 1384, pp.329-338. ⟨10.17660/ActaHortic.2023.1384.43⟩
resume
Stone fruit production must address an urgent societal and environmental demand for pesticide reduction in a context of unexpected epidemiological changes due to climate change. Cultivar improvement is a promising strategy to operate a sustainable transition towards low phytosanitary management. However, to date we lack cultivars bearing multiple resistances against pests and diseases and genetic resources are underused. To tackle this issue, two core collections composed by 150 apricot and 206 peach accessions have been set up. These collections have been planted respectively in two and three sites along a North-South gradient between Valence and Perpignan (France), between 2017 and 2019. These orchards are managed under low phytosanitary protection to observe the damages of pests and diseases present in natural conditions as well as phenological variables relevant as epidemiological covariates. Thus far, we have monitored three phenological traits of interest in these young orchards: blooming date, vegetative bud break and flower density. We observed a wide phenotypic diversity within the orchards, which illustrates the high genetic diversity represented in our core collections. Moreover, we observed high values of broad sense heritability (between 0.67 and 0.90) and we identified a strong effect of the environment and of genotype by environment interactions. Our results highlight the importance of a multi-site and multi-annual design to account for these effects for breeding perennials. To our knowledge, our design deployed with the objective of studying the multiple resistances to pests and diseases in apricot and peach, is the first of such amplitude. This project paves the way for future genome-wide association studies aiming at identifying candidate genes for multiple resistances to develop marker assisted selection.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies
auteur
Johan Rollin, Rachelle Bester, Yves Brostaux, Kadriye Caglayan, Kris de Jonghe, Ales Eichmeier, Yoika Foucart, Annelies Haegeman, Igor Koloniuk, Petr Kominek, Hans Maree, Serkan Onder, Susana Posada Céspedes, Vahid Roumi, Dana Šafářová, Olivier Schumpp, Cigdem Ulubas Serce, Merike Sõmera, Lucie Tamisier, Eeva Vainio, Rene Aa van der Vlugt, Sebastien Massart
article
PeerJ, 2023, 11, pp.e15816. ⟨10.7717/peerj.15816⟩
resume
Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04185674/file/2023_Rollin_PeerJ.pdf BibTex
titre
Going beyond consensus genome sequences: an innovative SNP-based methodology reconstructs different Uganda cassava brown streak virus haplotypes at a nationwide scale in Rwanda.
auteur
Chantal Nyirakanani, Lucie Tamisier, Jean Pierre Bizimana, Johan Rollin, Athanase Nduwumuremyi, Vincent de Paul Bigirimana, Ilhem Selmi, Ludivine Lasois, Hervé Vanderschuren, Sébastien Massart
article
Virus Evolution, In press, ⟨10.1093/ve/vead053⟩
resume
Cassava Brown Streak Disease (CBSD), which is caused by cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), represents one of the most devastating threats to cassava production in Africa, including in Rwanda where a dramatic epidemic in 2014 dropped cassava yield from 3.3 million to 900,000 tonnes (1). Studying viral genetic diversity at the genome level is essential in disease management, as it can provide valuable information on the origin and dynamics of epidemic events. To fill the current lack of genome-based diversity studies of UCBSV, we performed a nationwide survey of cassava ipomovirus genomic sequences in Rwanda by high-throughput sequencing (HTS) of pools of plants sampled from 130 cassava fields in 13 cassava-producing districts, spanning seven agro-ecological zones with contrasting climatic conditions and different cassava cultivars. HTS allowed the assembly of a nearly complete consensus genome of UCBSV in 12 districts. The phylogenetic analysis revealed high homology between UCBSV genome sequences, with a maximum of 0.8 % divergence between genomes at the nucleotide level. An in-depth investigation based on Single Nucleotide Polymorphisms (SNP) was conducted to explore the genome diversity beyond the consensus sequences. First, to ensure the validity of the result, a panel of SNPs was confirmed by independent RT-PCR and Sanger sequencing. Furthermore, the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNPs patterns identified three different UCBSV haplotypes geographically clustered. The haplotype 2 (H2) was restricted to the central regions, where the NAROCAS 1 cultivar is predominantly farmed. RT-PCR and Sanger sequencing of individual NAROCAS1 plants confirmed their association with H2. Haplotype 1 was widely spread, with a 100% occurrence in the Eastern region, while Haplotype 3 was only found in the Western region. These haplotypes’ associations with specific cultivars or regions would need further confirmation. Our results prove that a much more complex picture of genetic diversity can be deciphered beyond the consensus sequences, with practical implications on virus epidemiology, evolution, and disease management. Our methodology proposes a high-resolution analysis of genome diversity beyond the consensus between and within samples. It can be used at various scales, from individual plants to pooled samples of virus-infected plants. Our findings also showed how subtle genetic differences could be informative on the potential impact of agricultural practices, as the presence and frequency of a virus haplotype could be correlated with the dissemination and adoption of improved cultivars.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04193124/file/virusEvolution_Nyirakanani_23.pdf BibTex
titre
Arabidopsis eIF4E1 protects the translational machinery during TuMV infection and restricts virus accumulation
auteur
Delyan Zafirov, Nathalie Giovinazzo, Cécile Lecampion, Ben Field, Julia Novion Ducassou, Yohann Couté, Karen S Browning, Christophe Robaglia, Jean-Luc Gallois
article
PLoS Pathogens, 2023, 19 (11), pp.e1011417. ⟨10.1371/journal.ppat.1011417⟩
resume
Successful subversion of translation initiation factors eIF4E determines the infection success of potyviruses, the largest group of viruses affecting plants. In the natural variability of many plant species, resistance to potyvirus infection is provided by polymorphisms at eIF4E that renders them inadequate for virus hijacking but still functional in translation initiation. In crops where such natural resistance alleles are limited, the genetic inactivation of eIF4E has been proposed for the engineering of potyvirus resistance. However, recent findings indicate that knockout eIF4E alleles may be deleterious for plant health and could jeopardize resistance efficiency in comparison to functional resistance proteins. Here, we explored the cause of these adverse effects by studying the role of the Arabidopsis eIF4E1 , whose inactivation was previously reported as conferring resistance to the potyvirus clover yellow vein virus (ClYVV) while also promoting susceptibility to another potyvirus turnip mosaic virus (TuMV). We report that eIF4E1 is required to maintain global plant translation and to restrict TuMV accumulation during infection, and its absence is associated with a favoured virus multiplication over host translation. Furthermore, our findings show that, in the absence of eIF4E1, infection with TuMV results in the production of a truncated eIFiso4G1 protein. Finally, we demonstrate a role for eIFiso4G1 in TuMV accumulation and in supporting plant fitness during infection. These findings suggest that eIF4E1 counteracts the hijacking of the plant translational apparatus during TuMV infection and underscore the importance of preserving the functionality of translation initiation factors eIF4E when implementing potyvirus resistance strategies.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04447408/file/2023e%20Zafirov%20Plos%20Pathogens.pdf BibTex
titre
Volatile organic compound emissions from almond shoots during spring: dissociation between reproductive and vegetative organs
auteur
Anjélica Leconte, Nicolas Barthes, Bruno Buatois, Eugénie Coutagne, Henri Duval, Philippe Lucas, Michael Staudt
article
Comptes Rendus. Chimie, 2023, 26 (S2), pp.1-16. ⟨10.5802/crchim.241⟩
resume
Prunus dulcis, a fruit tree of global economic and nutritional importance, is infested by Eurytoma amygdali, the almond wasp, due to the lack of biocontrol measures. This study characterizes the volatile organic compounds (VOCs) emitted by almond trees. We identified and quantified by GC-MS 44 VOCs emitted during spring. VOCs emitted during flowering were benzaldehyde and 1,4-dimethoxybenzene, while VOCs emitted during fruit and leaf growth were mainly sesquiterpenes. Emissions increased with temperature but light did not affect short-term emissions. VOCs identified in this study could be used to develop a biocontrol method to prevent infestation.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04193216/file/CRCHIM_2023__leconte.pdf BibTex
titre
A single nonsynonymous substitution in the RNA-dependent RNApolymerase of Potato virus y allows the simultaneous breakdown of two different forms of antiviral resistance in Capsicum annuum
auteur
Benoît Moury, Thierry Michon, Vincent Simon, Alain Palloix
article
Viruses, 2023, 15, pp.1081. ⟨10.3390/v15051081⟩
resume
The dominant Pvr4 gene in pepper (Capsicum annuum) confers resistance to members of six potyvirus species, all of which belong to the Potato virus Y (PVY) phylogenetic group. The corresponding avirulence factor in the PVY genome is the NIb cistron (i.e., RNA-dependent RNA polymerase). Here, we describe a new source of potyvirus resistance in the Guatemalan accession C. annuum cv. PM949. PM949 is resistant to members of at least three potyvirus species, a subset of those controlled by Pvr4. The F1 progeny between PM949 and the susceptible cultivar Yolo Wonder was susceptible to PVY, indicating that the resistance is recessive. The segregation ratio between resistant and susceptible plants observed in the F2 progeny matched preferably with resistance being determined by two unlinked recessive genes independently conferring resistance to PVY. Inoculations by grafting resulted in the selection of PVY mutants breaking PM949 resistance and, less efficiently, Pvr4–mediated resistance. The codon substitution E472K in the NIb cistron of PVY, which was shown previously to be sufficient to break Pvr4 resistance, was also sufficient to break PM949 resistance, a rare example of cross-pathogenicity effect. In contrast, the other selected NIb mutants showed specific infectivity in PM949 or Pvr4 plants. Comparison of Pvr4 and PM949 resistance, which share the same target in PVY, provides interesting insights into the determinants of resistance durability.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04086320/file/2023_Moury_Viruses-V0.pdf BibTex
titre
Monitoring systemic infection by cucumber mosaic virus using a small fluorescent protein iLOV in plants
auteur
Ayaka Kawakubo, Jean-Luc Gallois, Kenji Nakahara
article
Journal of General Plant Pathology, 2023, 89, pp.47-52. ⟨10.1007/s10327-022-01100-6⟩
resume
Tracking virus infection in plants is useful to assess plant susceptibility or resistance. The recombinant cucumber mosaic virus (CMV) expressing a 2b-fused green fluorescent protein (GFP, 25 kDa) gradually loses (within weeks) the GFP gene in plants. Here, we constructed CMV expressing a flavin-based small fluorescent protein (iLOV, 10 kDa). CMV-iLOV still retains iLOV after 28 dpi in upper leaves of inoculated Nicotiana benthamiana and allows long-term monitoring of its distribution in plants. Using CMV-iLOV, we showed that pot1, a recessive allele for resistance to potyviruses, does not confer CMV resistance in tomato.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Exploration of bacterial diversity in leaves and rhizosphere soil of flood affected and unaffected apricot trees
auteur
Hedia Bourguiba, Chahnez Naccache, Salwa Zehdi-Azouzi, Fatma Amdouni, Neila Trifi-Farah, Jean-Marc Audergon, Fabrice Armougom, Maha Mezghani-Khemakhem
article
Biologia, In press, 78, pp.217-227. ⟨10.1007/s11756-022-01228-y⟩
resume
Plants harbor diverse and taxonomically structured communities of protective microorganisms that confer beneficial characteristics in plant growth and protection against biotic and abiotic stresses. The aim of this study is to characterize the composition of endophytic bacterial communities in leaves and rhizobacterial communities of the flood affected and unaffected apricot trees by 16S rRNA genes metabarcoding. Results showed a slight bacterial diversity reduction in flood affected condition compared to the unaffected one. The relative bacterial abundance analysis showed that the bacterial taxa were almost uniformly distributed between the leaves. However, a clear differential taxa abundance was observed in rhizosphere soil which may be associated with apricot tree environmental status. In fact, the flood affected rhizosphere soil showed a significant increase in several bacterial taxa including particularly Bacillusfrigoritolerans and Pseudoarthrobacterphenanthrenivorans which are known to be beneficial to soil. However, some Actinobacteria genera that promote growth of plants, including Nocardioidessp.,Streptomycessp.,BlastococcusandGeodermatophilus were decreased in abundance. This distribution of abundance and diversity of the bacterial community in the flood affected tree can be correlated to abiotic stress. These results provide new insights into rhizosphere-associated microbes that are likely playing a crucial role in plant growth and survival.
typdoc
Journal articles
Accès au bibtex
BibTex

2022

Journal articles

titre
Genetic diversity in a new peach core-collection designed for resilience breeding
auteur
Morgane Roth, Marie Serrie, Naïma Dlalah, Véronique Signoret, Sabrina Viret, Frederic Gilles, Yannick Montrognon, Bénédicte Quilot-Turion
article
Acta Horticulturae, 2022, 1352, pp.141-148. ⟨10.17660/ActaHortic.2022.1352.19⟩
resume
Understanding and harnessing crop genetic diversity is critical for a sustainable use of genetic resources. In peach, the narrow genetic basis in the cultivated pool could threaten future cultivar improvement but extant genetic resources can be mobilized to alleviate this issue. To this aim, populations called core-collections can be created to represent species’ diversity in an optimal way. In this context, we selected a large panel of individuals among elite and exotic peach genetic pools to design a peach core-collection of 206 accessions and aimed at validating its suitability for genetic analyses and resilience breeding. Among them, 192 accessions could be successfully genotyped with the IRSC 16k Illumina SNP-array. Structure analyses via discriminant analysis of principal components and sparse non-negative matrix factorization were congruent and showed the existence of three main genetic groups with moderate admixture, which was coherent with the current knowledge on peach genetic structuration. We also report wide variations in phenology and in leaf spot susceptibility, illustrating the large genetic diversity and breeding potential of this core-collection. Further phenotyping this population in a multisite experimental design under low pesticide cover will allow us to accelerate the discovery of useful variants for resilience breeding.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
auteur
Nelina Angelova, Theodoros Danis, Jacques Lagnel, Costas S Tsigenopoulos, Tereza Manousaki
article
BMC Research Notes, 2022, 15 (1), pp.98. ⟨10.1186/s13104-022-05978-5⟩
resume
Objective The rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through genome analyses. The foremost challenges of the field involve coping with questions emerging from the swift development and application of new algorithms, as well as the establishment of standardized analysis approaches that promote transparency and transferability in research. Results Here, we present SnakeCube, an automated and containerized whole de novo genome assembly pipeline that runs within isolated, secured environments and scales for use in High Performance Computing (HPC) domains. SnakeCube was optimized for its performance and tested for its effectiveness with various inputs, highlighting its safe and robust universal use in the field.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03842053/file/angelova.bmc.2022.pdf BibTex
titre
Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper
auteur
Gaëtan Maillot, Emmanuel Szadkowski, Anne Massire, Véronique Brunaud, Guillem Rigaill, Bernard Caromel, Joël Chadœuf, Alexandre Bachellez, Nasradin Touhami, Ingo Hein, Kurt Lamour, Sandrine Balzergue, Véronique Lefebvre
article
Frontiers in Plant Science, 2022, 13 (980587), pp.1-19. ⟨10.3389/fpls.2022.980587⟩
resume
Partial resistance in plants generally exerts a low selective pressure on pathogens, and thus ensuring their durability in agrosystems. However, little is known about the effect of partial resistance on the molecular mechanisms of pathogenicity, a knowledge that could advance plant breeding for sustainable plant health. Here we investigate the gene expression of Phytophthora capsici during infection of pepper ( Capsicum annuum L.), where only partial genetic resistance is reported, using Illumina RNA-seq. Comparison of transcriptomes of P. capsici infecting susceptible and partially resistant peppers identified a small number of genes that redirected its own resources into lipid biosynthesis to subsist on partially resistant plants. The adapted and non-adapted isolates of P. capsici differed in expression of genes involved in nucleic acid synthesis and transporters. Transient ectopic expression of the RxLR effector genes CUST_2407 and CUST_16519 in pepper lines differing in resistance levels revealed specific host-isolate interactions that either triggered local necrotic lesions (hypersensitive response or HR) or elicited leave abscission (extreme resistance or ER), preventing the spread of the pathogen to healthy tissue. Although these effectors did not unequivocally explain the quantitative host resistance, our findings highlight the importance of plant genes limiting nutrient resources to select pepper cultivars with sustainable resistance to P. capsici .
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03908269/file/fpls-13-980587.pdf BibTex
titre
The control of carpel determinacy pathway leads to sex determination in cucurbits
auteur
Siqi Zhang, Feng-Quan Tan, Ching-Hui Chung, Filip Slavkovic, Ravi Sureshbhai Devani, Christelle Troadec, Fabien Marcel, Halima Morin, Céline Camps, Maria Victoria Gomez Roldan, Moussa Benhamed, Catherine Dogimont, Adnane Boualem, Abdelhafid Bendahmane
article
Science, 2022, 378 (6619), pp.543-549. ⟨10.1126/science.add4250⟩
resume
Male and female unisexual flowers evolved from hermaphroditic ancestors, and control of flower sex is useful for plant breeding. We isolated a female-to-male sex transition mutant in melon and identified the causal gene as the carpel identity gene CRABS CLAW (CRC) . We show that the master regulator of sex determination in cucurbits, the transcription factor WIP1 whose expression orchestrates male flower development, recruits the corepressor TOPLESS to the CRC promoter to suppress its expression through histone deacetylation. Impairing TOPLESS-WIP1 physical interaction leads to CRC expression, carpel determination, and consequently the expression of the stamina inhibitor, the aminocyclopropane-1-carboxylic acid synthase 7 ( CmACS7 ), leading to female flower development. Our findings suggest that sex genes evolved to interfere with flower meristematic function, leading to unisexual flower development.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Pepper variome reveals the history and key loci associated with fruit domestication and diversification
auteur
Yacong Cao, Kang Zhang, Hailong Yu, Shumin Chen, Donghui Xu, Hong Zhao, Zhenghai Zhang, Yinqing Yang, Xiaozhen Gu, Xinyan Liu, Haiping Wang, Yaxin Jing, Yajie Mei, Xiang Wang, Véronique Lefebvre, Weili Zhang, Yuan Jin, Dongliang An, Risheng Wang, Paul Bosland, Xixiang Li, Ilan Paran, Baoxi Zhang, Giovanni Giuliano, Lihao Wang, Feng Cheng
article
Molecular Plant, 2022, 15 (11), pp.1744-1758. ⟨10.1016/j.molp.2022.09.021⟩
resume
Pepper (Capsicum spp.) is an important vegetable crop that provides a unique pungent sensation when eaten. Through construction of a pepper variome map, we examined the main groups that emerged during domestication and breeding of C. annuum, their relationships and temporal succession, and the molecular events underlying the main transitions. The results showed that the initial differentiation in fruit shape and pungency, increase in fruit weight, and transition from erect to pendent fruits, as well as the recent appearance of large, blocky, sweet fruits (bell peppers), were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions. Furthermore, we identified Up, which encodes a BIG GRAIN protein involved in auxin transport, as a key domestication gene that controls erect vs pendent fruit orientation. The up mutation gained increased expression especially in the fruit pedicel through a 579bp sequence deletion in its 5 0 upstream region, resulting in the phenotype of pendent fruit. The function of Up was confirmed by virus-induced gene silencing. Taken together, these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04132419/file/Cao_2022_MolPlant_PepperCapsicumAnnuumVariomeFruitDomestication.pdf BibTex
titre
The Molecular Characterization of a New Prunus-Infecting Cheravirus and Complete Genome Sequence of Stocky Prune Virus
auteur
Maryam Khalili, Thierry Candresse, Yoann Brans, Chantal Faure, Jean-Marc Audergon, Véronique Decroocq, Guillaume Roch, Armelle Marais
article
Viruses, 2022, 14 (11), pp.2325. ⟨10.3390/v14112325⟩
resume
As part of a virome characterization of Prunus species, a novel cheravirus was discovered in two wild species, Prunus brigantina and P. mahaleb, and in an apricot (P. armeniaca) accession. The sequence of the two genomic RNAs was completed for two isolates. The Pro-Pol conserved region showed 86% amino acid (aa) identity with the corresponding region of trillium govanianum cheravirus (TgCV), a tentative Cheravirus member, whereas the combined coat proteins (CPs) shared only 40% aa identity with TgCV CPs, well below the species demarcation threshold for the genus. This suggests that the new virus should be considered a new species for which the name alpine wild prunus virus (AWPV) is proposed. In parallel, the complete genome sequence of stocky prune virus (StPV), a poorly known cheravirus for which only partial sequences were available, was determined. A phylogenetic analysis showed that AWPV, TgCV and StPV form a distinct cluster, away from other cheraviruses.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03833094/file/2022-Khalili-Viruses.pdf BibTex
titre
Molecular mechanisms of resistance to Myzus persicae conferred by the peach Rm2 gene: A multi-omics view
auteur
Pauline Le Boulch, Jean-Luc Poëssel, David Roux, Raphaël Lugan
article
Frontiers in Plant Science, 2022, 13, pp.992544. ⟨10.3389/fpls.2022.992544⟩
resume
The transcriptomic and metabolomic responses of peach to Myzus persicae infestation were studied in Rubira, an accession carrying the major resistance gene Rm2 causing antixenosis, and GF305, a susceptible accession. Transcriptome and metabolome showed both a massive reconfiguration in Rubira 48 hours after infestation while GF305 displayed very limited changes. The Rubira immune system was massively stimulated, with simultaneous activation of genes encoding cell surface receptors involved in pattern-triggered immunity and cytoplasmic NLRs (nucleotide-binding domain, leucine-rich repeat containing proteins) involved in effector-triggered immunity. Hypersensitive reaction featured by necrotic lesions surrounding stylet punctures was supported by the induction of cell death stimulating NLRs/helpers couples, as well as the activation of H 2 O 2 -generating metabolic pathways: photorespiratory glyoxylate synthesis and activation of the futile P5C/proline cycle. The triggering of systemic acquired resistance was suggested by the activation of pipecolate pathway and accumulation of this defense hormone together with salicylate. Important reduction in carbon, nitrogen and sulphur metabolic pools and the repression of many genes related to cell division and growth, consistent with reduced apices elongation, suggested a decline in the nutritional value of apices. Finally, the accumulation of caffeic acid conjugates pointed toward their contribution as deterrent and/or toxic compounds in the mechanisms of resistance.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04047701/file/2022_Le%20Boulch_Front_Plant_Sci.pdf BibTex
titre
Field phenotyping of root architectural diversity in aubergine ( Solanum melongena L.) and related species
auteur
A. Hereil, J. Salinier, M. Daunay, R. Stevens
article
Acta Horticulturae, 2022, 1348, pp.163-172. ⟨10.17660/ActaHortic.2022.1348.22⟩
resume
Root architecture and plant biomass traits were investigated for 25 aubergine-genepool accessions representative of 9 Solanum L. species, including S. melongena L. The accessions were grown in the field in southeastern France and had previously been phenotyped in 1-m high PVC tubes. Few or weak correlations existed for the traits measured in the field with traits measured using the tubes: root diameters measured using the two methods showed some correlation. In the field, S. melongena genotypes had the highest harvest index but showed different strategies for carbon allocation to fruits, roots and shoots. Variation for biomass and harvest index traits existed in the collection as well as for the different root traits, including their: number, diameter, volume and angle frequency. These results indicate possibilities for adaptation of aubergine accessions to different environments that could be tested as rootstocks.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Phenolic profiling in ten apricot clones using an efficient method (Thioacidolysis-UFLC) and determination of their antioxidant potential
auteur
Jamal Ayour, Jean-Marc Audergon, Catherine M.G.C. Renard, Mohamed Benichou, Carine Le Bourvellec
article
Food Bioscience, 2022, 49, pp.101880. ⟨10.1016/j.fbio.2022.101880⟩
resume
The polyphenols of ten Moroccan apricot clones were analyzed using a Thioacidolysis-UFLC combination technology in order to evaluate their evolution pattern and their contribution to antioxidant activity during ripening. Procyanidins were the predominant polyphenol class with concentrations varied from 30 to 1091 mg kg(-1) in M1 (commercial stage) and from 398 to 1411 mg kg(-1) in M2 (consumption stage). Procyanidins with catechins, the two classes constitute the principal contributors to antioxidant activity of studied apricots. The impact of ripening was very limited compared to genotype, especially for size and skin color of the fruit. The Thioacidolysis-UFLC technology highlighted the contribution of procyanidins to antioxidant activity of apricot and established a typology based on the clone skin color. Indeed, dark red and orange apricots had higher phenolic contents and antioxidant activities than clear ones. This indicates the importance of fruit color to predict apricot bioactive compounds and the crucial role of phenolic compounds in the antioxidant activity of these fruits.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The Rm1 and Rm2 Resistance Genes to Green Peach Aphid (Myzus persicae) Encode the Same TNL Proteins in Peach (Prunus persica L.)
auteur
Henri Duval, Laure Heurtevin, Naïma Dlalah, Caroline Callot, Jacques Lagnel
article
Genes, 2022, 13 (8), ⟨10.3390/genes13081489⟩
resume
The green peach aphid (GPA), Myzus persicae, is an important pest of the peach crop. Three major dominant resistance genes have already been detected, Rm1 in the Weeping Flower Peach (WFP) clone, Rm2 in the Rubira clone, and Rm3 in the Fen Shouxing clone. In this study, after NGS resequencing of WFP and Rubira, we found that their genomic sequences in the Rm1 and Rm2 region were similar but very different from that of the susceptible reference peach Lovell. We constructed a BAC library for the GPA-resistant WFP and screened four BAC clones to sequence the target region. The new sequence was 61.7 Kb longer than Lovell and was annotated with four different TIR_NBS_LRR genes. Among them, the TNL1 gene was very overexpressed in WFP leaves 24 h after GPA infestation. This gene was also present and expressed in the Rubira clone and had the same sequence as the candidate Rm3 gene, supporting the hypothesis that the three genes share the same origin. In addition, we identified a second TNL, TNL2, located at 35.4 Kb from TNL1 and slightly overexpressed after GPA infestation. Kasp and size molecular markers were designed for use in marker-assisted selection and were validated in a peach segregating population.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Deployment of quality management systems in the biological resource centres of the AgroBRC infrastructure
auteur
Mélanie Martignon, Valerie Bergheaud, S. Buff, Victoria Chuat, Roland Cottin, Juliette Goussopoulos, Deborah Jardet, Michèle Tixier-Boichard, Florence Valence
article
NOV'AE, 2022, Numéro Spécial 02, RARe, pp.174-182. ⟨10.17180/novae-2022-NS02-art22⟩
resume
The quality management system of a structure is a management support tool. This article presents several of the systems deployed or in the process of formulation in the biological resource centres of the AgroBRC/RARe research infrastructure. They form a panel of situations present in each of the five pillars (animal, environment, forest, microorganisms and plants), and represent the diversity that exists in terms of maturity, certification standards, and specific contexts. For each of the cases presented, we analyse the benefits perceived and the difficulties encountered. The external recognition of the level of organisation provided by certification is an expected goal of the research infrastructure. That is why it organises events for the biological resource centres to foster sharing experiences and improving the skills of the teams involved.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://vetagro-sup.hal.science/hal-03720198/file/Qualit%C3%A9%20CRB_Ressources_agronomiques.pdf BibTex
titre
Inheritance of Secondary Metabolites and Gene Expression Related to Tomato Fruit Quality
auteur
Estelle Bineau, José Luis Rambla, Renaud Duboscq, Marie-Noëlle Corre, Frédérique Bitton, Raphaël Lugan, Antonio Granell, Clémence Plissonneau, Mathilde Causse
article
International Journal of Molecular Sciences, 2022, 23 (11), pp.6163. ⟨10.3390/ijms23116163⟩
resume
Flavour and nutritional quality are important goals for tomato breeders. This study aimed to shed light upon transgressive behaviors for fruit metabolic content. We studied the metabolic contents of 44 volatile organic compounds (VOCs), 18 polyphenolics, together with transcriptome profiles in a factorial design comprising six parental lines and their 14 F1 hybrids (HF1) among which were five pairs of reciprocal HF1. After cluster analyses of the metabolome dataset and co-expression network construction of the transcriptome dataset, we characterized the mode of inheritance of each component. Both overall and per-cross mode of inheritance analyses revealed as many additive and non-additive modes of inheritance with few reciprocal effects. Up to 66% of metabolites displayed transgressions in a HF1 relative to parental values. Analysis of the modes of inheritance of metabolites revealed that: (i) transgressions were mostly of a single type whichever the cross and poorly correlated to the genetic distance between parental lines; (ii) modes of inheritance were scarcely consistent between the 14 crosses but metabolites belonging to the same cluster displayed similar modes of inheritance for a given cross. Integrating metabolome, transcriptome and modes of inheritance analyses suggested a few candidate genes that may drive important changes in fruit VOC contents.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03842733/file/Bineau_ijms-2022.pdf BibTex
titre
Exploring New Routes for Genetic Resistances to Potyviruses: The Case of the Arabidopsis thaliana Phosphoglycerates Kinases (PGK) Metabolic Enzymes
auteur
Mamoudou Diop, Jean-Luc Gallois
article
Viruses, 2022, 14 (6), pp.1245. ⟨10.3390/v14061245⟩
resume
The development of recessive resistance by loss of susceptibility is a consistent strategy to combat and limit damages caused by plant viruses. Susceptibility genes can be turned into resistances, a feat that can either be selected among the plant’s natural diversity or engineered by biotechnology. Here, we summarize the current knowledge on the phosphoglycerate kinases (PGK), which have emerged as a new class of susceptibility factors to single-stranded positive RNA viruses, including potyviruses. PGKs are metabolic enzymes involved in glycolysis and the carbon reduction cycle, encoded by small multigene families in plants. To fulfil their role in the chloroplast and in the cytosol, PGKs genes encode differentially addressed proteins. Here, we assess the diversity and homology of chloroplastic and cytosolic PGKs sequences in several crops and review the current knowledge on their redundancies during plant development, taking Arabidopsis as a model. We also show how PGKs have been shown to be involved in susceptibility—and resistance—to viruses. Based on this knowledge, and drawing from the experience with the well-characterized translation initiation factors eIF4E, we discuss how PGKs genes, in light of their subcellular localization, function in metabolism, and susceptibility to viruses, could be turned into efficient genetic resistances using genome editing techniques.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03842615/file/diop_viruses-2022.pdf BibTex
titre
European traditional tomatoes galore: a result of farmers’ selection of a few diversity-rich loci
auteur
Jose Blanca, Clara Pons, Javier Montero-Pau, David Sanchez-Matarredona, Peio Ziarsolo, Lilian Fontanet, Josef Fisher, Mariola Plazas, Joan Casals, Jose Luis Rambla, Alessandro Riccini, Samuela Pombarella, Alessandra Ruggiero, Maria Sulli, Stephania Grillo, Angelos Kanellis, Giovanni Giuliano, Richard Finkers, Maria Cammareri, Silvana Grandillo, Andrea Mazzucato, Mathilde Causse, Maria José Díez, Jaime Prohens, Dani Zamir, Joaquin Cañizares, Antonio Jose Monforte, Antonio Granell
article
Journal of Experimental Botany, 2022, 73 (11), pp.3431-3445. ⟨10.1093/jxb/erac072⟩
resume
A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent secondary centers of diversity with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a genome-wide association study with fruit morphological traits in the European traditional collection. The corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise a low-diversity population suggests a history of balancing selection, in which tomato farmers likely maintained the morphological variation by inadvertently applying a high selective pressure within different varietal types.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03657385/file/erac072.pdf BibTex
titre
CmLHP1 proteins play a key role in plant development and sex determination in melon ( Cucumis melo )
auteur
Natalia Yaneth Rodriguez‐granados, Juan Sebastian Ramirez‐prado, Rim Brik‐chaouche, Jing An, Deborah Manza‐mianza, Sanchari Sircar, Christelle Troadec, Melissa Hanique, Camille Soulard, Rafael Costa, Catherine Dogimont, David Latrasse, Cécile Raynaud, Adnane Boualem, Moussa Benhamed, Abdelhafid Bendahmane
article
The Plant Journal, 2022, 109 (5), pp.1213-1228. ⟨10.1111/tpj.15627⟩
resume
In monoecious melon (Cucumis melo), sex is determined by the differential expression of sex determination genes (SDGs) and adoption of sex-specific transcriptional programs. Histone modifications such as H3K27me3 have been previously shown to be a hallmark associated to unisexual flower development in melon; yet, no genetic approaches have been conducted for elucidating the roles of H3K27me3 writers, readers, and erasers in this process. Here we show that melon homologs to Arabidopsis LHP1, CmLHP1A and B, redundantly control several aspects of plant development, including sex expression. Cmlhp1ab double mutants displayed an overall loss and redistribution of H3K27me3, leading to a deregulation of genes involved in hormone responses, plant architecture, and flower development. Consequently, double mutants display pleiotropic phenotypes and, interestingly, a general increase of the male:female ratio. We associated this phenomenon with a general deregulation of some hormonal response genes and a local activation of male-promoting SDGs and MADS-box transcription factors. Altogether, these results reveal a novel function for CmLHP1 proteins in maintenance of monoecy and provide novel insights into the polycomb-mediated epigenomic regulation of sex lability in plants.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Prime Editing in the model plant Physcomitrium patens and its potential in the tetraploid potato
auteur
Pierre-François Perroud, Anouchka Guyon-Debast, Florian Veillet, Marie-Paule Kermarrec, Laura Chauvin, Jean-Eric Chauvin, Jean-Luc Gallois, Fabien Nogué
article
Plant Science, 2022, 316, pp.111162. ⟨10.1016/j.plantsci.2021.111162⟩
resume
Since its discovery and first applications for genome editing in plants, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology has revolutionized plant research and precision crop breeding. Although the classical CRISPR-Cas9 system is a highly efficient tool for disruptive targeted mutagenesis, this system is mostly inefficient for the introduction of precise and predictable nucleotide substitutions. Recently, Prime Editing technology has been developed, allowing the simultaneous generation of nucleotide transitions and transversions but also short defined indels. In this study, we report on the successful use of Prime Editing in two plants of interest: the plant model Physcomitrium patens and the tetraploid and highly heterozygous potato (Solanum tuberosum). In both cases editing rates were lower than with other CRISPR-Cas9 based techniques, but we were able to successfully introduce nucleotide transversions into targeted genes, a unique feature of Prime Editing. Additionally, the analysis of potential off-target mutation sites in P. patens suggested very high targeting fidelity in this organism. The present work paves the way for the use Prime Editing in Physcomitrium patens and potato, however highlighting the limitations that need to be overcome for more efficient precision plant breeding.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03632448/file/Perroud_1-s2.0-S0168945221003587-main.pdf BibTex
titre
CRISPR-based knock-out of eIF4E2 in a cherry tomato background successfully recapitulates resistance to pepper veinal mottle virus
auteur
Kyoka Kuroiwa, Christina Thenault, Fabien Nogué, Laura Perrot, Marianne Mazier, Jean-Luc Gallois
article
Plant Science, 2022, 316, pp.1-7. ⟨10.1016/j.plantsci.2021.111160⟩
resume
The host susceptibility factors are important targets to develop genetic resistances in crops. Genome editing tools offer exciting prospects to develop resistances based on these susceptibility factors, directly in the cultivar of choice. Translation initiation factors 4E have long been known to be a susceptibility factor to the main genus of Potyviridae, potyviruses, but the inactivation of the eIF4E2 gene has only recently been shown to provide resistance to some isolates of pepper veinal mottle virus (PVMV) in big-fruit tomato plants. Here, using CRISPR-Cas9-NG, we show how eIF4E2 can be targeted and inactivated in cherry tomato plants. Three independent knockout alleles caused by indel in the first exon of eIF4E2, resulted in the complete absence of the eIF4E2 protein. All three lines displayed a narrow resistance spectrum to potyvirus, similar to the one described earlier for an eIF4E2 EMS mutant of M82, a big-fruit tomato cultivar; the plants were fully resistant to PVMV-Ca31, partially to PVMV-IC and were fully susceptible to two isolates of PVY assayed: N605 and LYE84. These results show how easily a resistance based on eIF4E2 can be transferred across tomato cultivar, but also confirm that gene redundancy can narrow the resistances based on eIF4E knockout.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The INRAE Centre for Vegetable Germplasm: Geographically and Phenotypically Diverse Collections and Their Use in Genetics and Plant Breeding
auteur
Jérémy Salinier, Véronique Lefebvre, Didier Besombes, Hélène Burck, Mathilde Causse, Marie-Christine Daunay, Catherine Dogimont, Juliette Goussopoulos, Christophe Gros, Brigitte Maisonneuve, Louis Mcleod, Fatiha Tobal, Rebecca Stevens
article
Plants, 2022, 11 (3), pp.1-19. ⟨10.3390/plants11030347⟩
resume
The French National Research Institute for Agriculture, Food and the Environment (INRAE) conserves and distributes five vegetable collections as seeds: the aubergine* (in this article the word aubergine refers to eggplant), pepper, tomato, melon and lettuce collections, together with their wild or cultivated relatives, are conserved in Avignon, France. Accessions from the collections have geographically diverse origins, are generally well-described and fixed for traits of agronomic or scientific interest and have available passport data. In addition to currently conserving over 10,000 accessions (between 900 and 3000 accessions per crop), the centre maintains scientific collections such as core collections and bi- or multi-parental populations, which have also been genotyped with SNP markers. Each collection has its own merits and highlights, which are discussed in this review: the aubergine collection is a rich source of crop wild relatives of Solanum; the pepper, melon and lettuce collections have been screened for resistance to plant pathogens, including viruses, fungi, oomycetes and insects; and the tomato collection has been at the heart of genome-wide association studies for fruit quality traits and environmental stress tolerance.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03551518/file/2022_plants_salinier.pdf BibTex
titre
I-SceI and customized meganucleases-mediated genome editing in tomato and oilseed rape
auteur
Benoit Danilo, Émilie Montes, Héloïse Archambeau, Maryse Lodé-Taburel, Mathieu Rousseau-Gueutin, Anne-Marie Chèvre, Marianne Mazier
article
Transgenic Research, 2022, 31 (1), pp.87-105. ⟨10.1007/s11248-021-00287-2⟩
resume
Meganucleases are rare cutting enzymes that can generate DNA modifications and are part of the plant genome editing toolkit although they lack versatility. Here, we evaluated the use of two meganucleases, I-SceI and a customized meganuclease, in tomato and oilseed rape. Different strategies were explored for the use of these meganucleases. The activity of a customized and a I-SceI meganucleases was first estimated by the use of a reporter construct GFFP with the target sequences and enabled to demonstrate that both meganucleases can generate double-strand break and HDR mediated recombination in a reporter gene. Interestingly, I-SceI seems to have a higher DSB efficiency than the customized meganuclease: up to 62.5% in tomato and 44.8% in oilseed rape. Secondly, the same exogenous landing pad was introduced in both species. Despite being less efficient compared to I-SceI, the customized meganuclease was able to generate the excision of an exogenous transgene (large deletion of up to 3316 bp) present in tomato. In this paper, we also present some pitfalls to be considered before using meganucleases (e.g., potential toxicity) for plant genome editing.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral Cucurbitaceae karyotype
auteur
Clement Pichot, Anis Djari, Joseph Tran, Marion Verdenaud, William Marande, Cécile C. Huneau, David Latrasse, Vivien Sommard, V. Gautier, Judit Szecsi, Sandrine Arribat, Christelle Troadec, Charles Poncet, Mohammed Bendahmane, Catherine Dogimont, Jerome Salse, Moussa Benhamed, Mohamed Zouine, Adnane Boualem, Abdelhafid Bendahmane
article
iScience, 2022, 25 (1), pp.103696. ⟨10.1016/j.isci.2021.103696⟩
resume
Cucumis melo displays a large diversity of horticultural groups with cantaloupe melon the most cultivated type. Using a combination of single-molecule sequencing, 10X Genomics link-reads, high-density optical and genetic maps, and chromosome conformation capture (Hi-C), we assembled a chromosome scale C. melo var. cantalupensis Charentais mono genome. Integration of RNA-seq, MeDip-seq, ChIP-seq, and Hi-C data revealed a widespread compartmentalization of the melon genome, segregating constitutive heterochromatin and euchromatin. Genome-wide comparative and evolutionary analysis between melon botanical groups identified Charentais mono genome increasingly more divergent from Harukei-3 (reticulatus), Payzawat (inodorus), and HS (ssp. agrestis) genomes. To assess the paleohistory of the Cucurbitaceae, we reconstructed the ancestral Cucurbitaceae karyotype and compared it to sequenced cucurbit genomes. In contrast to other species that experienced massive chromosome shuffling, melon has retained the ancestral genome structure. We provide comprehensive genomic resources and new insights in the diversity of melon horticultural groups and evolution of cucurbits.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03507170/file/Pichot_2022.pdf BibTex
titre
Genetic architecture and genomic predictive ability of apple quantitative traits across environments
auteur
Michaela Jung, Beat Keller, Morgane Roth, Maria José Aranzana, Annemarie Auwerkerken, Walter Guerra, Mehdi Al-Rifaï, Mariusz Lewandowski, Nadia Sanin, Marijn Rymenants, Frédérique Didelot, Christian Dujak, Carolina Font I Forcada, Andrea Knauf, François Laurens, Bruno Studer, Helene Muranty, Andrea Patocchi
article
Horticulture research, 2022, 9, pp.uhac028. ⟨10.1093/hr/uhac028⟩
resume
Abstract Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18–0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03661146/file/pmc_8976694.pdf BibTex
titre
Insertion of a mMoshan transposable element in PpLMI1, is associated with the absence or globose phenotype of extrafloral nectaries in peach [Prunus persica (L.) Batsch
auteur
Patrick Lambert, Carole Confolent, Laure Heurtevin, Naïma Dlalah, Véronique Signoret, Bénédicte Quilot-Turion, Thierry Pascal
article
Horticulture research, 2022, 9, pp.1-13. ⟨10.1093/hortre/uhab044⟩
resume
Most commercial peach [Prunus persica (L.) Batsch] cultivars have leaves with extraf loral nectaries (EFNs). Breeders have selected this character over time, as they observed that the eglandular phenotype resulted in high susceptibility to peach powdery mildew, a major disease of peach trees. EFNs are controlled by a Mendelian locus (E), mapped on chromosome 7. However, the genetic factor underlying E was unknown. In order to address this point, we developed a mapping population of 833 individuals derived from the selfing of "Malo Konare", a Bulgarian peach cultivar, heterozygous for the trait. This progeny was used to investigate the E-locus region, along with additional resources including peach genomic resequencing data, and 271 individuals from various origins used for validation. High-resolution mapping delimited a 40.6 kbp interval including the E-locus and four genes. Moreover, three doublerecombinants allowed identifying Prupe.7G121100, a LMI1-like homeodomain leucine zipper (HD-Zip) transcription factor, as a likely candidate for the trait. By comparing peach genomic resequencing data from individuals with contrasted phenotypes, a MITE-like transposable element of the hAT superfamily (mMoshan) was identified in the third exon of Prupe.7G121100. It was associated with the absence or globose phenotype of EFNs. The insertion of the transposon was positively correlated with enhanced expression of Prupe.7G121100. Furthermore, a PCR marker designed from the sequence-variants, allowed to properly assign the phenotypes of all the individuals studied. These findings provide valuable information on the genetic control of a trait poorly known so far although selected for a long time in peach.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03539501/file/Peach%20nectary%20paper_Lambert_26june_VF.pdf BibTex
titre
Atlas of phenotypic, genotypic and geographical diversity present in the European traditional tomato
auteur
Clara Pons, Joan Casals, Samuela Palombieri, Lilian Fontanet, Alessandro Riccini, Jose Luis Rambla, Alessandra Ruggiero, Maria del Rosario Figás, Mariola Plazas, Athanasios Koukounaras, Maurizio E Picarella, Maria Sulli, Josef Fisher, Peio Ziarsolo, Jose Blanca, Joaquin Cañizares, Maria Cammareri, Antonella Vitiello, Giorgia Batelli, Angelos Kanellis, Matthijs Brouwer, Richard Finkers, Konstantinos Nikoloudis, Salvador Soler, Giovanni Giuliano, Stephania Grillo, Silvana Grandillo, Dani Zamir, Andrea Mazzucato, Mathilde Causse, Maria José Díez, Jaime Prohens, Antonio Jose Monforte, Antonio Granell
article
Horticulture research, 2022, 9 (uhac112), ⟨10.1093/hr/uhac112⟩
resume
The Mediterranean basin countries are considered secondary centres of tomato diversification. However, information on phenotypic and allelic variation of local tomato materials is still limited. Here we report on the evaluation of the largest traditional tomato collection, which includes 1499 accessions from Southern Europe. Analyses of 70 traits revealed a broad range of phenotypic variability with different distributions among countries, with the culinary end use within each country being the main driver of tomato diversification. Furthermore, eight main tomato types (phenoclusters) were defined by integrating phenotypic data, country of origin, and end use. Genome-wide association study (GWAS) meta-analyses identified associations in 211 loci, 159 of which were novel. The multidimensional integration of phenoclusters and the GWAS meta-analysis identified the molecular signatures for each traditional tomato type and indicated that signatures originated from differential combinations of loci, which in some cases converged in the same tomato phenotype. Our results provide a roadmap for studying and exploiting this untapped tomato diversity.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03744877/file/Pons_uhac_22.pdf BibTex
titre
Multiple haplotype-based analyses provide genetic and evolutionary insights into tomato fruit weight and composition
auteur
Jiantao Zhao, Christopher Sauvage, Frédérique Bitton, Mathilde Causse
article
Horticulture research, 2022, 9 (uhab009), pp.1-14. ⟨10.1093/hr/uhab009⟩
resume
Improving fruit quality traits such as metabolic composition remains a challenge for tomato breeders. To better understand the genetic architecture of these traits and decipher the demographic history of the loci controlling tomato quality traits, we applied an innovative approach using multiple haplotype-based analyses, aiming to test the potentials of haplotype based study in association and genomic prediction studies. We performed and compared haplotype vs SNP-based associations (hapQTL) with multi-locus mixed model (MLMM), focusing on tomato fruit weight and metabolite contents (i.e. sugars, organic acids and amino acids). Using a panel of 163 tomato accessions genotyped with 5995 SNPs, we detected a total of 784 haplotype blocks, with an average size of haplotype blocks ~58 kb. A total of 108 significant associations for 26 traits were detected thanks to Haplotype/SNP-based Bayes models. Haplotype-based Bayes model (97 associations) outperformed SNP-based Bayes model (50 associations) and MLMM (53 associations) in identifying marker-trait associations as well as in genomic prediction (especially for those traits with moderate to low heritability). To decipher the demographic history, we identified 24 positive selective sweeps using the integrated haplotype score (iHS). Most of the significant associations for tomato quality traits were located within selective sweeps (54.63% and 71.7% in hapQTL and MLMM models, respectively). Promising candidate genes were identified controlling tomato fruit weight and metabolite contents. We thus demonstrated the benefits of using haplotypes for evolutionary and genetic studies, providing novel insights into tomato quality improvement and breeding history.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03657384/file/zhao.horticulturaleResearch_2024.pdf BibTex
titre
Unravelling cucumber resistance to several viruses via genome-wide association studies highlighted resistance hotspots and new QTLs
auteur
Severine Monnot, Melissa Cantet, Tristan Mary-Huard, Laurence Moreau, Rebecca Lowdon, Maurine van Haesendonck, Agnès Ricard, Nathalie Boissot
article
Horticulture research, 2022, 9, pp.uhac184. ⟨10.1093/hr/uhac184⟩
resume
Abstract The mapping and introduction of sustainable resistance to viruses in crops is a major challenge in modern breeding, especially regarding vegetables. We hence assembled a panel of cucumber elite lines and landraces from different horticultural groups for testing with six virus species. We mapped 18 quantitative trait loci (QTL) with a multiloci genome wide association studies (GWAS), some of which have already been described in the literature. We detected two resistance hotspots, one on chromosome 5 for resistance to the cucumber mosaic virus (CMV), cucumber vein yellowing virus (CVYV), cucumber green mottle mosaic virus (CGMMV) and watermelon mosaic virus (WMV), colocalizing with the RDR1 gene, and another on chromosome 6 for resistance to the zucchini yellowing mosaic virus (ZYMV) and papaya ringspot virus (PRSV) close to the putative VPS4 gene location. We observed clear structuring of resistance among horticultural groups due to plant virus coevolution and modern breeding which have impacted linkage disequilibrium (LD) in resistance QTLs. The inclusion of genetic structure in GWAS models enhanced the GWAS accuracy in this study. The dissection of resistance hotspots by local LD and haplotype construction helped gain insight into the panel’s resistance introduction history. ZYMV and CMV resistance were both introduced from different donors in the panel, resulting in multiple resistant haplotypes at same locus for ZYMV, and in multiple resistant QTLs for CMV.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03971463/file/Monnot_uhac184_2022.pdf BibTex
titre
Concurrent evolution of resistance and tolerance to potato virus Y in Capsicum annuum revealed by genome‐wide association
auteur
Lucie Tamisier, Marion Szadkowski, Gregory Girardot, Caroline Djian-Caporalino, Alain Palloix, Judith Hirsch, Benoît Moury
article
Molecular Plant Pathology, 2022, 23, pp.254-264. ⟨10.1111/mpp.13157⟩
resume
We performed a genome-wide association study of pepper (Capsicum annuum) tolerance to potato virus Y (PVY). For 254 pepper accessions, we estimated the tolerance to PVY as the coefficient of regression of the fresh weight (or height) of PVY-infected and mock-inoculated plants against within-plant virus load. Small (strongly negative) coefficients of regression indicate low tolerance because plant biomass or growth decreases sharply as virus load increases. The tolerance level varied largely, with some pepper accessions showing no symptoms or fairly mild mosaics, whereas about half (48%) of the accessions showed necrotic symptoms. We found two adjacent single-nucleotide polymorphisms (SNPs) at one extremity of chromosome 9 that were significantly associated with tolerance to PVY. Similarly, in three biparental pepper progenies, we showed that the induction of necrosis on PVY systemic infection segregated as a monogenic trait determined by a locus on chromosome 9. Our results also demonstrate the existence of a negative correlation between resistance and tolerance among the cultivated pepper accessions at both the phenotypic and genetic levels. By comparing the distributions of the tolerance-associated SNP alleles and previously identified PVY resistance-associated SNP alleles, we showed that cultivated pepper accessions possess favourable alleles for both resistance and tolerance less frequently than expected under random associations, while the minority of wild pepper accessions frequently combined resistance and tolerance alleles. This divergent evolution of PVY resistance and tolerance could be related to pepper domestication or farmer's selection.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03418676/file/2021_Tamisier_MPP.pdf BibTex
titre
Improving genomic predictions with inbreeding and nonadditive effects in two admixed maize hybrid populations in single and multienvironment contexts
auteur
Morgane Roth, Aurélien Beugnot, Tristan Mary-Huard, Laurence Moreau, Alain Charcosset, Julie Fiévet
article
Genetics, 2022, 220 (4), pp.1-18. ⟨10.1093/genetics/iyac018⟩
resume
Genetic admixture, resulting from the recombination between structural groups, is frequently encountered in breeding populations. In hybrid breeding, crossing admixed lines can generate substantial nonadditive genetic variance and contrasted levels of inbreeding which can impact trait variation. This study aimed at testing recent methodological developments for the modeling of inbreeding and nonadditive effects in order to increase prediction accuracy in admixed populations. Using two maize (Zea mays L.) populations of hybrids admixed between dent and flint heterotic groups, we compared a suite of five genomic prediction models incorporating (or not) parameters accounting for inbreeding and nonadditive effects with the natural and orthogonal interaction approach in single and multienvironment contexts. In both populations, variance decompositions showed the strong impact of inbreeding on plant yield, height, and flowering time which was supported by the superiority of prediction models incorporating this effect (þ0.038 in predictive ability for mean yield). In most cases dominance variance was reduced when inbreeding was accounted for. The model including additivity, dominance, epistasis, and inbreeding effects appeared to be the most robust for prediction across traits and populations (þ0.054 in predictive ability for mean yield). In a multienvironment context, we found that the inclusion of nonadditive and inbreeding effects was advantageous when predicting hybrids not yet observed in any environment. Overall, comparing variance decompositions was helpful to guide model selection for genomic prediction. Finally, we recommend the use of models including inbreeding and nonadditive parameters following the natural and orthogonal interaction approach to increase prediction accuracy in admixed populations.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-03659124/file/Roth_2022_Genetics_to_share.pdf BibTex
titre
A single substitution in Vacuolar protein sorting 4 is responsible for resistance to Watermelon mosaic virus in melon
auteur
Aimeric Agaoua, Vincent Rittener, Christelle Troadec, Cecile Desbiez, Abdelhafid Bendahmane, Frédéric Moquet, Catherine Dogimont
article
Journal of Experimental Botany, 2022, 73, pp.4008-4021. ⟨10.1093/jxb/erac135⟩
resume
In plants, introgression of genetic resistance is a proven strategy for developing new resistant lines. While host proteins involved in genome replication and cell to cell movement are widely studied, other cell mechanisms responsible for virus infection remain under investigated. Endosomal sorting complexes required for transport (ESCRT) play a key role in membrane trafficking in plants and are involved in the replication of several plant RNA viruses. In this work, we describe the role of the ESCRT protein CmVPS4 as a new susceptibility factor to the Potyvirus Watermelon mosaic virus (WMV) in melon. Using a worldwide collection of melons, we identified three different alleles carrying non-synonymous substitutions in CmVps4. Two of these alleles were shown to be associated with WMV resistance. Using a complementation approach, we demonstrated that resistance is due to a single non-synonymous substitution in the allele CmVps4P30R. This work opens up new avenues of research on a new family of host factors required for virus infection and new targets for resistance.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03671982/file/Agaoua%20et%20al%202022%20JEXBOT%20version%20accept%C3%A9e%20avec%20figures.pdf BibTex
titre
Genetic control of tomato fruit quality: from QTL mapping to Genome Wide Association studies and breeding
auteur
Mathilde Causse, Juliette Bénéjam, Frédérique Bitton, Marie Brault, Yolande Carretero, Henri Desaint, Alexandre Hereil, Karine Pellegrino, Esther Pelpoir, Jiantao Zhao
article
Comptes Rendus. Biologies, 2022, 345 (4), pp.3-13. ⟨10.5802/crbiol.99⟩
resume
Consumers began to complain about the taste of tomato varieties in the late 1990's. Although tomato taste is influenced by environmental and post-harvest conditions, varieties show a large diversity for fruit quality traits. We herein review our past and present research work intended to improve tomato fruit quality. First, results from sensory analysis allowed identifying important traits for consumer preferences. Then, we dissected the genetic control of flavor related traits by mapping several QTL in the last 20 years, and identified the genes corresponding to a few major QTL. Since the availability of the tomato genome sequence, genome-wide association studies were performed on several panels of tomato accessions. We discovered a large number of associations for fruit composition and identified relevant allele combinations for breeding. We then performed a meta-analysis combining the results of several studies. We also checked the inheritance of quality traits at the hybrid level and assessed how genomic prediction could help selecting better tomato varieties
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04169924/file/CRBIOL_2022_Causse.pdf BibTex
titre
Mapping the intensity function of a non-stationary point process in unobserved areas
auteur
Edith Gabriel, Francisco Rodríguez-Cortés, Jérôme Coville, Jorge Mateu, Joël Chadœuf
article
Stochastic Environmental Research and Risk Assessment, In press, ⟨10.1007/s00477-022-02304-0⟩
resume
Seismic networks provide data that are used as basis both for public safety decisions and for scientific research. Their configuration affects the data completeness, which in turn, critically affects several seismological scientific targets (e.g., earthquake prediction, seismic hazard...). In this context, a key aspect is how to map earthquakes density in seismogenic areas from censored data or even in areas that are not covered by the network. We propose to predict the spatial distribution of earthquakes from the knowledge of presence locations and geological relationships, taking into account any interaction between records. Namely, in a more general setting, we aim to estimate the intensity function of a point process, conditional to its censored realization, as in geostatistics for continuous processes. We define a predictor as the best linear unbiased combination of the observed point pattern. We show that the weight function associated to the predictor is the solution of a Fredholm equation of second kind. Both the kernel and the source term of the Fredholm equation are related to the first- and second-order characteristics of the point process through the intensity and the pair correlation function. Results are presented and illustrated on simulated non-stationary point processes and real data for mapping Greek Hellenic seismicity in a region with unreliable and incomplete records.
typdoc
Journal articles
Accès au bibtex
https://arxiv.org/pdf/2111.14403 BibTex
titre
Introduction process, approaches and tools for managing the health of stone fruits of the BRC Prunus-Juglans
auteur
Marine Delmas, Jean Leonetti, Delphine Racofier, Marie-Laure Greil, Frédéric Gauillard, Alain Blanc, Jean-Marc Audergon
article
NOV'AE, 2022, Numéro Spécial 02, RARe, pp.10-15. ⟨10.17180/novae-2022-NS02-art01⟩
resume
The collections of the BRC Prunus-Juglans of INRAE conserve around 2,800 accessions of stone fruits (Prunus), in the PACA and Nouvelle-Aquitaine regions of France. These species, mostly obtained through vegetative propagation, are particularly vulnerable to health risks, notably viruses and bacteria. To protect the collections and permit their exploitation, two points of vigilance are ensured with the SRAL on the regulatory level: the introduction of healthy plant material, and monitoring the collections. European health regulations and phytosanitary passport, and the fruit tree certification system, are two key elements of this process. They ensure that the material introduced is as safe as possible, and the sustainable protection of the resources in the collection. Depending on the risks, isolation, control and prevention measures are decided and taken by the employees of the BRC.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04623668/file/NOVAE2022_Ressources_art01.pdf BibTex
titre
Specificity of resistance and tolerance to cucumber vein yellowing virus in melon accessions and evidence for resistance breaking associated with a single mutation in VPg
auteur
Cecile Desbiez, Maria Luisa Domingo Calap, Michel Pitrat, Catherine Wipf-Scheibel, Gregory Girardot, Inmaculada Ferriol, Juan Jose Lopez-Moya, Hervé Lecoq
article
Phytopathology, 2022, 112 (5), pp.1185-1191. ⟨10.1094/PHYTO-06-21-0263-R⟩
resume
Cucumber vein yellowing virus (CVYV) is an emerging virus on cucurbits in the Mediterranean Basin, against which few resistance sources are available, particularly in melon. The melon accession PI 164323 displays complete resistance to isolate CVYV-Esp, and accession HSD 2458 presents a tolerance, i.e. very mild symptoms in spite of virus accumulation in inoculated plants. The resistance is controlled by a dominant allele Cvy-1 1 , while the tolerance is controlled by a recessive allele cvy-2, independent from Cvy-1 1 . Before introducing the resistance or tolerance in commercial cultivars through a long breeding process, it is important to estimate their specificity and durability. Upon inoculation with eight molecularly diverse CVYV isolates, the resistance was found to be isolate-specific since many CVYV isolates induced necrosis on PI 164323, whereas the tolerance presented a broader range. A resistance-breaking isolate inducing severe mosaic on PI 164323 was obtained. This isolate differed from the parental strain by a single amino acid change in the VPg coding region. An infectious CVYV cDNA clone was obtained, and the effect of the mutation in the VPg cistron on resistance to PI 164323 was confirmed by reverse genetics. This represents the first determinant for resistance-breaking in an ipomovirus. Our results indicate that the use of the Cvy-1 1 allele alone will not provide durable resistance to CVYV and that, if used in the field, it should be combined with other control methods such as cultural practices and pyramiding of resistance genes to achieve long-lasting resistance against CVYV.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03428436/file/2021_Desbiez_Phytopath.pdf BibTex
titre
The stem rust effector protein AvrSr50 escapes Sr50 recognition by a substitution in a single surface‐exposed residue
auteur
Diana Ortiz, Jian Chen, Megan Outram, Isabel Saur, Narayana Upadhyaya, Rohit Mago, Daniel Ericsson, Stella Cesari, Chunhong Chen, Simon Williams, Peter Dodds
article
New Phytologist, 2022, 234 (2), pp.592-606. ⟨10.1111/nph.18011⟩
resume
Pathogen effectors are crucial players during plant colonisation and infection. Plant resistance mostly relies on effector recognition to activate defence responses. Understanding how effector proteins escape from plant surveillance is important for plant breeding and resistance deployment. Here we examined the role of genetic diversity of the stem rust (Puccinia graminis f. sp. tritici (Pgt)) AvrSr50 gene in determining recognition by the corresponding wheat Sr50 resistance gene. We solved the crystal structure of a natural variant of AvrSr50 and used site-directed mutagenesis and transient expression assays to dissect the molecular mechanisms explaining gain of virulence. We report that AvrSr50 can escape recognition by Sr50 through different mechanisms including DNA insertion, stop codon loss or by amino-acid variation involving a single substitution of the AvrSr50 surface-exposed residue Q121. We also report structural homology of AvrSr50 to cupin superfamily members and carbohydrate-binding modules indicating a potential role in binding sugar moieties. This study identifies key polymorphic sites present in AvrSr50 alleles from natural stem rust populations that play important roles to escape from Sr50 recognition. This constitutes an important step to better understand Pgt effector evolution and to monitor AvrSr50 variants in natural rust populations.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03610628/file/Ortiz-NP-2022-CC-BU-NC-ND.pdf BibTex

2021

Journal articles

titre
Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars
auteur
Felipe Pérez de Los Cobos, Pedro J Martínez-García, Agustí Romero, Xavier Miarnau, Iban Eduardo, Werner Howad, Mourad Mnejja, Federico Dicenta, Rafel Socias I Company, Maria J Rubio-Cabetas, Thomas M Gradziel, Michelle Wirthensohn, Henri Duval, Doron Holland, Pere Arús, Francisco J Vargas, Ignasi Batlle
article
Horticulture research, 2021, 8 (1), pp.1-11. ⟨10.1038/s41438-020-00444-4⟩
resume
Abstract Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the S f allele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Stochastic models support rapid peopling of Late Pleistocene Sahul
auteur
Corey Bradshaw, Kasih Norman, Sean Ulm, Alan Williams, Chris Clarkson, Joël Chadœuf, Sam Lin, Zenobia Jacobs, Richard Roberts, Michael Bird, Laura Weyrich, Simon Haberle, Sue O’connor, Bastien Llamas, Tim Cohen, Tobias Friedrich, Peter Veth, Matthew Leavesley, Frédérik Saltré
article
Nature Communications, 2021, 12 (1), ⟨10.1038/s41467-021-21551-3⟩
resume
The peopling of Sahul (the combined continent of Australia and New Guinea) represents the earliest continental migration and settlement event of solely anatomically modern humans, but its patterns and ecological drivers remain largely conceptual in the current literature. We present an advanced stochastic-ecological model to test the relative support for scenarios describing where and when the first humans entered Sahul, and their most probable routes of early settlement. The model supports a dominant entry via the northwest Sahul Shelf first, potentially followed by a second entry through New Guinea, with initial entry most consistent with 50,000 or 75,000 years ago based on comparison with bias-corrected archaeological map layers. The model’s emergent properties predict that peopling of the entire continent occurred rapidly across all ecological environments within 156–208 human generations (4368–5599 years) and at a plausible rate of 0.71–0.92 km year −1 . More broadly, our methods and approaches can readily inform other global migration debates, with results supporting an exit of anatomically modern humans from Africa 63,000–90,000 years ago, and the peopling of Eurasia in as little as 12,000–15,000 years via inland routes.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Effect of long-term drought on tomato leaves: the impact on metabolic and antioxidative response
auteur
Ivana Petrović, Slađana Savić, Justine Gricourt, Mathilde Causse, Zorica Jovanović, Radmila Stikić
article
Physiology and Molecular Biology of Plants, 2021, 27 (12), pp.2805-2817. ⟨10.1007/s12298-021-01102-2⟩
resume
Water deficit triggers physiological, biochemical, and molecular changes in leaves that could be important for overall plant adaptive response and it can affect tomato yield and quality. To assess the influence of long-term moderate drought on leaves, four tomato accessions from MAGIC TOM populations were selected on the basis of their differences in fruit size and were grown in a glasshouse under control and water deficit conditions. Drought affected stomatal conductance more in large fruit genotypes compared to cherry genotypes and this could be related to higher abscisic acid (ABA) leaf content. Compared to large fruits, cherry tomato genotypes coped better with water stress by reducing leaf area and maintaining photochemical efficiency as important adaptive responses. Accumulation of soluble sugars in the cherry genotypes and organic acid in the leaves of the larger fruit genotypes indicated their role in the osmoregulation and the continuum of source/sink gradient under stress conditions. Long-term moderate drought induced upregulation of NCED gene in all four genotypes that was associated with ABA production. The increase in the expression of ZEP gene was found only in the LA1420 cherry genotype and indicated its possible role in the protection against photooxidative stress induced by prolonged water stress. In addition, upregulation of the APX genes, higher accumulation of vitamin C and total antioxidant capacity in cherry genotype leaves highlighted their greater adaptive response against long-term drought stress compared to larger fruit genotypes that could also reflect at fruit level.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances
auteur
Severine Monnot, Henri Desaint, Tristan Mary-Huard, Laurence Moreau, Valerie Schurdi-Levraud, Nathalie Boissot
article
Cells, 2021, 10 (11), pp.3080. ⟨10.3390/cells10113080⟩
resume
Growing virus resistant varieties is a highly effective means to avoid yield loss due to infection by many types of virus. The challenge is to be able to detect resistance donors within plant species diversity and then quickly introduce alleles conferring resistance into elite genetic backgrounds. Until now, mainly monogenic forms of resistance with major effects have been introduced in crops. Polygenic resistance is harder to map and introduce in susceptible genetic backgrounds, but it is likely more durable. Genome wide association studies (GWAS) offer an opportunity to accelerate mapping of both monogenic and polygenic resistance, but have seldom been implemented and described in the plant–virus interaction context. Yet, all of the 48 plant–virus GWAS published so far have successfully mapped QTLs involved in plant virus resistance. In this review, we analyzed general and specific GWAS issues regarding plant virus resistance. We have identified and described several key steps throughout the GWAS pipeline, from diversity panel assembly to GWAS result analyses. Based on the 48 published articles, we analyzed the impact of each key step on the GWAS power and showcase several GWAS methods tailored to all types of viruses.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-03424384/file/2021-Monnot-cells.pdf BibTex
titre
Sensory Traits and Consumer’s Perceived Quality of Traditional and Modern Fresh Market Tomato Varieties: A Study in Three European Countries
auteur
Fiorella Sinesio, Maria Cammareri, Valentine Cottet, Lilian Fontanet, Michel Jost, Elisabetta Moneta, Samuela Palombieri, Marina Peparaio, Roser Romero del Castillo, Eleonora Saggia Civitelli, Patrizia Spigno, Antonella Vitiello, Brigitte Navez, Joan Casals, Mathilde Causse, Antonio Granell, Silvana Grandillo
article
Foods, 2021, 10 (11), pp.1-22. ⟨10.3390/foods10112521⟩
resume
Consumer dissatisfaction with the flavor quality of many modern fresh market tomato varieties has fostered breeders’ interest in sensory quality improvement, and the demand for traditional varieties, which are generally associated with better flavor. To achieve further knowledge on the factors influencing the sensory quality and consumers’ preferences and perception, European traditional and modern fresh market tomato varieties were grown and evaluated in France, Italy, and Spain. Different growing conditions were tested in France (soilless vs. soil) and in Spain (open field vs. greenhouse), while in Italy fruits were evaluated at two ripening stages. Fruit quality was assessed by integrating physicochemical analyses, sensory profiles, and consumer tests. In all three countries, overall modern varieties were perceived as having more intense “tomato flavor” and “overall flavor” than traditional ones. In France and Spain, consumers’ preferences were more oriented towards modern varieties than traditional ones. Significant growing condition effects were found on sensory and physicochemical traits, while the effect on consumers’ overall liking was not significant, largely depending on the genotype. A fair agreement between product configurations from descriptive analysis by trained assessors and Check-All-That-Apply (CATA) questions by consumers was observed. Penalty-lift analysis based on CATA allowed identifying positive and negative drivers of liking.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03543114/file/foods-10-02521-v3.pdf BibTex
titre
Membrane Trafficking Proteins: A New Target to Identify Resistance to Viruses in Plants
auteur
Aimeric Agaoua, Abdelhafid Bendahmane, Frédéric Moquet, Catherine Dogimont
article
Plants, 2021, 10 (10), pp.1-12. ⟨10.3390/plants10102139⟩
resume
Replication cycles from most simple-stranded positive RNA viruses infecting plants involve endomembrane deformations. Recent published data revealed several interactions between viral proteins and plant proteins associated with vesicle formation and movement. These plant proteins belong to the COPI/II, SNARE, clathrin and ESCRT endomembrane trafficking mechanisms. In a few cases, variations of these plant proteins leading to virus resistance have been identified. In this review, we summarize all known interactions between these plant cell mechanisms and viruses and highlight strategies allowing fast identification of variant alleles for membrane-associated proteins.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids
auteur
Estelle Bineau, José Luis Rambla, Santiago Priego-Cubero, Alexandre Hereil, Frédérique Bitton, Clémence Plissonneau, Antonio Granell, Mathilde Causse
article
Genes, 2021, 12 (9), pp.1443. ⟨10.3390/genes12091443⟩
resume
Tomato flavour is an important goal for breeders. Volatile organic compounds (VOCs) are major determinants of tomato flavour. Although most tomato varieties for fresh market are F1 hybrids, most studies on the genetic control of flavour-related traits are performed on lines. We quantified 46 VOCs in a panel of 121 small fruited lines and in a test cross panel of 165 hybrids (the previous panel plus 44 elite cherry tomato lines crossed with a common line). High and consistent heritabilities were assessed for most VOCs in the two panels, and 65% of VOC contents were strongly correlated between lines and hybrids. Additivity was observed for most VOCs. We performed genome wide association studies (GWAS) on the two panels separately, along with a third GWAS on the test cross subset carrying only F1 hybrids corresponding to the line panel. We identified 205, 183 and 138 associations, respectively. We identified numerous overlapping associations for VOCs belonging to the same metabolic pathway within each panel; we focused on seven chromosome regions with clusters of associations simultaneously involved in several key VOCs for tomato aroma. The study highlighted the benefit of testcross panels to create tasty F1 hybrid varieties.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03543122/file/genes-12-01443-v2.pdf BibTex
titre
Genomics accelerated isolation of a new stem rust avirulence gene–wheat resistance gene pair
auteur
Narayana M Upadhyaya, Rohit Mago, Vinay Panwar, Tim Hewitt, Ming Luo, Jian Chen, Jana Sperschneider, Hoa Nguyen-Phuc, Aihua Wang, Diana Vallejo Ortiz, Luch Hac, Dhara Bhatt, Feng Li, Jianping Zhang, Michael Ayliffe, Melania Figueroa, Kostya Kanyuka, Jeffrey G Ellis, Peter N Dodds
article
Nature Plants, 2021, 7 (9), pp.1220-1228. ⟨10.1038/s41477-021-00971-5⟩
resume
Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled in the latter half of the twentieth century, new virulent strains of Pgt, such as Ug99, have recently evolved1,2. These strains have caused notable losses worldwide and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases3. A number of rust resistance genes have been characterized in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class4, which recognize pathogen effector proteins known as avirulence (Avr) proteins5. However, only two Avr genes have been identified in Pgt so far, AvrSr35 and AvrSr50 (refs. 6,7), and none in other cereal rusts8,9. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye10. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale), which is a wheat–rye hybrid and is a host for Pgt11,12. Sr27 is effective against Ug99 (ref. 13) and other recent Pgt strains14,15. Here, we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-03906041/file/Upadhyaya%20et%20al%202021.%20Genomics%20accelerated%20isolation%20of%20a%20new%20stem%20rust%20avirulence%20gene.pdf BibTex
titre
0s and 1s in marine molecular research: a regional HPC perspective
auteur
Jacques Lagnel, Haris Zafeiropoulos, Anastasia Gioti, Stelios Ninidakis, Antonis Potirakis, Savvas Paragkamian, Nelina Angelova, Aglaia Antoniou, Theodoros Danis, Eliza Kaitetzidou, Panagiotis Kasapidis, Jon Bent Kristoffersen, Vasileios Papadogiannis, Christina Pavloudi, Quoc Viet Ha, Nikos Pattakos, Giorgos Perantinos, Dimitris Sidirokastritis, Panagiotis Vavilis, Georgios Kotoulas, Tereza Manousaki, Elena Sarropoulou, Costas Tsigenopoulos, Christos Arvanitidis, Antonios Magoulas, Evangelos Pafilis
article
GigaScience, 2021, 10 (8), pp.1-12. ⟨10.1093/gigascience/giab053⟩
resume
Abstract High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Global range expansion history of pepper ( Capsicum spp.) revealed by over 10,000 genebank accessions
auteur
Pasquale Tripodi, Mark Timothy Rabanus-Wallace, Lorenzo Barchi, Sandip Kale, Salvatore Esposito, Alberto Acquadro, Roland Schafleitner, Maarten van Zonneveld, Jaime Prohens, Maria José Diez, Andreas Börner, Jérémy Salinier, Bernard Caromel, Arnaud Bovy, Filiz Boyaci, Gancho Pasev, Ronny Brandt, Axel Himmelbach, Ezio Portis, Richard Finkers, Sergio Lanteri, Ilan Paran, Véronique Lefebvre, Giovanni Giuliano, Nils Stein
article
Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (34), pp.e2104315118. ⟨10.1073/pnas.2104315118⟩
resume
Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker–trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper ( Capsicum spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed Capsicum annuum to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method ReMIXTURE— using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Tactics of host manipulation by intracellular effectors from plant pathogenic fungi
auteur
Melania Figueroa, Diana Vallejo Ortiz, Eva C Henningsen
article
Current Opinion in Plant Biology, In press, 62, ⟨10.1016/j.pbi.2021.102054⟩
resume
Fungal pathogens can secrete hundreds of effectors, some of which are known to promote host susceptibility. This biological complexity, together with the lack of genetic tools in some fungi, presents a substantial challenge to develop a broad picture of the mechanisms these pathogens use for host manipulation. Nevertheless, recent advances in understanding individual effector functions are beginning to flesh out our view of fungal pathogenesis. This review discusses some of the latest findings that illustrate how effectors from diverse species use similar strategies to modulate plant physiology to their advantage. We also summarize recent breakthroughs in the identification of effectors from challenging systems, like obligate biotrophs, and emerging concepts such as the 'iceberg model' to explain how the activation of plant immunity can be turned off by effectors with suppressive activity.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03227294/file/Figueroa%2C%20Ortiz%20and%20Henningsen%202021.%20Host%20manipulation%20by%20intracellular%20effectors%20in%20fungi.pdf BibTex
titre
Chloroplastic and nuclear diversity of endemic Prunus armeniaca L. species in the oasis agroecosystems
auteur
Hedia Bourguiba, Mohamed-Amine Batnini, Chahnez Naccache, Nadia Zitouna, Neila Trifi-Farah, Jean-Marc Audergon, Lamia Krichen
article
Genetica, 2021, 149 (4), pp.239-251. ⟨10.1007/s10709-021-00127-5⟩
resume
Tunisia is characterized by the presence of specific seed-propagated apricot (Prunus armeniaca L.) material which is found in the oasis agroecosystems. In order to highlight the genetic diversity, population structure, and demographic history of this germplasm, 33 apricot accessions collected from six different oasis regions in southwestern Tunisia were genotyped using 24 microsatellite markers. A total number of 111 alleles was detected with an average of 4.62 alleles per locus. Bayesian model-based clustering analysis indicated four subdivisions within the collection sampled that corresponded mainly to the geographic origin of the material. The analysis of the 33 accessions using chloroplast markers allowed the identification of 32 haplotypes. Overall, the present study highlighted the high Tunisian apricot's diversity in the traditional oasis agroecosystems with low genetic differentiation. Understanding the structure of seed-propagated apricot collection is crucial for managing collections in regard to adaptive traits for Arid and Saharan climates as well as for identifying interesting genotypes that can be integrated into international coordinated actions of breeding programs.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Population genomics of apricots unravels domestication history and adaptive events
auteur
Alexis Groppi, Shuo Liu, A. Cornille, David Tricon, Quynh Trang Bui, Corinne Cruaud, Sandrine Arribat, Caroline Belser, William Marande, Jérôme Salse, Cécile C. Huneau, Nathalie Rodde, Wassim Rhalloussi, Stéphane Cauet, Benjamin Istace, Erwan Denis, Sébastien Carrère, Jean-Marc Audergon, Guillaume Roch, Patrick Lambert, Tetyana Zhebentyayeva, Wei-Sheng Liu, Olivier Bouchez, Céline Lopez-Roques, Rémy-Félix Serre, Robert Debuchy, Joseph Tran, Patrick Wincker, Xilong Chen, Pierre Pétriacq, Aurélien Barré, Macha Nikolski, Jean-Marc Aury, Albert Glenn Abbott, Tatiana E Giraud, Véronique Decroocq
article
Nature Communications, 2021, 12 (1), pp.3956. ⟨10.1038/s41467-021-24283-6⟩
resume
Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03282504/file/2021-Groppi-Nature_Communications.pdf BibTex
titre
Aphis gossypii/Aphis frangulae collected worldwide: Microsatellite markers data and genetic cluster assignment
auteur
Pascale Mistral, Flavie Vanlerberghe-Masutti, Sonia Elbelt, Nathalie Boissot
article
Data in Brief, 2021, 36, pp.106967. ⟨10.1016/j.dib.2021.106967⟩
resume
Aphis gossypii is a cosmopolitan aphid species able to colonize hundreds of plant species from various families [1]. It causes serious damage to a wide range of crops and it is considered a major pest of cucurbits and cotton [2]. It reproduces clonally, by obligate parthenogenesis, on secondary hosts present throughout the year in the intertropical area. At higher latitude, some lineages clonally overwinter but part of the population may have a sexual reproduction in autumn on primary host such as Hibiscus syriacus, to generate cold resistant overwintering eggs [3]. It is highly challenging to distinguish A. gossypii from its sister species Aphis frangulae as both are colonizing solanaceous plants as secondary hosts but the primary host of A. frangulae is Frangula alnus[4]. This paper describes a worldwide collection of both species from December 1989 to September 2019. Aphids were collected individually on plants (19 families) or in traps. The location, the morph type and the botanical family of the host plant were registered. DNA was extracted from each aphid and amplified at 8 microsatellite loci [5]. Amplicons were analysed with ABI technology and their size was defined with Genemapper software. We named each unique combination of alleles, called a multilocus genotype (MLG), and then each individual was given its MLG. The matrix of alleles of all MLGs was run for a Bayesian analysis to describe the genetic structure of the diversity collected and then each MLG had a probability to belong to a genetic group [6,7]. Probability of assignation to each genetic group revealed by the analysis was reported to each individual according to its MLG. This dataset can be used to analyze host plant specificities in A. gossypii, genetic diversity in A. gossypii and relative incidence of variants in diverse geographical regions, admixture between two sister species (Aphis gossypii and Aphis frangulae).
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03229073/file/DataBrief-03-2021.pdf BibTex
titre
Conservation of horticultural genetic resources in France
auteur
Michel Roux-Cuvelier, Michel Grisoni, Arnaud Bellec, Emmanuel Bloquel, Carine Charron, Magalie Delalande, Marine Delmas, Audrey Didier, Charles-Eric Durel, Charles-Henry Duval, Florence Esnault, Laurence Feugey, Emmanuel E. Geoffriau, Bouchaib Khadari, Sandra Lepers-Andrzejewski, Luro François, Cécile Marchal, Alix Pernet, Jérémy Salinier, Marc M. Seguin, Rebecca Stevens, Bernice van Issum-Groyer, Rémi Kahane
article
Chronica Horticulturae, 2021, 61 (2)
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.univ-reunion.fr/hal-03372865/file/French-Hort-BRC-published-in-Chronica-Hort-61022021.pdf BibTex
titre
Tester la résistance à Xanthomonas
auteur
Bénédicte Quilot-Turion, Naïma Dlalah, Yannick Montrognon
article
Réussir Fruits et Légumes, 2021, 30
resume
Un nouveau test ADN américain permet de déterminer les variétés de pêches résistantes ou sensibles à la bactérie Xanthomonas. Une avancée pour la création de variétés résistantes à cette bactérie.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Phenotyping Brown Rot Susceptibility in Stone Fruit: A Literature Review with Emphasis on Peach
auteur
Majid Hassan Mustafa, Daniele Bassi, Marie-Noëlle Corre, Leandro Oliveira Lino, Véronique Signoret, Bénédicte Quilot-Turion, Marco Cirilli
article
Horticulturae, 2021, 7 (5), pp.115. ⟨10.3390/horticulturae7050115⟩
resume
Plant disease phenotyping methodologies can vary considerably among testers and often suffer from shortcomings in their procedures and applications. This has been an important challenge in resistance breeding to brown rot, one of the most severe pre-and postharvest stone fruit diseases caused by Monilinia spp. Literature about methodologies for evaluating stone fruit susceptibility to brown rot is abundant but displays significant variations across the described approaches, limiting the ability to compare results from different studies. This is despite the fact that authors largely agree on the main factors influencing brown rot development, such as Monilinia inocula, environmental conditions, cultivars, fruit stage, and management practices. The present review first discusses ways to control or at least account for major factors affecting brown rot phenotyping studies. The second section describes in detail the different steps of fruit infection assays, comparing different protocols available in the literature with the objective of highlighting best practices and further improvement of phenotyping for brown rot susceptibility. Finally, experimental results from multi-year evaluation trials are also reported, highlighting year-to-year variability and exploring correlations of evaluation outcomes among years and assay types, suggesting that choice of phenotyping methodology must be carefully considered in breeding programs.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A blueprint for gene function analysis through Base Editing in the model plant Physcomitrium (Physcomitrella) patens
auteur
Anouchka Guyon-Debast, Alessandro Alboresi, Zoé Terret, Florence Charlot, Floriane Berthier, Pol Vendrell-Mir, Josep M. Casacuberta, Florian Veillet, Tomas Morosinotto, Jean-Luc Gallois, Fabien Nogue
article
New Phytologist, 2021, 230 (3), pp.1258-1272. ⟨10.1111/nph.17171⟩
resume
CRISPR-Cas9 has proven to be highly valuable for genome editing in plants, including the model plant Physcomitrium patens. However, the fact that most of the editing events produced using the native Cas9 nuclease correspond to small insertions and deletions is a limitation. CRISPR-Cas9 base editors enable targeted mutation of single nucleotides in eukaryotic genomes and therefore overcome this limitation. Here, we report two programmable base-editing systems to induce precise cytosine or adenine conversions in P. patens. Using cytosine or adenine base editors, site-specific single-base mutations can be achieved with an efficiency up to 55%, without off-target mutations. Using the APT gene as a reporter of editing, we could show that both base editors can be used in simplex or multiplex, allowing for the production of protein variants with multiple amino-acid changes. Finally, we set up a co-editing selection system, named selecting modification of APRT to report gene targeting (SMART), allowing up to 90% efficiency site-specific base editing in P. patens. These two base editors will facilitate gene functional analysis in P. patens, allowing for site-specific editing of a given base through single sgRNA base editing or for in planta evolution of a given gene through the production of randomly mutagenised variants using multiple sgRNA base editing.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-03163698/file/New%20Phytologist%20-%202021%20-%20Guyon-Debast%20-%20A%20blueprint%20for%20gene%20function%20analysis%20through%20Base%20Editing%20in%20the%20model%20plant.pdf BibTex
titre
Resistance to root-knot Nematodes in the genus Lactuca: hope for breeding resistant lettuce
auteur
Brigitte Maisonneuve, Claire Jouan, Benjamin Gard, Stéphanie Gimenez, Claire Goillon, Loic Jean, Yannie Trottin, Hélène Védie, Michel Pitrat
article
Innovations Agronomiques, 2021, 84, pp.11-23. ⟨10.15454/02s5-ab94⟩
resume
Lactuca germplasm was evaluated by testing young plants in laboratory with Meloidogyne incognita. After inoculation with 400 juveniles (J2) per pot, the number of egg masses per plant was used to identify resistant accession. No accession among the 569 tested was immune. But 3% out of 409 L. sativa cultivars and 54% out of 160 wild Lactuca accessions exhibited less than 10 egg masses per plant and were selected as resistant accessions. Resistance of 52 out of the 102 resistant accessions screened on two plants was checked in three laboratories with two isolates; 14 cultivars and 36 L. serriola accessions confirmed low egg mass numbers. Few from these accessions were also resistant (height L. serriola) or partly resistant (PI 419140) to M. arenaria in laboratory. After a strong inoculation (2000 J2/plant), the high level of resistance of four accessions of L. serriola was confirmed. Moreover, 10 resistant accessions were tested in two agricultural soils contaminated with Meloidogyne populations especially M. arenaria. On six L. serriola which were resistant to M. incognita and M. arenaria in laboratory, egg mass number and number of eggs per gall were low in comparison with L. serriola control susceptible to M. arenaria in laboratory. But, the lowest numbers of galls and of egg masses were found on one L. virosa susceptible to M. arenaria in laboratory. In conclusion, some useful accessions were identified for lettuce breeding program for resistance to nematodes.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02617666/file/2021_Maisonneuve_Innovations%20Agronomiques%2084.pdf BibTex
titre
Tomato response to water stress
auteur
Mathilde Causse, Nadia Bertin
article
Innovations Agronomiques, 2021, 84, pp.135-144. ⟨10.15454/gv9k-py55⟩
resume
In a context of climate change, especially the scarcity of natural resources (particularly water), production systems must evolve towards less intensive and more sustainable systems. In this project, the fundamental knowledge acquired in genetics, ecophysiology and modeling on the mechanisms of adaptation to water stress and the development of fruit quality, have been used in an attempt to define tomato variety ideotypes adapted to the water constraint and improved for fruit quality traits. For this purpose, plant and fruit function models have been used to predict the behavior of allelic combinations at QTL in variable stress situations as well as multi-criteria optimization algorithms. A population of recombinant inbred lines from a cross between a cherry tomato variety and a medium-sized tomato was genotyped and phenotyped under control and water stress conditions to map stress response QTL, related to plant growth and fruit quality. These QTL were used on the one hand, to look for possible colocalisations with candidate genes, on the other hand to feed the modeling part and to identify physiological parameters and genes likely to be involved in tolerance to water stress. At the same time, a collection of 140 cultivated tomato accessions was characterized under the same conditions, in order to evaluate the genetic diversity of stress responses and to look for associations between genotypes and phenotypes. This project has identified ideotypes, resources, markers and genes potentially useful for the selection of varieties that will be less demanding for water and having a good quality.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03632730/file/2021_Causse_Innovations%20Agronomiques%2084.pdf BibTex
titre
Building a cluster of NLR genes conferring resistance to pests and pathogens: the story of the Vat gene cluster in cucurbits
auteur
Véronique Chovelon, Rafael Feriche-Linares, Guillaume Barreau, Joël Chadoeuf, Caroline Callot, Véronique Gautier, Marie-Christine Le Paslier, Aurélie Berad, Patricia Faivre-Rampant, Jacques Lagnel, Nathalie Boissot
article
Horticulture research, 2021, 8 (1), ⟨10.1038/s41438-021-00507-0⟩
resume
Most molecularly characterized plant resistance genes (R genes) belong to the nucleotide-binding-site-leucine-rich-repeat (NLR) receptor family and are prone to duplication and transposition with high sequence diversity. In this family, the Vat gene in melon is one of the few R genes known for conferring resistance to insect, i.e., Aphis gossypii , but it has been misassembled and/or mispredicted in the whole genomes of Cucurbits. We examined 14 genomic regions (about 400 kb) derived from long-read assemblies spanning Vat -related genes in Cucumis melo , Cucumis sativus, Citrullus lanatus, Benincasa hispida, Cucurbita argyrosperma , and Momordica charantia . We built the phylogeny of those genes. Investigating the paleohistory of the Vat gene cluster, we revealed a step by step process beginning from a common ancestry in cucurbits older than 50 my. We highlighted Vat exclusively in the Cucumis genera, which diverged about 20 my ago. We then focused on melon, evaluating a minimum duplication rate of Vat in 80 wild and cultivated melon lines using generalist primers; our results suggested that duplication started before melon domestication. The phylogeny of 44 Vat-CDS obtained from 21 melon lines revealed gain and loss of leucine-rich-repeat domains along diversification. Altogether, we revealed the high putative recognition scale offered in melon based on a combination of SNPs, number of leucine-rich-repeat domains within each homolog and number of homologs within each cluster that might jointly confer resistance to a large pest and pathogen spectrum. Based on our findings, we propose possible avenues for breeding programs.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03216497/file/2021_Chovelon_Horticulture%20Research.pdf BibTex
titre
The Genetic Control of Nectary Development
auteur
Filip Slavković, Catherine Dogimont, Halima Morin, Adnane Boualem, Abdelhafid Bendahmane
article
Trends in Plant Science, 2021, 26 (3), pp.260-271. ⟨10.1016/j.tplants.2020.11.002⟩
resume
Nectar is the most important reward offered by flowering plants to pollinators for pollination services. Since pollinator decline has emerged as a major threat for agriculture, and the food demand is growing globally, studying the nectar gland is of utmost importance. Although the genetic mechanisms that control the development of angiosperm flowers have been quite well understood for many years, the development and maturation of the nectar gland and the secretion of nectar in synchrony with the maturation of the sexual organs appears to be one of the flower's best-kept secrets. Here we review key findings controlling these processes. We also raise key questions that need to be addressed to develop crop ecological functions that take into consideration pollinators' needs.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03633112/file/S1360138520303381.pdf BibTex
titre
Changes in cell wall neutral sugar composition related to pectinolytic enzyme activities and intra-flesh textural property during ripening of ten apricot clones
auteur
Jamal Ayour, Carine Le Bourvellec, Barbara Gouble, Jean-Marc Audergon, Mohamed Benichou, Catherine M.G.C. Renard
article
Food Chemistry, 2021, 339, pp.128096. ⟨10.1016/j.foodchem.2020.128096⟩
resume
The changes of texture and cell wall characteristics of apricot were investigated in ten clones at two maturity stages. Fruit firmness, cell wall composition and enzyme activity of three apricot flesh zones were analysed. The AIS (alcohol-insoluble solids) were characterised by high amounts of uronic acid (179-300 mg g-1 AIS) and relatively high amounts of cellulosic glucose (118-214 mg g-1 AIS). The methylesterification degree varied significantly among the different clones ranging from 58 to 97 in Ab 5 and Mans 15 respectively. Conversely to zones firmness, enzymatic activity was higher in pistil followed by equatorial and peduncle zones. The ripening effect has been observed in firmness evolution according to enzymatic activity. This correlation allowed a classification of clones depending on softening. Among studied clones, Ab 5, Marouch 16, Mans 15 and Cg 2 were less influenced by softening and have the advantage of a technological valorisation for the processing industry.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02979871/file/S0308814620319580.pdf BibTex
titre
The Di2/pet Variant in the PETALOSA Gene Underlies a Major Heat Requirement-Related QTL for Blooming Date in Peach [ Prunus persica (L.) Batsch]
auteur
Marco Cirilli, Stefano Gattolin, Remo Chiozzotto, Bénédicte Quilot-Turion, Irina Baccichet, Thierry Pascal, Laura Rossini, Daniele Bassi
article
Plant and Cell Physiology, 2021, 62 (2), pp.356-365. ⟨10.1093/pcp/pcaa166⟩
resume
Environmental adaptation of deciduous fruit trees largely depends on their ability to synchronize growth and development with seasonal climate change. Winter dormancy of flower buds is a key process to prevent frost damage and ensure reproductive success. Temperature is a crucial environmental stimulus largely influencing the timing of flowering, only occurring after fulfillment of certain temperature requirements. Nevertheless, genetic variation affecting chilling or heat-dependent dormancy release still remains largely unknown. In this study, a major QTL able to delay blooming date in peach by increasing heat requirement was finely mapped in three segregating progenies, revealing a strict association with a genetic variant (petDEL) in a PETALOSA gene, previously shown to also affect flower morphology. Analysis of segregating genome-edited tobacco plants provided further evidence of the potential ability of PET variations to delay flowering time. Potential applications of the petDEL variant for improving phenological traits in peach are discussed.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genomic inference of complex domestication histories in three Solanaceae species
auteur
Stéphanie Arnoux, Christelle Fraïsse, Christopher Sauvage
article
Journal of Evolutionary Biology, 2021, 34 (2), pp.270-283. ⟨10.1111/jeb.13723⟩
resume
Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a "protracted period" of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Evaluation of tomato, eggplant and pepper accessions for resistance to Ralstonia solanacearum species complex (RSSC) strains from Louisiana
auteur
Melanie Lewis Ivey, Alejandra Jimenez Madrid, Marie-Christine Daunay, Denis Shah
article
European Journal of Plant Pathology, 2021, 159 (2), pp.279-293. ⟨10.1007/s10658-020-02160-0⟩
resume
Bacterial wilt (BW), caused by Ralstonia solanacearum species complex (RSSC), is a major disease affecting tomato and other solanaceous crops produced in Louisiana and worldwide. The most effective and economic management strategy for BW is the use of crop genetic resistance. However, regional genetic variation among RSSC strains has made stable and durable resistance elusive. A collection of tomato, eggplant and pepper (TEP) accessions that responds to globally diverse strains in the RSSC was screened for resistance to six RSSC strains, belonging to phylotypes I and II, from Louisiana, United States (US). Wilt severity was quantified from six days up to 25 days post-inoculation (DPI). Wilting increased most rapidly to 10 DPI and was generally more severe with Phylotype II strains. However, wilt response profiles depended on the accession-strain combination. Differences in aggressiveness, as measured by the area under the disease progress stairs, were observed among the phylotype I and II strains on TEP. Wilting responses were the most severe with the tomato accessions. Hawaii 7996, TML46, CLN1463 and R3034 were highly resistant to all phylotype I strains, but Hawaii 7996 displayed the best resistance to phylotype II strains. Remarkably, eggplant accession Ceylan SM 164 was resistant to all six strains. Eggplant accessions SM6, Surya, and AG91-25, as well as pepper accessions CA8 and MC4, were moderately to highly resistant to all six strains. Although resistance spectrum and levels of these tomato, eggplant and pepper accessions need to be confirmed by further experiments, our results already indicate that these accessions are potential BW-resistant rootstock candidates for grafting to susceptible market-driven tomato, eggplant and pepper produced in this US state.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Validated MAGIC and GWAS population mapping reveals the link between vitamin E content and natural variation in chorismate metabolism in tomato
auteur
Estanislao Burgos, Maria Belen de Luca, Isidore Diouf, Luis Haro, Elise Albert, Christopher Sauvage, Zhao Tao, Luisa Bermudez, Ramon Asís, Adriano Nesi, Michel Matringe, Claire Bréhélin, Thomas Guiraud, Carine Ferrand, Isabelle Atienza, Joana Jorly, Jean-Philippe Mauxion, Pierre Baldet, Alisdair Fernie, Leandro Quadrana, Christophe Rothan, Mathilde Causse, Fernando Carrari
article
The Plant Journal, 2021, 105 (4), pp.907-923. ⟨10.1111/tpj.15077⟩
resume
Tocochromanols constitute the different forms of vitamin E (VTE), essential components of the human diet, and display a high membrane protectant activity. By combining interval mapping and genome-wide association studies (GWAS), we unveiled the genetic determinants of tocochromanol accumulation in tomato (Solanum lycopersicum) fruits. To enhance the nutritional value of this highly consumed vegetable, we dissected the natural intraspecific variability of tocochromanols in tomato fruits and genetically engineered their biosynthetic pathway. These analyses allowed the identification of a total of 25 quantitative trait loci interspersed across the genome pinpointing the chorismate-tyrosine pathway as a regulatory hub controlling the supply of the aromatic head group for tocochromanol biosynthesis. To validate the link between the chorismate-tyrosine pathway and VTE, we engineered tomato plants to bypass the pathway at the arogenate branch point. Transgenic tomatoes showed moderate increments in tocopherols (up to approximately 20%) and a massive accumulation of tocotrienols (up to approximately 3400%). Gene expression analyses of these plants reveal a trade-off between VTE and natural variation in chorismate metabolism explained by transcriptional reprogramming of specific structural genes of the pathway. By restoring the accumulation of alpha-tocotrienols (alpha-t3) in fruits, the plants produced here are of high pharmacological and nutritional interest.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat
auteur
Ming Luo, Liqiong Xie, Soma Chakraborty, Aihua Wang, Oadi Matny, Michelle Jugovich, James A Kolmer, Terese Richardson, Dhara Bhatt, Mohammad Hoque, Mehran Patpour, Chris Sørensen, Diana Vallejo Ortiz, Peter Dodds, Burkhard Steuernagel, Brande B H Wulff, Narayana M Upadhyaya, Rohit Mago, Sambasivam Periyannan, Evans Lagudah, Roger Freedman, T Lynne Reuber, Brian J Steffenson, Michael Ayliffe
article
Nature Biotechnology, 2021, 39, pp.561 - 566. ⟨10.1038/s41587-020-00770-x⟩
resume
Breeding wheat with durable resistance to the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), a major threat to cereal production, is challenging due to the rapid evolution of pathogen virulence. Increased durability and broad-spectrum resistance can be achieved by introducing more than one resistance gene, but combining numerous unlinked genes by breeding is laborious. Here we generate polygenic Pgt resistance by introducing a transgene cassette of five resistance genes into bread wheat as a single locus and show that at least four of the five genes are functional. These wheat lines are resistant to aggressive and highly virulent Pgt isolates from around the world and show very high levels of resistance in the field. The simple monogenic inheritance of this multigene locus greatly simplifies its use in breeding. However, a new Pgt isolate with virulence to several genes at this locus suggests gene stacks will need strategic deployment to maintain their effectiveness. Pgt continues to overcome resistant wheat cultivars, with three new, highly virulent isolates emerging in the last 20 years, and the disease reappearing in Europe and the UK 1. Two classes of Pgt resistance genes have been cloned from wheat: all-stage resistance (ASR) genes and adult plant resistance (APR) genes 2. ASR genes (for example, Sr22 (ref. 3), Sr35 (ref. 4), Sr45 (ref. 3) and Sr50 (ref. 5)) generally encode nucleotide-binding, leucine-rich repeat (NLR) proteins that recognize a specific Pgt molecule (an effector) introduced into host plant cells by the fungus to promote parasitism, whereupon a plant defense response is activated 2. The presence, absence or allelic variation of the fungal effector determines which Pgt isolates an ASR gene is effective against. ASR genes are extremely valuable for crop protection but, when deployed singly, often show transient resistance, as pathogen effectors rapidly evolve to avoid recognition. Combining ASR genes increases their durability, and theoretical estimates suggest that the chance of a single Pgt isolate gaining virulence for five or more ASR genes in wheat is infinitesimally small 6. The second gene class, APR genes, can be remarkably durable and, in some cases, effective against multiple pathogen species. However, these genes generally provide partial resistance that is often insufficient for crop protection during severe pathogen epidemics.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03906159/file/A%20five%20transgenne%20cassette%20confers%20broad-spectrum%20resistance.pdf BibTex
titre
Phenolic compounds identified in apricot branch tissues and their role in the control of Monilinia laxa growth
auteur
Jorge del Cueto, Agnieszka Kosinska-Cagnazzo, Patrick Stefani, Julien Heritier, Guillaume Roch, Thomas Oberhänsli, Jean-Marc Audergon, Danilo Christen
article
Scientia Horticulturae, 2021, 275, pp.109707. ⟨10.1016/j.scienta.2020.109707⟩
resume
Secondary metabolites, such as phenolics, are plant defence substances. In the present study, the impact of Monilinia laxa inoculation under controlled conditions on phenolic content of apricot branches was investigated. A bi-parental hybrid population issued from Bergeron and Bakour cultivars (BerBa) and consisting of 192 hybrids was studied. The susceptibility of the BerBa population to M. laxa was evaluated by measuring the length of the necrosed tissues and the concentration of fungal DNA by qPCR in the branches 8 days post-inoculation. The results exhibit significant differences between the two parental cultivars in terms of necrosis length, which confirm their different susceptibility to the pathogen. A considerably high content of 2′,6′-dihydroxy-4′–methoxyacetophenone hexoside was found in branch tissues of Bakour (tolerant parental cultivar), amounting to 1.72 mg/g and 1.41 mg/g of fresh weight in non-inoculated and inoculated samples, respectively. The content of this compound in Bergeron branch tissues was several times lower, amounting to 0.24 mg/g and 0.14 mg/g of fresh weight in non-inoculated and inoculated samples, respectively. In the inoculated branches, scopolin was almost twice as abundant in the tolerant parental cultivar branch tissues as in the susceptible ones. In general, after inoculation a lower content of phenolic compounds was observed for hybrids with longer necrosed tissue. A Principal Component Analysis showed that at 8 days post-inoculation M. laxa concentration in the branches and the content of phenolic compounds, such as scopolin and chlorogenic acids, were negatively correlated. Additionally, the antifungal activity of pure phenolic compounds against M. laxa mycelial growth and spore germination was investigated. At a concentration of 500 mg/L, up to 40 % inhibition of M. laxa mycelial growth by scopoletin, up to 60 % inhibition by 2′,4′,6′-trihydroxyacetophenone and total inhibition by 2′-hydroxy-4′-methoxyacetophenone was observed. Scopoletin and 2′,4′,6′-trihydroxyacetophenone also inhibited spore germination by about 50 %. These results can serve to improve breeding programs aiming to develop apricot cultivars resistant to brown rot blossom blight.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
FRUINOV – Participatory research of fruit varieties adapted to the Provence-Alpes-Cote d'Azur area
auteur
S.-J. Ondet, G. Gaspari, J.-P. Talichet, M. Meignan, H. Duval, C. Assegond, V. Ayme-Sévenier, D. Desclaux, Yuna Chiffoleau
article
Innovations Agronomiques, 2021, 82, pp.151-163. ⟨10.15454/hy3j-zv57⟩
resume
The FRUINOV CASDAR project (2016-2019) evaluated and described regional varieties and varieties of regional interest, and also selected and upgraded varieties less susceptible to pests and diseases of 7 fruit species of economic interest (almond, apricot, cherry, peach, pear, apple and plum), adapted to soil conditions and climate of the Provence-Alpes-Côte-d'Azur area. These studied varieties are kept in collection orchards without inputs or under very low level of organic inputs depending on the species. The use of varieties adapted to the local conditions is a compulsory basis for the development of organic agriculture, agroforestry and more widely to consider a reduction of inputs in agriculture. The varieties were selected according to a participatory methodology and were initially intended to supply short and local food chains, and then other types of markets. This methodology included the diversity of actors in the sector, from producers to consumers. This project is also included in the current “produce differently” approach of the educational campaign and thus raises awareness among the farmers of the future. All the results obtained are gathered on the website to facilitate the search for information on regional varieties of PACA and to find a professional of this regional fruit sector.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03469599/file/2021_Ondet_Innovations%20Agronomiques%2082.pdf BibTex
titre
Self-(in)compatibility analysis of apricot germplasm in Tunisia: S-RNase allele identification, S-genotype determination and crop history evolution
auteur
Ayda Boubakri, Lamia Krichen, Mohamed-Amine Batnini, Neila Trifi-Farah, Guillaume Roch, Jean-Marc Audergon, Hedia Bourguiba
article
Scientia Horticulturae, 2021, 276, pp.109758. ⟨10.1016/j.scienta.2020.109758⟩
resume
Apricot (Prunus armeniaca L.) exhibits a gametophytic self-incompatibility (GSI) system and is mostly considered to be a self-incompatible species though numerous self-compatible exceptions occur. A set of 68 local Tunisian apricot accessions coming from different geographic areas was examined by PCR analysis of the S-loci genotypes. Up to nine S-alleles were detected within the Tunisian apricot germplasm allocating the studied accessions into 14 cross-incompatibility groups, nine of them newly identified in this study. Self-compatible accessions carrying the SC-allele were revealed for the first time within the Tunisian apricot germplasm. The heterogeneous distribution of the apricot S-alleles confirmed the species’ domestication and diffusion history from the Irano-Caucasian region to North-Africa. The knowledge of incompatibility relationships among apricot accessions can be a highly valuable tool for the development of future breeding programs by selecting the appropriate parents and for efficient orchard design by planting a combination of self-compatible and inter-compatible accessions.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
When a knockout is an Achilles’ heel: Resistance to one potyvirus species triggers hypersusceptibility to another one in Arabidopsis thaliana
auteur
Delyan Zafirov, Nathalie Giovinazzo, Anna Bastet, Jean‐luc Gallois
article
Molecular Plant Pathology, 2021, 22 (3), pp.334-347. ⟨10.1111/mpp.13031⟩
resume
The translation initiation factors 4E are a small family of major susceptibility factors to potyviruses. It has been suggested that knocking out these genes could provide genetic resistance in crops when natural resistance alleles, which encode functional eIF4E proteins, are not available. Here, using the well-characterized Arabidopsis thaliana-potyvirus pathosystem, we evaluate the resistance spectrum of plants knocked out for eIF4E1, the susceptibility factor to clover yellow vein virus (ClYVV). We show that besides resistance to ClYVV, the eIF4E1 loss of function is associated with hypersusceptibility to turnip mosaic virus (TuMV), a potyvirus known to rely on the paralog host factor eIFiso4E. On TuMV infection, plants knocked out for eIF4E1 display striking developmental defects such as early senescence and primordia development stoppage. This phenotype is coupled with a strong TuMV overaccumulation throughout the plant, while remarkably the levels of the viral target eIFiso4E remain uninfluenced. Our data suggest that this hypersusceptibility cannot be explained by virus evolution leading to a gain of TuMV aggressiveness. Furthermore, we report that a functional eIF4E1 resistance allele engineered by CRISPR/Cas9 base-editing technology successfully circumvents the increase of TuMV susceptibility conditioned by eIF4E1 disruption. These findings in Arabidopsis add to several previous findings in crops suggesting that resistance based on knocking out eIF4E factors should be avoided in plant breeding, as it could also expose the plant to the severe threat of potyviruses able to recruit alternative eIF4E copies. At the same time, it provides a simple model that can help understanding of the homeostasis among eIF4E proteins in the plant cell and what makes them available to potyviruses.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Population Genomics of the “Arcanum” Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages
auteur
Ana Florez-Rueda, Mathias Scharmann, Thomas Städler, Morgane Roth
article
Frontiers in Plant Science, 2021, 12, pp.1-16. ⟨10.3389/fpls.2021.624442⟩
resume
Given their diverse mating systems and recent divergence, wild tomatoes ( Solanum section Lycopersicon ) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the “Arcanum” group, comprising the nominal species Solanum arcanum , Solanum chmielewskii , and Solanum neorickii . The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological “selfing syndrome.” Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species’ geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum ; only the self-incompatible lineage known as “var. marañón” has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii , respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S -locus diversity in the two independently derived self-compatible species.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-03631554/file/Florez-Rueda_2021.pdf BibTex
titre
A revival of effective ploidy: the asymmetry of parental roles in endosperm-based hybridization barriers
auteur
Thomas Städler, Ana Florez-Rueda, Morgane Roth
article
Current Opinion in Plant Biology, 2021, 61, pp.1-7. ⟨10.1016/j.pbi.2021.102015⟩
resume
Interest in understanding hybrid seed failure (HSF) has mushroomed, both in terms of identifying underlying molecular processes and their evolutionary drivers. We review phenotypic and molecular advances with a focus on the 'effective ploidy' concept, witnessing a recent revival after long obscurity. Endosperm misdevelopment has now been shown to underlie HSF in many inter-specific, homoploid crosses. The consistent asymmetries in seed size and developmental trajectories likely reflect parental divergence in key, dosage-sensitive processes. Transcriptomic and epigenomic studies reveal genome-wide, polarized expression perturbations and shifts in parental expression proportions, consistent with small-RNA imbalances between parental roles. Among-species differences in levels of parental conflict over resource allocation enjoy strong support in explaining why differences in effective ploidy may evolve.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-03631570/file/Sta%CC%88dler_2021_COPB.pdf BibTex
titre
Genetic diversity of tomato response to heat stress at the QTL and transcriptome levels
auteur
Estelle Bineau, Isidore Diouf, Yolande Carretero, Renaud Duboscq, Frédérique Bitton, Anis Djari, Mohamed Zouine, Mathilde Causse
article
The Plant Journal, In press, ⟨10.1111/tpj.15379⟩
resume
Tomato is a widely cultivated crop, which can grow in many environments. However, temperature above 30 degrees C impairs its reproduction, subsequently impacting fruit yield. We assessed the impact of high-temperature stress (HS) in two tomato experimental populations, a multi-parental advanced generation intercross (MAGIC) population and a core-collection (CC) of small-fruited tomato accessions. Both populations were evaluated for 11 traits related to yield components, phenology and fruit quality in optimal and HS conditions. HS significantly impacted all traits in both populations, but a few genotypes with stable yield under HS were identified. A plasticity index was computed for each individual to measure the extent of the heat impact for each trait. Quantitative trait loci (QTL) were detected in control and HS conditions as well as for plasticity index. Linkage and genome-wide association analyses in the MAGIC and CC populations identified a total of 98 and 166 QTLs, respectively. Taking the two populations together, 69 plasticity QTLs (pQTLs) were involved in tomato heat response for 11 traits. The transcriptome changes in the ovary of six genotypes with contrasted responses to HS were studied, and 837 genes differentially expressed according to the conditions were detected. Combined with previous transcriptome studies, these results were used to propose candidate genes for HS response QTLs.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Large-scale geography survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa
auteur
S.G. Olvera-Vazquez, C. Remoué, A. Venon, A. Rousselet, O. Grandcolas, M. Azrine, L. Momont, M. Galan, L. Benoit, G. David, A. Alhmedi, T. Beliën, G. Alins, Pierre P. Franck, S.K. Jacobsen, A. Haddioui, R. Andreev, Simon Sylvaine, L. Sigsgaard, E. Guibert, L. Tournant, F. Gazel, K. Mody, Y. Khachtib, A. Roman, T.M. Ursu, H. Belcram, I.A. Zakharov, M. Harry, A. Agnello, Jean-Christophe Simon, S. Oram, J.M. Ricard, Morgane Roth, E. Beers, J. Engelman, I. Balti, A. Salhi-Hannachi, H. Zhang, H. Tu, C. Mottet, B. Barrès, A. Degrave, J. Razmjou, Tatiana Giraud, M. Falque, E. Dapena, M. Miñarro, L. Jardillier, P. Deschamps, Emmanuelle Jousselin, A Cornille
article
Peer Community Journal, 2021, 1, pp.e34. ⟨10.24072/pcjournal.26⟩
resume
With frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may also be involved in or affected by colonization processes, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its microbiota. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the ones from Morocco and North America that are likely the result of recent colonization events. Coalescent-based inferences revealed high levels of gene flow among populations during the colonization but did not allow determining the sequence of colonization of Europe, North America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. We found that D. plantaginea rarely hosts other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play an important role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03605093/file/Olvera-Vazquez.pdf BibTex
titre
Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure
auteur
Ana Florez-Rueda, Flurin Fiscalini, Ueli Grossniklaus, Thomas Städler, Morgane Roth
article
Genome Biology and Evolution, 2021, 13 (8), pp.1-15. ⟨10.1093/gbe/evab107⟩
resume
Crosses between the wild tomato species Solanum peruvianum and Solanum chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origindependent expression of alleles, is perturbed in the hybrid endosperm, with many of the normally paternally expressed genes losing their imprinted status. Here, we report transcriptome-based analyses of gene and small RNA (sRNA) expression levels. We identified 2,295 genes and 387 sRNA clusters as differentially expressed when comparing reciprocal hybrid seed to seeds and endosperms from the two within-species crosses. Our analyses uncovered a pattern of overdominance in endosperm gene expression in both hybrid cross directions, in marked contrast to the patterns of sRNA expression in whole seeds. Intriguingly, patterns of increased gene expression resemble the previously reported increased maternal expression proportions in hybrid endosperms. We identified physical clusters of sRNAs; differentially expressed sRNAs exhibit reduced transcript abundance in hybrid seeds of both cross directions. Moreover, sRNAs map to genes coding for key proteins involved in epigenetic regulation of gene expression, suggesting a regulatory feedback mechanism. We describe examples of genes that appear to be targets of sRNA-mediated gene silencing; in these cases, reduced sRNA abundance is concomitant with increased gene expression in hybrid seeds. Our analyses also show that S. peruvianum dominance impacts gene and sRNA expression in hybrid seeds. Overall, our study indicates roles for sRNA-mediated epigenetic regulation in HSF between closely related wild tomato species.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-03631559/file/Florez-Rueda_2021_GBE_sRNA_endosperm.pdf BibTex
titre
The Melon Zym Locus Conferring Resistance to ZYMV: High Resolution Mapping and Candidate Gene Identification
auteur
Nastacia Adler-Berke, Yitzchak Goldenberg, Yariv Brotman, Irina Kovalski, Amit Gal-On, Tirza Doniger, Rotem Harel-Beja, Christelle Troadec, Abdelhafid Bendahmane, Michel Pitrat, Catherine Dogimont, Nurit Katzir, Rafael Perl-Treves
article
Agronomy, 2021, 11 (12), pp. 2427. ⟨10.3390/agronomy11122427⟩
resume
Zucchini yellow mosaic virus (ZYMV; potyviridae) represents a major pathogen of Cucurbitaceae crops. ZYMV resistance in melon PI 414723 is conditioned by a dominant allele at the Zym locus. This resistant accession restricts viral spread and does not develop mosaic symptoms, but necrosis sometimes develops in response to inoculation. In previous studies, Zym has been mapped to linkage group II of the melon genetic map. In the present study, positional cloning of the locus was undertaken, starting from the CM-AG36 SSR marker at approximately 2 cm distance. We utilized five mapping populations that share the same resistant parent, PI 414723, and analyzed a total of 1630 offspring, to construct a high-resolution genetic map of the Zym locus. Two melon BAC libraries were used for chromosome walking and for developing new markers closer to the resistance gene by BAC-end sequencing. A BAC contig was constructed, and we identified a single BAC clone, from the ZYMV susceptible genotype MR-1, that physically encompasses the resistance gene. A second clone was isolated from another susceptible genotype, WMR 29, and the two clones were fully sequenced and annotated. Additional markers derived from the sequenced region delimited the region to 17.6 kb of a sequence that harbors a NAC-like transcription factor and, depending on the genotype, either two or three R-gene homologs with a CC-NBS-LRR structure. Mapping was confirmed by saturating the map with SNP markers using a single mapping population. The same region was amplified and sequenced also in the ZYMV resistant genotype PI 414723. Because numerous polymorphic sites were noted between genotypes, we could not associate resistance with a specific DNA polymorphism; however, this study enables molecular identification of Zym and paves the way to functional studies of this important locus.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03828614/file/Adler-berke_agronomy-2022.pdf BibTex
titre
The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions
auteur
Benoît Moury, Jean-Marc Audergon, Sylvie Baudracco-Arnas, Safa Ben Krima, François Bertrand, Nathalie Boissot, Mireille Buisson, Valérie Caffier, Melissa Cantet, Sylvia Chanéac, Carole Constant, François Delmotte, Catherine Dogimont, Juliette Doumayrou, Frédéric Fabre, Sylvain Fournet, Valérie Grimault, Thierry Jaunet, Isabelle Justafré, Véronique Lefebvre, Denis Losdat, Thierry Marcel, Josselin Montarry, Cindy E. Morris, Mariem Omrani, Manon Paineau, Sophie Perrot, Marie-Laure Pilet-Nayel, Youna Ruellan
article
Peer Community Journal, 2021, 1, pp.e44. ⟨10.24072/pcjournal.51⟩
resume
Understanding the relationships between host range and pathogenicity for parasites, and between the efficiency and scope of immunity for hosts are essential to implement efficient disease control strategies. In the case of plant parasites, most studies have focused on describing qualitative interactions and a variety of genetic and evolutionary models has been proposed in this context. Although plant quantitative resistance benefits from advantages in terms of durability, we presently lack models that account for quantitative interactions between plants and their parasites and the evolution of these interactions. Nestedness and modularity are important features to unravel the overall structure of host-parasite interaction matrices. Here, we analysed these two features on 32 matrices of quantitative pathogenicity trait data gathered from 15 plant-parasite pathosystems consisting of either annual or perennial plants along with fungi or oomycetes, bacteria, nematodes, insects and viruses. The performance of several nestedness and modularity algorithms was evaluated through a simulation approach, which helped interpretation of the results. We observed significant modularity in only six of the 32 matrices, with two or three modules detected. For three of these matrices, modules could be related to resistance quantitative trait loci present in the host. In contrast, we found high and significant nestedness in 30 of the 32 matrices. Nestedness was linked to other properties of plant-parasite interactions. First, pathogenicity trait values were explained in majority by a parasite strain effect and a plant accession effect, with no or minor parasite-plant interaction term. Second, correlations between the efficiency and scope of the resistance of plant genotypes, and between the host range breadth and pathogenicity level of parasite strains were overall positive. This latter result questions the efficiency of strategies based on the deployment of several genetically-differentiated cultivars of a given crop species in the case of quantitative plant immunity.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03461843/file/2021_Moury_PeerCommunityJournal.pdf BibTex

2020

Journal articles

titre
Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality
auteur
Mariem Nsibi, Barbara Gouble, Sylvie Bureau, Timothée Flutre, Christopher Sauvage, Jean-Marc Audergon, Jean-Luc Regnard
article
G3, 2020, 10 (12), pp.4513-4529. ⟨10.1534/g3.120.401452⟩
resume
Genomic selection (GS) is a breeding approach which exploits genome-wide information and whose unprecedented success has shaped several animal and plant breeding schemes through delivering their genetic progress. This is the first study assessing the potential of GS in apricot (Prunus armeniaca) to enhance postharvest fruit quality attributes. Genomic predictions were based on a F1 pseudo-testcross population, comprising 153 individuals with contrasting fruit quality traits. They were phenotyped for physical and biochemical fruit metrics in contrasting climatic conditions over two years. Prediction accuracy (PA) varied from 0.31 for glucose content with the Bayesian LASSO (BL) to 0.78 for ethylene production with RR-BLUP, which yielded the most accurate predictions in comparison to Bayesian models and only 10% out of 61,030 SNPs were sufficient to reach accurate predictions. Useful insights were provided on the genetic architecture of apricot fruit quality whose integration in prediction models improved their performance, notably for traits governed by major QTL. Furthermore, multivariate modeling yielded promising outcomes in terms of PA within training partitions partially phenotyped for target traits. This provides a useful framework for the implementation of indirect selection based on easy-to-measure traits. Thus, we highlighted the main levers to take into account for the implementation of GS for fruit quality in apricot, but also to improve the genetic gain in perennial species.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03057805/file/2020%20-%20Publi%2032%20-%20Nsibi%20-%20G3.pdf BibTex
titre
‘Candidatus Liberibacter solanacearum’ distribution and diversity in Scotland and the characterisation of novel haplotypes from Craspedolepta spp. (Psyllidae: Aphalaridae)
auteur
Jason Sumner-Kalkun, Fiona Highet, Yvonne Arnsdorf, Emma Back, Mairi Carnegie, Siobhán Madden, Silvia Carboni, William Billaud, Zoë Lawrence, David Kenyon
article
Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-73382-9⟩
resume
The phloem limited bacterium 'Candidatus Liberibacter solanacearum' (Lso) is associated with disease in Solanaceous and Apiaceous crops. This bacterium has previously been found in the UK in Trioza anthrisci, but its impact on UK crops is unknown. Psyllid and Lso diversity and distribution among fields across the major carrot growing areas of Scotland were assessed using real-time PCR and DNA barcoding techniques. Four Lso haplotypes were found: C, U, and two novel haplotypes. Lso haplotype C was also found in a small percentage of asymptomatic carrot plants (9.34%, n=139) from a field in Milnathort where known vectors of this haplotype were not found. This is the first report of Lso in cultivated carrot growing in the UK and raises concern for the carrot and potato growing industry regarding the potential spread of new and existing Lso haplotypes into crops. Trioza anthrisci was found present only in sites in Elgin, Moray with 100% of individuals harbouring Lso haplotype C. Lso haplotype U was found at all sites infecting Trioza urticae and at some sites infecting Urtica dioica with 77.55% and 24.37% average infection, respectively. The two novel haplotypes were found in Craspedolepta nebulosa and Craspedolepta subpunctata and named Cras1 and Cras2. This is the first report of Lso in psyllids from the Aphalaridae. These new haplotypes were most closely related to Lso haplotype H recently found in carrot and parsnip. Lso was also detected in several weed plants surrounding carrot and parsnip fields. These included two Apiaceous species Aegropodium podagraria (hap undetermined) and Anthriscus sylvestris (hap C); one Gallium sp. (Rubiaceae) (hap undetermined); and Chenopodium album (Amaranthaceae) (hap undetermined).
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The apple REFPOP—a reference population for genomics-assisted breeding in apple
auteur
Michaela Jung, Morgane Roth, Maria José Aranzana, Annemarie Auwerkerken, Marco Bink, Caroline Denancé, Christian Dujak, Charles-Eric Durel, Carolina Font I Forcada, Celia Cantin, Walter Guerra, Nicholas Howard, Beat Keller, Mariusz Lewandowski, Matthew Ordidge, Marijn Rymenants, Nadia Sanin, Bruno Studer, Edward Zurawicz, François Laurens, Andrea Patocchi, Hélène Muranty
article
Horticulture research, 2020, 7 (1), ⟨10.1038/s41438-020-00408-8⟩
resume
Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker-trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker-trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://univ-angers.hal.science/hal-03016720/file/s41438-020-00408-8.pdf BibTex
titre
Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif
auteur
Kelsey Wood, Munir Nur, Juliana D B Gil, Kyle Fletcher, Kim Lakeman, Dasan Gann, Ayumi Gothberg, Tina Khuu, Jennifer Kopetzky, Sanye Naqvi, Archana Pandya, Chi Zhang, Brigitte Maisonneuve, Mathieu Pel, Richard Michelmore
article
PLoS Pathogens, 2020, 16 (10), pp.e1009012. ⟨10.1371/journal.ppat.1009012⟩
resume
Pathogens that infect plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen Bremia lactucae by searching the predicted proteome for the WY domain, a structural fold found in effectors that has been implicated in immune suppression as well as effector recognition by host resistance proteins. We predicted 55 WY domain containing proteins in the genome of B. lactucae and found substantial variation in both sequence and domain architecture. These candidate effectors exhibit several characteristics of pathogen effectors, including an N-terminal signal peptide, lineage specificity, and expression during infection. Unexpectedly, only a minority of B. lactucae WY effectors contain the canonical N-terminal RXLR motif, which is a conserved feature in the majority of cytoplasmic effectors reported in Phytophthora spp. Functional analysis of 21 effectors containing WY domains revealed 11 that elicited cell death on wild accessions and domesticated lettuce lines containing resistance genes, indicative of recognition of these effectors by the host immune system. Only two of the 11 recognized effectors contained the canonical RXLR motif, suggesting that there has been an evolutionary divergence in sequence motifs between genera; this has major consequences for robust effector prediction in oomycete pathogens.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03106412/file/Wood_ppat_2020.pdf BibTex
titre
Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population
auteur
Isidore Diouf, Laurent Derivot, Shai Koussevitzky, Yolande Carretero, Frédérique Bitton, Laurence Moreau, Mathilde Causse
article
Journal of Experimental Botany, 2020, 71 (18), pp.5365-5376. ⟨10.1093/jxb/eraa265⟩
resume
Deciphering the genetic basis of phenotypic plasticity and genotype x environment interactions (GxE) is of primary importance for plant breeding in the context of global climate change. Tomato (Solanum lycopersicum) is a widely cultivated crop that can grow in different geographical habitats and that displays a great capacity for expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore GxE and plasticity for multiple traits measured in a multi-environment trial (MET) comprising optimal cultural conditions together with water deficit, salinity, and heat stress over 12 environments. Substantial GxE was observed for all the traits measured. Different plasticity parameters were estimated by employing Finlay-Wilkinson and factorial regression models and these were used together with genotypic means for quantitative trait loci (QTL) mapping analyses. In addition, mixed linear models were also used to investigate the presence of QTL x environment interactions. The results highlighted a complex genetic architecture of tomato plasticity and GxE. Candidate genes that might be involved in the occurrence of GxE are proposed, paving the way for functional characterization of stress response genes in tomato and for breeding climate-adapted cultivars.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02952485/file/eraa265.pdf BibTex
titre
Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple
auteur
Morgane Roth, Helene Muranty, Mario Di Guardo, Walter Guerra, Andrea Patocchi, Fabrizio Costa
article
Horticulture research, 2020, 7, pp.148-161. ⟨10.1038/s41438-020-00370-5⟩
resume
Texture is a complex trait and a major component of fruit quality in apple. While the major effect of MdPG1, a genecontrolling firmness, has already been exploited in elite cultivars, the genetic basis of crispness remains poorlyunderstood. To further improve fruit texture, harnessing loci with minor effects via genomic selection is thereforenecessary. In this study, we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture. Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers. The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance (0.64). Predictions for biparental families using the entire training set varied from low to high accuracy, depending on the family considered. While adding siblings or half-siblings into the training set did not clearly improve predictions, we performed an optimization of the training set size and composition for each validation set. This allowed us to increase prediction accuracies by 0.17 on average, with a maximal accuracy of 0.81 when predicting firmness in the ‘Gala’ × ‘Pink Lady’ family. Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple. In particular, we advise to rely on a large training population, with high phenotypic variability from which a ‘tailored training population’ can be extracted using a priori information on genetic relatedness, in order to predict a specific target population.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02926794/file/s41438-020-00370-5.pdf BibTex
titre
Selections issued from CEP INNOVATION, CENTREX and INRA: apricot breeding program in France
auteur
C. Auvinet, A. Blanc, F. Gilles, G. Clauzel, E. Hostalnou, N. Courthieu, G. Roch, B. Gouble, S. Bureau, C. Pitiot, J.M. Audergon
article
Acta Horticulturae, 2020, 1290, pp.31-34. ⟨10.17660/ActaHortic.2020.1290.6⟩
resume
The French apricot production is located in the southeastern part of the country with a focused zone in the Rhone valley and close to the Mediterranean Sea. The north of Rhone valley is characterized by a continental climate while the southern region (Rhone valley and Mediterranean area) is characterized by a typical Mediterranean climate. Due to economic and adaptation constraints the apricot fruit production depends on the development of a specific range of cultivars in the different areas of cultivation. In order to enlarge the panel of, a breeding program is developed at a national level in France with the participation of CEP INNOVATION, CENTREX and INRA. The main goals of the breeding program are: the elaboration of cultivars suitable for a durable production (including resistance to pests and diseases), production regularity (including self-fertility and quality of the flowers), and fruit quality (including taste, attractiveness, and suitability for the transport). Out of a first evaluation stage in nursery, based on a MAS approach targeted onto sharka susceptibility and Self-fertility, the agronomical evaluation is performed in orchard and followed by an evaluation of the pre-selections after grafting in the 3 main areas of cultivation for integrating the adaptability. Then the ‘elite’ agronomic and commercial assessments are conducted in small orchards. The main results issued from this program are here presented with 10 blushy and purple-red cultivars including five PPV resistant ‘Aramis®’ cultivars.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Evaluation of apricot fruit quality diversity in two countries, France and New Zealand
auteur
B. Gouble, C. Scofield, A. Mcglone, H. Boldingh, C. Clark, J.M. Audergon, S. Bureau, J. Stanley
article
Acta Horticulturae, 2020, 1290, pp.147-154. ⟨10.17660/ActaHortic.2020.1290.27⟩
resume
New Zealand and French stone fruit industries desire new long-storing, sweettasting apricot cultivars. The climacteric nature of apricots (a high ethylene production that stimulates softening via cell wall degradation) shortens their storage life. Breeders in France (FR) and New Zealand (NZ) have some apricot populations producing fruit with unusually low climacteric behavior and with a large range of total soluble solids (TSS). Trials in FR and NZ shared the same research protocols, for optimal comparison and verification. Up to 60 genotypes representative of fruit diversity in each country were studied in June-July 2016 in FR and January-February 2017 in NZ, with four cultivars in common. For each genotype, six fruits, selected according to firmness, were characterized for fruit quality traits on the day of harvest. Measurements were intact fruit: compression firmness, near infrared spectroscopy (NIRS), ethylene production, skin color, and penetrometer; and fruit tissue samples: TSS, titratable acidity (TA), and individual sugar and organic acid contents. A large diversity was observed for firmness, from 4 to 55 N in NZ and 1 to 36 N in FR. Ethylene production ranged from 0 to 740 nmol h-1 kg-1 in NZ and 0 to 4257 nmol h-1 kg-1 in FR, and discriminated between known lowand high-ethylene cultivars. Conversely, the variability was larger in NZ than in FR for biochemical content: TSS ranged from 8 to 24 °Brix in NZ and 10 to 22 °Brix in FR and TA from 85 to 514 meq kg-1 in NZ and 24 to 350 meq kg-1 in FR. NIRS has the ability to discriminate across countries. The fruit genetic variability opens new opportunities for breeding programs.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Precision breeding made real with CRISPR: illustration through genetic resistance to pathogens
auteur
Florian Veillet, Mickaël Durand, Thomas Kroj, Stella Cesari, Jean-Luc Gallois
article
Plant Communications, 2020, 1 (5), pp.100102. ⟨10.1016/j.xplc.2020.100102⟩
resume
Since its discovery as a bacterial adaptive immune system and its development for genome editing in eukaryotes, the CRISPR technology has revolutionized plant research and precision crop breeding. The CRISPR toolbox holds great promise in the production of crops with genetic disease resistance to increase agriculture resilience and reduce chemical crop protection with a strong impact on the environment and public health. In this review, we provide an extensive overview on recent breakthroughs in CRISPR technology, including the newly developed prime editing system that allows precision gene editing in plants. We present how each CRISPR tool can be selected for optimal use in accordance with its specific strengths and limitations, and illustrate how the CRISPR toolbox can foster the development of genetically pathogen-resistant crops for sustainable agriculture.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02908429/file/2020_veillet_plant_communications.pdf BibTex
titre
Integration of QTL, Transcriptome and Polymorphism Studies Reveals Candidate Genes for Water Stress Response in Tomato
auteur
Isidore Diouf, Elise Albert, Renaud Duboscq, Sylvain Santoni, Frédérique Bitton, Justine Gricourt, Mathilde Causse
article
Genes, 2020, 11 (8), pp.900. ⟨10.3390/genes11080900⟩
resume
Water deficit (WD) leads to significant phenotypic changes in crops resulting from complex stress regulation mechanisms involving responses at the physiological, biochemical and molecular levels. Tomato growth and fruit quality have been shown to be significantly affected by WD stress. Understanding the molecular mechanism underlying response to WD is crucial to develop tomato cultivars with relatively high performance under low watering conditions. Transcriptome response to WD was investigated through the RNA sequencing of fruit and leaves in eight accessions grown under two irrigation conditions, in order to get insight into the complex genetic regulation of WD response in tomato. Significant differences in genotype WD response were first observed at the phenotypic level for fruit composition and plant development traits. At the transcriptome level, a total of 14,065 differentially expressed genes (DEGs) in response to WD were detected, among which 7393 (53%) and 11,059 (79%) were genotype- and organ-specific, respectively. Water deficit induced transcriptome variations much stronger in leaves than in fruit. A significant effect of the genetic background on expression variation was observed compared to the WD effect, along with the presence of a set of genes showing a significant genotype x watering regime interaction. Integrating the DEGs with previously identified WD response quantitative trait loci (QTLs) mapped in a multi-parental population derived from the crossing of the eight genotypes narrowed the candidate gene lists to within the confidence intervals surrounding the QTLs. The results present valuable resources for further study to decipher the genetic determinants of tomato response to WD.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02952488/file/genes-11-00900.pdf BibTex
titre
Ecological Specialization and Rarity of Arable Weeds: Insights from a Comprehensible Survey in France
auteur
François Munoz, Guillaume Fried, Laura Armengot, Bérenger Bourgeois, Vincent Bretagnolle, Joel J. Chadoeuf, Lucie Mahaut, Christine Plumejeaud, Jonathan Storkey, Cyrille Violle, Sabrina Gaba
article
Plants, 2020, 9 (7), pp.824. ⟨10.3390/plants9070824⟩
resume
The definition of “arable weeds” remains contentious. Although much attention has been devoted to specialized, segetal weeds, many taxa found in arable fields also commonly occur in other habitats. The extent to which adjacent habitats are favorable to the weed flora and act as potential sources of colonizers in arable fields remains unclear. In addition, weeds form assemblages with large spatiotemporal variability, so that many taxa in weed flora are rarely observed in plot-based surveys. We thus addressed the following questions: How often do weeds occur in other habitats than arable fields? How does including field edges extend the taxonomic and ecological diversity of weeds? How does the weed flora vary across surveys at different spatial and temporal scales? We built a comprehensive dataset of weed taxa in France by compiling weed flora, lists of specialized segetal weeds, and plot-based surveys in agricultural fields, with different spatial and temporal coverages. We informed life forms, biogeographical origins and conservation status of these weeds. We also defined a broader dataset of plants occupying open habitats in France and assessed habitat specialization of weeds and of other plant species absent from arable fields. Our results show that many arable weeds are frequently recorded in both arable fields and non-cultivated open habitats and are, on average, more generalist than species absent from arable fields. Surveys encompassing field edges included species also occurring in mesic grasslands and nitrophilous fringes, suggesting spill-over from surrounding habitats. A total of 71.5% of the French weed flora was not captured in plot-based surveys at regional and national scales, and many rare and declining taxa were of Mediterranean origin. This result underlines the importance of implementing conservation measures for specialist plant species that are particularly reliant on arable fields as a habitat, while also pointing out biotic homogenization of agricultural landscapes as a factor in the declining plant diversity of farmed landscapes. Our dataset provides a reference species pool for France, with associated ecological and biogeographical information.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02886083/file/plants-09-00824-v3.pdf BibTex
titre
Cuticular waxes of nectarines during fruit development in relation to surface conductance and susceptibility to Monilinia laxa
auteur
Leandro Oliveira Lino, Bénédicte Quilot-Turion, Claire Dufour, Marie-Noëlle Corre, René Lessire, Michel Génard, Jean-Luc Poessel
article
Journal of Experimental Botany, 2020, ⟨10.1093/jxb/eraa284⟩
resume
The cuticle is composed of cutin and cuticular waxes, and it is the first protective barrier to abiotic and biotic stresses in fruit. In this study, we analysed the composition of and changes in cuticular waxes during fruit development in nectarine (Prunus persica L. Batsch) cultivars, in parallel with their conductance and their susceptibility to Monilinia laxa. The nectarine waxes were composed of triterpenoids, mostly ursolic and oleanolic acids, phytosterols, and very-long-chain aliphatics. In addition, we detected phenolic compounds that were esterified with sugars or with triterpenoids, which are newly described in cuticular waxes. We quantified 42 compounds and found that they changed markedly during fruit development, with an intense accumulation of triterpenoids during initial fruit growth followed by their decrease at the end of endocarp lignification and a final increase in very-long-chain alkanes and hydroxylated triterpenoids until maturity. The surface conductance and susceptibility to Monilinia decreased sharply at the beginning of endocarp lignification, suggesting that triterpenoid deposition could play a major role in regulating fruit permeability and susceptibility to brown rot. Our results provide new insights into the composition of cuticular waxes of nectarines and their changes during fruit development, opening new avenues of research to explore brown rot resistance factors in stone fruit.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Phenotyping with fast fluorescence sensors approximates yield component measurements in pepper (Capsicum annuum L.)
auteur
S. Lenk, J.A. Dieleman, Véronique Lefebvre, E. Heuvelink, J.J. Magan, A. Palloix, F.A. Eeuwijk, A. Barocsi
article
Photosynthetica, 2020, 58, pp.622-637. ⟨10.32615/ps.2020.016⟩
resume
Molecular breeding, a powerful technique to increase crop yield, tries to predict yield by crop growth models with genotype specific, environment-independent yield components and environmental indices as inputs. A fluorescence-trait-based approach is presented to approximate some costly and time-consuming measurements of yield components. Temporal monitoring of chlorophyll a fluorescence resulted in fluorescence traits with high heritability (0.60-0.82) that could act as proxies for model inputs. Medium-sized Pearson's correlations were calculated between fluorescence traits, light-use efficiency (LUE), and fruit related parameters up to 0.53. Multi-trait quantitative trait locus (QTL) analyses identified genomic regions of pepper (Capsicum annuum L.) involved in the phenotypic variation of the fluorescence traits. Fluorescence QTLs found on linkage groups P6, P7, and P11 corresponded to QTLs for number of fruits, partitioning into fruits, and LUE. Fluorescence parameters within 1 min of the fluorescence response curve can thus be useful to approximate yield component traits.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic Structure of a Worldwide Germplasm Collection of Prunus armeniaca L. Reveals Three Major Diffusion Routes for Varieties Coming From the Species’ Center of Origin
auteur
Hedia Bourguiba, Ivan Scotti, Christopher Sauvage, Tetyana Zhebentyayeva, Craig Ledbetter, Boris Krška, Arnaud A. Remay, Claudio D’onofrio, Hiroyuki Iketani, Danilo Christen, Lamia Krichen, Neila Trifi-Farah, Weisheng Liu, Guillaume Roch, Jean-Marc Audergon
article
Frontiers in Plant Science, 2020, 11, ⟨10.3389/fpls.2020.00638⟩
resume
The characterization of the largest worldwide representative data set of apricot (Prunus armeniaca L.) germplasm was performed using molecular markers. Genetic diversity and structure of the cultivated apricot genetic resources were analyzed to decipher the history of diffusion of this species around the world. A common set of 25 microsatellite markers was used for genotyping a total of 890 apricot accessions in different collections from the center of origin to the more recent regions of apricot culture. Using a Bayesian model-based clustering approach, the apricot genotypes can be structured into five different genetic clusters (F-ST = 0.174), correlated with the geographical regions of origin of the accessions. Accessions from China and Central Asia were clustered together and exhibited the highest levels of diversity, confirming an origin in this region. A loss of genetic diversity was observed from the center of origin to both western and eastern zones of recent apricot culture. Altogether, our results revealed that apricot spread from China and Central Asia, defined as the center of origin, following three major diffusion routes with a decreasing gradient of genetic variation in each geographical group. The identification of specific alleles outside the center of origin confirmed the existence of different secondary apricot diversification centers. The present work provides more understanding of the worldwide history of apricot species diffusion as well as the field of conservation of the available genetic resources. Data have been used to define an apricot core collection based on molecular marker diversity which will be useful for further identification of genomic regions associated with commercially important horticultural traits through genome-wide association studies to sustain apricot breeding programs.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Competitive interactions in plant-parasitic nematode communities affecting organic vegetable cropping systems
auteur
Thierry T. Mateille, Johannes Tavoillot, Claire Goillon, Laure Pares, Amélie Lefevre, Hélène Védie, Mireille Navarrete, Alain Palloix, Anne-Marie Sage-Palloix, Philippe Castagnone-Sereno, Ariane Fazari, Nathalie Marteu, Caroline Djian-Caporalino
article
Crop Protection, 2020, 135, pp.105206. ⟨10.1016/j.cropro.2020.105206⟩
resume
Plant-parasitic nematodes (PPN) are detected everywhere as mixed-species communities. Most non-chemical control strategies of PPN only target some species, thus raising questions about the consequences that this specificity may have on the residual community. In this respect, the long-term ecological sustainability of such strategies is challenged. In order to evaluate the impacts of agronomical practices on PPN communities, two four-year experiments that differed by the presence or absence of root-knot nematodes (RKN - Meloidogyne spp.) were carried out under cold shelters in the south of France, under native field conditions of vegetable cropping systems that included a nematicidal sorghum green manure and a pepper variety carrying a RKN resistance gene. At the site with RKN, RKN populations developed on susceptible vegetables. They were controlled by the green manure but not by the R-pepper, and were also vulnerable to low soil temperatures. At the site without RKN, Paratylenchidae populations developed on susceptible vegetables, but were controlled by both the green manure and the R-pepper, and not by low temperatures. At each site, populations of Telotylenchidae exhibited dynamics suggesting competition with RKN or Paratylenchidae. Hypotheses about competition models are discussed according to the specific life traits of the PPN involved, including ecto- vs. endoparasitism and sedentary vs. free-living behaviour, and to the antagonist mechanisms of the cover and resistant crops that must be introduced in vegetable cropping systems.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02649096/file/S0261219420301393.pdf BibTex
titre
Reducing a model of sugar metabolism in peach to catch different patterns among genotypes
auteur
Hussein Kanso, Bénédicte Quilot-Turion, Mohamed-Mahmoud Memah, Olivier Bernard, Jean-Luc Gouzé, Valentina Baldazzi
article
Mathematical Biosciences, 2020, 321, pp.108321. ⟨10.1016/j.mbs.2020.108321⟩
resume
Several studies have been conducted to understand the dynamic of primary metabolisms in fruit by translating them into mathematics models. An ODE kinetic model of sugar metabolism has been developed by Desnoues et al. (2018) to simulate the accumulation of different sugars during peach fruit development. Two major drawbacks of this model are (a) the number of parameters to calibrate and (b) its integration time that can be long due to non-linearity and time-dependent input functions. Together, these issues hamper the use of the model for a large panel of genotypes, for which few data are available. In this paper, we present a model reduction scheme that explicitly addresses the specificity of genetic studies in that: (i) it yields a reduced model that is adapted to the whole expected genetic diversity (ii) it maintains network structure and variable identity, in order to facilitate biological interpretation. The proposed approach is based on the combination and the systematic evaluation of different reduction methods. Thus, we combined multivariate sensitivity analysis, structural simplification and timescale-based approaches to simplify the number and the structure of ordinary differential equations of the model. The original and reduced models were compared based on three criteria, namely the corrected Aikake Information Criterion (AIC(C)), the calibration time and the expected error of the reduced model over a progeny of virtual genotypes. The resulting reduced model not only reproduces the predictions of the original one but presents many advantages including a reduced number of parameters to be estimated and shorter calibration time, opening new promising perspectives for genetic studies and virtual breeding. The validity of the reduced model was further evaluated by calibration on 30 additional genotypes of an inter-specific peach progeny for which few data were available.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02922359/file/Kanso2020.pdf BibTex
titre
Semantic concept schema of the linear mixed model of experimental observations
auteur
Hanna Ćwiek-Kupczyńska, Katarzyna Filipiak, Augustyn Markiewicz, Philippe Rocca-Serra, Alejandra N Gonzalez-Beltran, Susanna-Assunta Sansone, Emilie J Millet, Fred van Eeuwijk, Agnieszka Ławrynowicz, Paweł Krajewski
article
Scientific Data , 2020, 7 (1), pp.70. ⟨10.1038/s41597-020-0409-7⟩
resume
in the information age, smart data modelling and data management can be carried out to address the wealth of data produced in scientific experiments. In this paper, we propose a semantic model for the statistical analysis of datasets by linear mixed models. We tie together disparate statistical concepts in an interdisciplinary context through the application of ontologies, in particular the Statistics Ontology (STATO), to produce FAIR data summaries. We hope to improve the general understanding of statistical modelling and thus contribute to a better description of the statistical conclusions from data analysis, allowing their efficient exploration and automated processing.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04151050/file/wiek-Kupczy%C5%84ska%20et%20al.%20-%202020%20-%20Semantic%20concept%20schema%20of%20the%20linear%20mixed%20model%20.pdf BibTex
titre
Expanding the CRISPR Toolbox in P. patens Using SpCas9-NG Variant and Application for Gene and Base Editing in Solanaceae Crops
auteur
Florian Veillet, Laura Perrot, Anouchka Guyon-Debast, Marie-Paule Kermarrec, Laura Chauvin, Jean-Eric Chauvin, Jean-Luc Gallois, Marianne Mazier, Fabien Nogué
article
International Journal of Molecular Sciences, 2020, 21 (3), pp.1024. ⟨10.3390/ijms21031024⟩
resume
Genome editing has become a major tool for both functional studies and plant breeding in several species. Besides generating knockouts through the classical CRISPR-Cas9 system, recent development of CRISPR base editing holds great and exciting opportunities for the production of gain-of-function mutants. The PAM requirement is a strong limitation for CRISPR technologies such as base editing, because the base substitution mainly occurs in a small edition window. As precise single amino-acid substitution can be responsible for functions associated to some domains or agronomic traits, development of Cas9 variants with relaxed PAM recognition is of upmost importance for gene function analysis and plant breeding. Recently, the SpCas9-NG variant that recognizes the NGN PAM has been successfully tested in plants, mainly in monocotyledon species. In this work, we studied the efficiency of SpCas9-NG in the model moss Physcomitrella patens and two Solanaceae crops (Solanum lycopersicum and Solanum tuberosum) for both classical CRISPR-generated gene knock-out and cytosine base editing. We showed that the SpCas9-NG greatly expands the scope of genome editing by allowing the targeting of non-canonical NGT and NGA PAMs. The CRISPR toolbox developed in our study opens up new gene function analysis and plant breeding perspectives for model and crop plants.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03142023/file/Veillet-2020-Expanding%20the%20CRISPR%20Toolbox%20in%20P.%20patens.pdf BibTex
titre
Gearing Up for Warmer Times: Transcriptomic Response of Spongia officinalis to Elevated Temperatures Reveals Recruited Mechanisms and Potential for Resilience
auteur
Vasiliki Koutsouveli, Tereza Manousaki, Ana Riesgo, Jacques Lagnel, Spyros Kollias, Costas Tsigenopoulos, Christos Arvanitidis, Costas Dounas, Antonios Magoulas, Thanos Dailianis
article
Frontiers in Marine Science, 2020, 6, ⟨10.3389/fmars.2019.00786⟩
resume
The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism's response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure to temperatures of varying intensity and span on its gene expression profile, replicating gradients encountered in the species' native habitat. Analysis revealed major shifts in the organism's transcriptomic profile induced by temperatures corresponding to the standard seasonal maximum, triggering processes related to signal transduction, inflammation, and apoptotic pathway. Further elevation of temperature corresponding to local extremes activated further the immune response of the sponge along with protein ubiquitination. Following prolonged exposure, activation of endoplasmic reticulum stress related to accumulation of misfolded proteins and signs of resilience were observed. In the latter condition, categories such as cellular response to stress, wound repair, and diminution of pathological inflammation as also genes related to cell regeneration and cell growth were upregulated. Our results highlight the acknowledged sensitivity of S. officinalis to environmental shifts, providing an insight into the molecular mechanisms involved in the process. Furthermore, they suggest innate capacity for resilience at the current thermal extremes, implying a combination of factors and not temperature per se as the lethal agent. This sheds light on the mechanisms of pressure induced by the ongoing ocean warming trend to coastal sessile invertebrates.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
auteur
Tyler Alioto, Konstantinos Alexiou, Amélie Bardil, Fabio Barteri, Raúl Castanera, Fernando Cruz, Amit Dhingra, Henri Duval, Angel Fernandez I Marti, Leonor Frias, Beatriz Galán, José García, Werner Howad, Jèssica Gómez‐garrido, Marta Gut, Irene Julca, Jordi Morata, Pere Puigdomènech, Paolo Ribeca, María Rubio Cabetas, Anna Vlasova, Michelle Wirthensohn, Jordi Garcia‐mas, Toni Gabaldón, Josep Casacuberta, Pere Arús
article
The Plant Journal, 2020, 101 (2), pp.455-472. ⟨10.1111/tpj.14538⟩
resume
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Future development of apricot blossom blight under climate change in Southern France
auteur
Paul Tresson, Laurent Brun, Iñaki Garcia de Cortazar-Atauri, Jean-Marc Audergon, Sophie Buléon, Hélène Chenevotot, Freddy Combe, Doriane Dam, Maxime Jacquot, Baptiste Labeyrie, Vincent Mercier, Claude-Eric Parveaud, Marie Launay
article
European Journal of Agronomy, 2020, 112, pp.125960. ⟨10.1016/j.eja.2019.125960⟩
resume
Climate change will have several consequences for agro-systems, one of which will concern changes to the development of pathogens. Because of the losses it causes, particularly in organic farming, Monilinia laxa is an important pathogen affecting apricot crops. This study focuses on the consequences of climate change regarding blossom and twig blight (Monilinia laxa) of apricot. To achieve this, a Climatic Index of cumulated Blight risk (CIB) was built, to obtain the weighted sum of blossom blight incidence throughout the blooming period. An epidemiological model to calculate the incidence of blossom blight during every potentially infectious episode and based on biological parameters, was calibrated using a trap pot experiment where trees were placed in orchards and subject to various meteorological conditions. The CIB derived from this model was evaluated on field data, and was shown to be a robust and useful tool to predict the effects of climate change on the development of apricot blight. Then, using the CIB with a phenological model to predict blooming periods in the future, we estimated the risks of apricot blight until 2100 on four contrasted apricot cultivars and in three geographical zones under climate change scenarios RCP 4.5 and 8.5. This study revealed different effects of climate change depending on the cultivar and altitude. Apricot trees would bloom earlier (up to a difference of 50 days between 1950 and 2100) under climate change. Under the combined effects of these shifts of blooming period and changing climatic conditions, late cultivars such as Bergarouge might see a reduction in the risk of blossom blight (down to 31%) because of warmer but dryer blooming periods. Other varieties (e.g.: Bergeron) could experience an increase in this risk by up to 27% with a shift of the blooming period towards rainier conditions at the highest altitudes. The results of this study could be used to anticipate future changes as well as be used at present as a decision-support tool for farmers.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02361185/file/Tresson_et_al_2019_EJA_version_auteur.pdf BibTex
titre
Analysis of tomato spotted wilt virus RNA-dependent RNA polymerase adaptative evolution and constrained domains using homology protein structure modelling.
auteur
Zoé Terret-Welter, Grégori Bonnet, Benoît Moury, Jean-Luc Gallois
article
Journal of General Virology, 2020, 101, pp.334-346. ⟨10.1099/jgv.0.001380⟩
resume
Tomato spotted wilt virus (TSWV; genus Orthotospovirus, family Tospoviridae) has a huge impact on a large range of plants worldwide. In this study, we determined the sequence of the large (L) RNA segment that encodes the RNA-dependent RNA polymerase (RdRp) from a TSWV isolate (LYE51) collected in the south of France. Analysis of the phylogenetic relationships of TSWV-LYE51 with other TSWV isolates shows that it is closely related to other European isolates. A 3D model of TSWV-LYE51 RdRp was built by homology with the RdRp structure of the La Crosse virus (genus Orthobunyavirus, family Peribunyaviridae). Finally, an analysis of positive and negative selection was carried out on 30 TSWV full-length RNA L sequences and compared with the phylogeny and the protein structure data. We showed that the seven codons that are under positive selection are distributed all along the RdRp gene. By contrast, the codons associated with negative selection are especially concentrated in three highly constrained domains: the endonuclease in charge of the cap-snatching mechanism, the thumb domain and the mid domain. Those three domains could constitute good candidates to look for host targets on which genetic resistance by loss of susceptibility could be developed.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The multi-site PeachRefPop collection: a true cultural heritage and international scientific tool for fruit trees
auteur
Marco Cirilli, Sabrina Micali, Maria Jose Aranzana, Pere Arus, Annarosa Babini, Teresa Barreneche, Marco Cam Bink, Celia Cantín, Angelo Ciacciulli, José Cos-Terrer, Pavlina Drogoudi, Iban Eduardo, Stefano Foschi, Daniela Giovannini, Walter Guerra, Alessandro Liverani, Igor Pacheco, Thierry Pascal, Bénédicte Quilot-Turion, Ignazio Verde, Laura Rossini, Daniele Bassi
article
Plant Physiology, 2020, 184 (2), pp.632-646. ⟨10.1104/pp.19.01412⟩
resume
Plants have evolved a range of adaptive mechanisms that adjust their development and physiology to variable external conditions, particularly in perennial species subjected to long-term interplay with the environment. Exploiting the allelic diversity within available germplasm and leveraging the knowledge of the mechanisms regulating genotype interaction with the environment are crucial to address climatic challenges and assist the breeding of novel cultivars with improved resilience. The development of multisite collections is of utmost importance for the conservation and utilization of genetic materials and will greatly facilitate the dissection of genotype-by-environment interaction. Such resources are still lacking for perennial trees, especially with the intrinsic difficulties of successful propagation, material exchange and living collection maintenance. This work describes the concept, design and realization of the first multi-site peach [Prunus persica (L.) Batsch] reference collection (PeachRefPop: PRP) located across different European countries and sharing the same experimental design. Other than an invaluable tool for scientific studies in perennial species, the PRP provides a milestone in an international collaborative project for the conservation and exploitation of European peach germplasm resources and, ultimately, as a true heritage for future generations.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach
auteur
Jiali Yu, Anna O Conrad, Véronique Decroocq, Tetyana Zhebentyayeva, Daniel E Williams, Dennis Bennett, Guillaume Roch, Jean-Marc Audergon, Christopher Dardick, Zongrang Liu, Albert G. Abbott, Michael James Considine, Hisayo Yamane, Gabino Ríos, Carmen Leida, Margaret E Staton
article
Frontiers in Plant Science, 2020, 11, pp.180. ⟨10.3389/fpls.2020.00180⟩
resume
Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot (Prunus armeniaca) genotypes with contrasting bloom dates and peach (Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo-to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box (DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved Frontiers in Plant Science | www.frontiersin.org
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02534855/file/2020_Yu_Frontiers_In_Plant_Science.pdf BibTex
titre
Knock-out mutation of eukaryotic initiation factor 4E2 (eIF4E2) confers resistance to pepper veinal mottle virus in tomato
auteur
Benoît Moury, Caroline Lebaron, Marion Szadkowski, Mekki Ben Khalifa, Gregory Girardot, Bolou Antoine Bolou Bi, Daouda Koné, Léon W. Nitiema, Hatem Fakhfakh, Jean-Luc Gallois
article
Virology, 2020, 539, pp.11-17. ⟨10.1016/j.virol.2019.09.015⟩
resume
Translation initiation factors 4E (eIF4E) are the main source of resistance to potyvirus. We systematically assessed tomato single and double knock-out (KO) mutants of members of the eIF4E-coding gene family for resistance to Pepper veinal mottle virus (PVMV), a major constraint to tomato production. We show that the KO mutant of eIF4E2 has partial resistance to PVMV isolate IC, with plants harboring weak symptoms and low virus loads at the systemic level. The causal effect of eIF4E2 loss-of-function on resistance was confirmed on a progeny segregating for the KO mutation. The eIF4E2 KO mutant was resistant to six of the eight PVMV isolates tested and no resistance to other potyviruses was observed. This is the first evidence that mutation of eIF4E2 is in itself conferring resistance to a potyvirus and 3D protein modelling suggests that the eIF4E2 gene could be converted into a functional resistance allele.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding.
auteur
Lucie Tamisier, Marion Szadkowski, Ghislaine Nemouchi, Véronique Lefebvre, Emmanuel Szadkowski, Renaud Duboscq, Sylvain Santoni, Sarah Gautier, Christopher Sauvage, Alain Palloix, Benoît Moury
article
Molecular Plant Pathology, 2020, 21 (1), pp.03-16. ⟨10.1111/mpp.12874⟩
resume
In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02315849/file/2020_Tamisier_MPP.pdf BibTex
titre
Un nouveau tigre pour la faune de France : Dictyla indigena (Wollaston, 1858) (Hemiptera Tingidae)
auteur
Jean‐Claude Streito, Valérie Balmès, J. Kervella, H. Le Sann
article
L'Entomologiste, 2020, 76 (2), pp.121-124
typdoc
Journal articles
Accès au bibtex
BibTex

2019

Journal articles

titre
The gynoecious CmWIP1 transcription factor interacts with CmbZIP48 to inhibit carpel development
auteur
John Eleblu, Aimen Haraghi, Brahim Mania, Céline Camps, Dali Rashid, Halima H. Morin, Catherine Dogimont, Adnane Boualem, Abdelhafid Bendahmane
article
Scientific Reports, 2019, 9 (1), pp.5953-5966. ⟨10.1038/s41598-019-52004-z⟩
resume
In angiosperms, sex determination leads to development of unisexual flowers. In Cucumis melo, development of unisexual male flowers results from the expression of the sex determination gene, CmWIP1, in carpel primordia. To bring new insight on the molecular mechanisms through which CmWIP1 leads to carpel abortion in male flowers, we used the yeast two-hybrid approach to look for CmWIP1-interacting proteins. We found that CmWIP1 physically interacts with an S2 bZIP transcription factor, CmbZIP48. We further determined the region mediating the interaction and showed that it involves the N-terminal part of CmWIP1. Using laser capture microdissection coupled with quantitative real-time gene expression analysis, we demonstrated that CmWIP1 and CmbZIP48 share a similar spatiotemporal expression pattern, providing the plant organ context for the CmWIP1-CmbZIP48 protein interaction. Using sex transition mutants, we demonstrated that the expression of the male promoting gene CmWIP1 correlates with the expression of CmbZIP48. Altogether, our data support a model in which the coexpression and the physical interaction of CmWIP1 and CmbZIP48 trigger carpel primordia abortion, leading to the development of unisexual male flowers.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits
auteur
Guangwei Zhao, Qun Lian, Zhonghua Zhang, Qiushi Fu, Yuhua He, Shuangwu Ma, Valentino Ruggieri, Antonio Monforte, Pingyong Wang, Irene Julca, Huaisong Wang, Junpu Liu, Yong Xu, Runze Wang, Jiabing Ji, Zhihong Xu, Weihu Kong, Yang Zhong, Jianli Shang, Lara Pereira, Jason Argyris, Jian Zhang, Carlos Mayobre, Marta Pujol, Elad Oren, Diandian Ou, Jiming Wang, Dexi Sun, Shengjie Zhao, Yingchun Zhu, Na Li, Nurit Katzir, Amit Gur, Catherine Dogimont, Hanno Schaefer, Wei Fan, Abdelhafid Bendahmane, Zhangjun Fei, Michel Pitrat, Toni Gabaldón, Tao Lin, Jordi Garcia-Mas, Yongyang Xu, Sanwen Huang
article
Nature Genetics, 2019, 51 (11), pp.1607-1615. ⟨10.1038/s41588-019-0522-8⟩
resume
Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. Our results suggest that three independent domestication events occurred in melon, two in India and one in Africa. We detected two independent sets of domestication sweeps, resulting in diverse characteristics of the two subspecies melo and agrestis during melon breeding. Genome-wide association studies for 16 agronomic traits identified 208 loci significantly associated with fruit mass, quality and morphological characters. This study sheds light on the domestication history of melon and provides a valuable resource for genomics-assisted breeding of this important crop.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Renewable and sustainable strategies for improving the thermal environment of Chinese solar greenhouses
auteur
Kai Cao, Hongjun Xu, Rong Zhang, Dawei Xu, Lulu Yan, Yachen Sun, Liru Xia, Jiantao Zhao, Zhirong Zou, Encai Bao
article
Energy and Buildings, 2019, 202, pp.109414. ⟨10.1016/j.enbuild.2019.109414⟩
resume
Chinese solar greenhouses (CSGs) play an important role in horticultural development, providing high-efficiency thermal storage performance compared to the other greenhouse styles. CGSs are fully passive solar greenhouses for vegetables without auxiliary heating system during the winter. To improve the thermal environmental conditions of CSGs and produce better crops, some strategies have been investigated to improve the thermal environments. In this study, a comprehensive review is presented focusing on key strategies for improving the thermal environment in CSGs. The technologies considered within the scope of this research are mainly renewable and sustainable solutions such as structures (sunken CSG, variable south roof CSG, air channel heat exchange CSG), options for north wall materials (hollow wall, pebble wall, phase-change materials), and equipment for thermal storage (water circulation thermal storage, energy-efficient heat pump thermal storage, photovoltaic thermal storage). These new findings revealed that through the application of a single strategy or synergistic strategies, we can maximize the utilization of renewable and sustainable energy to provide indoor heating. This review also provides a reference for design, application and research on thermal storage and energy-saving strategies for CSGs.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The Solanum tuberosum GBSSI gene: a target for assessing gene and base editing in tetraploid potato
auteur
Florian Veillet, Laura Chauvin, Marie-Paule Kermarrec, François Sevestre, Mathilde Merrer, Zoé Terret, Nicolas Szydlowski, Pierre Devaux, Jean-Luc Gallois, Jean-Eric Chauvin
article
Plant Cell Reports, 2019, 38 (9), pp.1065-1080. ⟨10.1007/s00299-019-02426-w⟩
resume
The StGBSSI gene was successfully and precisely edited in the tetraploid potato using gene and base-editing strategies, leading to plants with impaired amylose biosynthesis. Genome editing has recently become a method of choice for basic research and functional genomics, and holds great potential for molecular plant-breeding applications. The powerful CRISPR-Cas9 system that typically produces double-strand DNA breaks is mainly used to generate knockout mutants. Recently, the development of base editors has broadened the scope of genome editing, allowing precise and efficient nucleotide substitutions. In this study, we produced mutants in two cultivated elite cultivars of the tetraploid potato (Solanum tuberosum) using stable or transient expression of the CRISPR-Cas9 components to knock out the amylose-producing StGBSSI gene. We set up a rapid, highly sensitive and cost-effective screening strategy based on high-resolution melting analysis followed by direct Sanger sequencing and trace chromatogram analysis. Most mutations consisted of small indels, but unwanted insertions of plasmid DNA were also observed. We successfully created tetra-allelic mutants with impaired amylose biosynthesis, confirming the loss of function of the StGBSSI protein. The second main objective of this work was to demonstrate the proof of concept of CRISPR-Cas9 base editing in the tetraploid potato by targeting two loci encoding catalytic motifs of the StGBSSI enzyme. Using a cytidine base editor (CBE), we efficiently and precisely induced DNA substitutions in the KTGGL-encoding locus, leading to discrete variation in the amino acid sequence and generating a loss-of-function allele. The successful application of base editing in the tetraploid potato opens up new avenues for genome engineering in this species.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Comparative Transcriptome Analysis of Gene Expression Patterns in Tomato Under Dynamic Light Conditions
auteur
Juanjuan Ding, Jiantao Zhao, Tonghua Pan, Linjie Xi, Jing Zhang, Zhirong Zou
article
Genes, 2019, 10 (9), pp.662. ⟨10.3390/genes10090662⟩
resume
Plants grown under highly variable natural light regimes differ strongly from plants grown under constant light (CL) regimes. Plant phenotype and adaptation responses are important for plant biomass and fitness. However, the underlying regulatory mechanisms are still poorly understood, particularly from a transcriptional perspective. To investigate the influence of different light regimes on tomato plants, three dynamic light (DL) regimes were designed, using a CL regime as control. Morphological, photosynthetic, and transcriptional differences after five weeks of treatment were compared. Leaf area, plant height, shoot /root weight, total chlorophyll content, photosynthetic rate, and stomatal conductance all significantly decreased in response to DL regimes. The biggest expression difference was found between the treatment with the highest light intensity at the middle of the day with a total of 1080 significantly up-/down-regulated genes. A total of 177 common differentially expressed genes were identified between DL and CL conditions. Finally, significant differences were observed in the levels of gene expression between DL and CL treatments in multiple pathways, predominantly of plant-pathogen interactions, plant hormone signal transductions, metabolites, and photosynthesis. These results expand the understanding of plant development and photosynthetic regulations under DL conditions by multiple pathways.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02877775/file/2019_ding_genes.pdf BibTex
titre
Crop plants with improved culture and quality traits for food, feed and other uses
auteur
Fabien Nogué, Philippe Vergne, Anne-Marie Chèvre, Jean-Eric Chauvin, Oumaya Bouchabke-Coussa, Annabelle Déjardin, Elisabeth Chevreau, Laurence Hibrand-Saint Oyant, Marianne Mazier, Pierre Barret, Emmanuel Guiderdoni, Christophe Sallaud, Séverine Foucrier, Pierre Devaux, Peter Rogowsky
article
Transgenic Research, 2019, 28 (S2), pp.65-73. ⟨10.1007/s11248-019-00135-4⟩
resume
The large French research project GENIUS (2012-2019, https://www6.inra.genius-project_eng/ ) provides a good showcase of current genome editing techniques applied to crop plants. It addresses a large variety of agricultural species (rice, wheat, maize, tomato, potato, oilseed rape, poplar, apple and rose) together with some models (Arabidopsis, Brachypodium, Physcomitrella). Using targeted mutagenesis as its work horse, the project is limited to proof of concept under confined conditions. It mainly covers traits linked to crop culture, such as disease resistance to viruses and fungi, flowering time, plant architecture, tolerance to salinity and plant reproduction but also addresses traits improving the quality of agricultural products for industrial purposes. Examples include virus resistant tomato, early flowering apple and low-amylose starch potato. The wide range of traits illustrates the potential of genome editing towards a more sustainable agriculture through the reduction of pesticides and to the emergence of innovative bio-economy sectors based on custom tailored quality traits.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A complex eIF4E locus impacts the durability of va resistance to Potato virus Y in tobacco
auteur
Vincent Michel, Emilie Julio, Thierry Candresse, Julien Cotucheau, Christophe Decorps, Roxane Volpatti, Benoît Moury, Laurent Glais, Emmanuel Jacquot, François Dorlhac de Borne, Véronique Decroocq, Jean-Luc Gallois, Sylvie German-Retana
article
Molecular Plant Pathology, 2019, 20 (8), pp.1051-1066. ⟨10.1111/mpp.12810⟩
resume
Many recessive resistances against potyviruses are mediated by eukaryotic translation initiation factor 4E (eIF4E). In tobacco, the va resistance gene commonly used to control Potato virus Y (PVY) corresponds to a large deletion affecting the eIF4E-1 gene on chromosome 21. Here, we compared the resistance durability conferred by various types of mutations affecting eIF4E-1 (deletions of various sizes, frameshift or nonsense mutations). The 'large deletion' genotypes displayed the broadest and most durable resistance, whereas frameshift and nonsense mutants displayed a less durable resistance, with rapid and frequent apparition of resistance-breaking variants. In addition, genetic and transcriptomic analyses revealed that resistance durability is strongly impacted by a complex genetic locus on chromosome 14, which contains three other eIF4E genes. One of these, eIF4E-3, is rearranged as a hybrid gene between eIF4E-2 and eIF4E-3 (eIF4E-2-3 ) in the genotypes showing the most durable resistance, while eIF4E-2 is differentially expressed between the tested varieties. RNA-seq and quantitative reverse transcriptase-polymerase chain reaction experiments demonstrated that eIF4E-2 expression level is positively correlated with resistance durability. These results suggest that besides the nature of the mutation affecting eIF4E-1, three factors linked with a complex locus may potentially impact va durability: loss of an integral eIF4E-3, presence of eIF4E-2-3 and overexpression of eIF4E-2. This latter gene might act as a decoy in a non-productive virus-plant interaction, limiting the ability of PVY to evolve towards resistance breaking. Taken together, these results show that va resistance durability can in large part be explained by complex redundancy effects in the eIF4E gene family.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02627932/file/2019_Michel_MPP_1.pdf BibTex
titre
New Data Completing the Spectrum of the Ma , RMia , and RMja Genes for Resistance to Root-Knot Nematodes ( Meloidogyne spp.) in Prunus
auteur
Henri Duval, Cyril van Ghelder, Ulysse Portier, Carole Confolent, Pablo Meza, Daniel Esmenjaud
article
Phytopathology, 2019, 109 (4), pp.615-622. ⟨10.1094/PHYTO-05-18-0173-R⟩
resume
Root-knot nematodes (RKN) (Meloidogyne spp.) are worldwide pests that affect a considerable number of plants, among which stone fruit (Prunus spp.) are severely attacked. Prevalent RKN species are Meloidogyne arenaria, M. incognita, and M. javanica in stone fruit but the emergent M. ethiopica and M. enterolobii are also reported to challenge perennial crops. In Prunus spp., the complete-spectrum resistance (R) gene Ma from plum and the more restricted-spectrum R genes RMia from peach and RMja from almond completely inhibit nematode multiplication and gall formation of the RKN species that they control. This study aimed to update the resistance spectra of these three major genes by evaluating their activity toward one isolate of the yet-untested RKN species mentioned above. To state whether a given gene controls a particular species, the principle of our experiment was to genotype with appropriate markers a number of individuals segregating for this gene and then to phenotype these individuals. A perfect matching of the genotype and the phenotype of individuals indicates that the gene of interest is active against and, thus, controls the corresponding isolate of this RKN species. Segregating materials used were an Ma F1 plum progeny, an RMia F2 peach progeny, and an RMja F2 almond progeny. In addition to previous data, our results establish a clear spectrum for each of the three genes toward isolates from both the three prevalent species and the two emerging species. Ultimately, our results reveal that (i) Ma controls all of them, (ii) RMja controls all species except M. incognita and M. floridensis, and (iii) RMia controls M. arenaria, M. incognita, and M. ethiopica but not M. javanica or M. enterolobii. Our data should have wide implications for RKN resistance management and breeding and for deciphering the molecular mechanisms of the spectrum of RKN R genes.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Efficient and transgene-free gene targeting using Agrobacterium-mediated delivery of the CRISPR/Cas9 system in tomato
auteur
Benoit Danilo, Laura Perrot, Kostlend Mara, Emmanuel Botton, Fabien Nogué, Marianne Mazier
article
Plant Cell Reports, 2019, 38 (4), pp.459-462. ⟨10.1007/s00299-019-02373-6⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Mimicking natural polymorphism in eIF4E by CRISPR-Cas9 base editing is associated with resistance to potyviruses
auteur
Anna Bastet, Delyan Zafirov, Nathalie Giovinazzo, Anouchka Guyon-Debast, Fabien Nogué, Christophe C. Robaglia, Jean-Luc Gallois
article
Plant Biotechnology Journal, 2019, 17 (9), pp.1-15. ⟨10.1111/pbi.13096⟩
resume
In many crop species, natural variation in eIF4E proteins confers resistance to potyviruses. Gene editing offers new opportunities to transfer genetic resistance to crops that seem to lack natural eIF4E alleles. However, because eIF4E are physiologically important proteins, any introduced modification for virus resistance must not bring adverse phenotype effects. In this study, we assessed the role of amino acid substitutions encoded by a Pisum sativum eIF4E virus-resistance allele (W69L, T80D S81D, S84A, G114R and N176K) by introducing them independently into the Arabidopsis thaliana eIF4E1 gene, a susceptibility factor to the Clover yellow vein virus (ClYVV). Results show that most mutations were sufficient to prevent ClYVV accumulation in plants without affecting plant growth. In addition, two of these engineered resistance alleles can be combined with a loss-of-function eIFiso4E to expand the resistance spectrum to other potyviruses. Finally, we use CRISPR-nCas9-cytidine deaminase technology to convert the Arabidopsis eIF4E1 susceptibility allele into a resistance allele by introducing the N176K mutation with a single-point mutation through C-to-G base editing to generate resistant plants. This study shows how combining knowledge on pathogen susceptibility factors with precise genome-editing technologies offers a feasible solution for engineering transgene-free genetic resistance in plants, even across species barriers.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://cea.hal.science/cea-02096102/file/Bastet_et_al-2019-Plant_Biotechnology_Journal.pdf BibTex
titre
Transgene-Free Genome Editing in Tomato and Potato Plants Using Agrobacterium-Mediated Delivery of a CRISPR/Cas9 Cytidine Base Editor
auteur
Florian Veillet, Laura Perrot, Laura Chauvin, Marie-Paule Kermarrec, Anouchka Guyon-Debast, Jean-Eric Chauvin, Fabien Nogué, Marianne Mazier
article
International Journal of Molecular Sciences, 2019, 20 (2), pp.402. ⟨10.3390/ijms20020402⟩
resume
Genome editing tools have rapidly been adopted by plant scientists for gene function discovery and crop improvement. The current technical challenge is to efficiently induce precise and predictable targeted point mutations valuable for crop breeding purposes. Cytidine base editors (CBEs) are CRISPR/Cas9 derived tools recently developed to direct a C-to-T base conversion. Stable genomic integration of CRISPR/Cas9 components through Agrobacterium-mediated transformation is the most widely used approach in dicotyledonous plants. However, elimination of foreign DNA may be difficult to achieve, especially in vegetatively propagated plants. In this study, we targeted the acetolactate synthase (ALS) gene in tomato and potato by a CBE using Agrobacterium-mediated transformation. We successfully and efficiently edited the targeted cytidine bases, leading to chlorsulfuron-resistant plants with precise base edition efficiency up to 71% in tomato. More importantly, we produced 12.9% and 10% edited but transgene-free plants in the first generation in tomato and potato, respectively. Such an approach is expected to decrease deleterious effects due to the random integration of transgene(s) into the host genome. Our successful approach opens up new perspectives for genome engineering by the co-edition of the ALS with other gene(s), leading to transgene-free plants harboring new traits of interest.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02628093/file/2019_Veillet_International%20Journal%20of%20Molecular%20Sciences_1.pdf BibTex
titre
Model-based QTL detection is sensitive to slight modifications in model formulation
auteur
Caterina Barrasso, Mohamed-Mahmoud Memah, Michel Génard, Bénédicte Quilot-Turion
article
PLoS ONE, 2019, 14 (10), pp.1-24. ⟨10.1371/journal.pone.0222764⟩
resume
Classical crop models have been developed to predict crop yield and quality, and they are based on physiological and environmental inputs. After molecular discoveries, models should integrate genetic variation to allow predictions that are more genotype-dependent. An interesting approach, Quantitative Trait Locus (QTL)-based ecophysiological modeling, has shown promising results for the design of ideotypes that are adapted to biotic and abiotic stresses, but there are still limitations to attaining a fully integrated model. The aim of this case study is to clarify the impact of choosing different model equations (closely related and with different numbers of parameters) and optimization methods on the detection of QTLs controlling the parameters of crop growth. Different growth equations were parameterized based on a genetic population by following different approaches. The correlations between parameters were analyzed, and two different strategies were adopted to address the correlation issue. QTL analysis was performed on the optimized values of the parameters of the growth equations and on the observed dry mass (DM) data to validate the QTLs detected. Overall, models and strategies resulted in different QTLs being detected. Similar LOD profiles but with peaks of different heights were observed, some of which were significant, resulting in different numbers of QTLs. In some cases, peaks had slightly different positions or were absent. Even closely related growth models led to the detection of different QTLs. The goodness of fit and complexity of the growth models were found to be insufficient to select the best model. Calculating parameters independently of observed data may not be a good strategy, whereas setting parameters independent of the genotype is recommended. Given the large-scale global optimization problem and the strong correlations between parameters, the two algorithms tested showed poor performance. Currently, the lack of effective algorithms is the main obstacle to answering the question posed. The authors therefore suggest testing different model formulations and comparing the QTLs detected before choosing the best formulation to use in an ecophysiological modeling approach based on QTLs.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02619010/file/2019_Barrasso_Plos%20One_1.pdf BibTex
titre
Resistance against melon chlorotic mosaic virus and tomato leaf curl New Delhi virus in melon
auteur
Gustavo Romay, Michel Pitrat, Hervé Lecoq, Catherine Wipf-Scheibel, Pauline Millot, Gregory Girardot, Cecile Desbiez
article
Plant Disease, 2019, 103 (11), pp.2913-2919. ⟨10.1094/PDIS-02-19-0298-RE⟩
resume
Thirty-one melon accessions were screened for resistance to the begomoviruses melon Melon chlorotic mosaic virus (MeCMV) and tomato Tomato leaf curl New Delhi virus (ToLCNDV). Five accessions presented nearly complete resistance to both viruses. Accession IC-274014, showing the highest level of resistance to both viruses, was crossed with the susceptible cultivar ‘Védrantais’. The F1, F2, F3/F4 and both back-cross progenies were mechanically inoculated with MeCMV. Plants without symptoms nor virus detection by ELISA and/or PCR were considered as resistant. The segregations were compatible with two recessive and one dominant independent genes simultaneously required for resistance. Inheritance of resistance to ToLCNDV in the F2 was best explained by one recessive gene and two independent dominant genes simultaneously required. Some F3 and F4 families selected for resistance to MeCMV were also resistant to ToLCNDV, suggesting that common or tightly linked genes were involved in resistance to both viruses. We propose the names begomovirus resistance-1 and Begomovirus resistance-2 for these genes (symbols bgm-1 and Bgm-2). Resistance to MeCMV in IC-274014 was controlled by bgm-1, Bgm-2 and the recessive gene melon chlorotic mosaic virus resistance (mecmv); resistance to ToLCNDV was controlled by bgm-1, Bgm-2 and the dominant gene Tomato leaf curl New Delhi virus resistance (Tolcndv).
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02619468/file/2019_Romay_PlantDis_postprint_1.pdf BibTex
titre
Genetic analysis of resistance to bacterial leaf spot in the heirloom lettuce cultivar Reine des Glaces
auteur
Germán V. Sandoya, Brigitte Maisonneuve, Maria Jose Truco, Carolee T. Bull, Ivan Simko, Mark Trent, Ryan J. Hayes, Richard W. Michelmore
article
Molecular Breeding, 2019, 39 (12), ⟨10.1007/s11032-019-1072-6⟩
resume
Bacterial leaf spot (BLS) is a disease that affects lettuce (Lactuca sativa L.) worldwide. The disease is caused by the bacterium Xanthomonas campestris pathovar vitians (Xcv), which exclusively infects lettuce and is particularly devastating in warm humid climates. Reine des Glaces (RG), an old Batavia-type cultivar, exhibited an uninvestigated partial resistance to Xcv. Quantitative trait loci (QTLs) were analyzed using two recombinant inbred line (RIL) populations derived from RG × Eruption and RG × Delsay using three isolates collected in California and Canada, each representing a different race, and an isolate collected in France. A major QTL was identified in linkage group 2 in both populations; additional, minor QTLs were also detected in other linkage groups. The major QTL collocates with the Xanthomonas resistance 1 (Xar1) and Xanthomonas campestris vitians resistance (Xcvr) genes that had previously been identified using RIL populations derived from Salinas 88 × La Brillante and PI 358001-1 × Tall Guzmaine. RG provides another resistance resource for combating BLS using data provided by this study for marker-assisted selection.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Association of the phenylpropanoid pathway with dormancy and adaptive trait variation in apricot (Prunus armeniaca).
auteur
Anna O Conrad, Jiali Yu, Margaret E Staton, Jean Marc Audergon, Guillaume Roch, Véronique Decroocq, Kevin Knagge, Huadong Chen, Tatyana Zhebentyayeva, Zongrang Liu, Christopher Dardick, C Dana Nelson, Albert G Abbott
article
Tree Physiology, 2019, 39, pp.1136-1148. ⟨10.1093/treephys/tpz053⟩
resume
Trees use many mechanisms to adapt and respond to stressful conditions. The phenylpropanoid pathway in particular is known to be associated with a diverse suite of plant stress responses. In this study, we explored the relationship between the phenylpropanoid pathway metabolite production, gene expression, and adaptive trait variation associated with floral bud reactivation during and following dormancy in Prunus armeniaca L. (apricot). Concentrations of eight phenylpropanoid metabolites were measured during chill accumulation and at developmental stages corresponding to the emergence of sepals and petals in floral buds of varieties that differ phenotypically in bloom date (BD). A significant interaction effect of chill hours and BD phenotype on the concentration of each of the compounds was observed (mixed ANOVA, P < 0.05), with the concentration of most phenylpropanoid metabolites dropping precipitously when sepals and petals emerged. While phenylpropanoid biosynthetic gene expression patterns were more variable in general, expression changed over time and was impacted, although to a lesser degree, by BD phenotype. Furthermore, separation of BD phenotypic groups was most pronounced when early and late BD varieties were at different developmental stages, i.e., 800 chill hours. Taken together, these results suggest that the phenylpropanoid pathway is associated with floral bud reactivation in apricot. Furthermore, we show that the phenylpropanoid pathway is also impacted by phenological trait variation associated with dormancy. A better understanding of how apricot and other perennial tree species respond and adapt to environmental perturbations will be critical for improvement programs aimed at identifying and breeding trees more suitable for rapidly changing environments.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics
auteur
Alexandros Tsakogiannis, Tereza Manousaki, Jacques Lagnel, Nikolaos Papanikolaou, Nikos Papandroulakis, Constantinos C. Mylonas, Costas S. Tsigenopoulos
article
Frontiers in Genetics, 2019, 9, ⟨10.3389/fgene.2018.00749⟩
resume
Sex-biased gene expression is the mode through which sex dimorphism arises from a nearly identical genome, especially in organisms without genetic sex determination. Teleost fishes show great variations in the way the sex phenotype forms. Among them, Sparidae, that might be considered as a model family displays a remarkable diversity of reproductive modes. In this study, we sequenced and analyzed the sex-biased transcriptome in gonads and brain (the tissues with the most profound role in sexual development and reproduction) of two sparids with different reproductive modes: the gonochoristic common dentex, Dentex dentex, and the protandrous hermaphrodite gilthead seabream, Sparus aurata. Through comparative analysis with other protogynous and rudimentary protandrous sparid transcriptomes already available, we put forward common male and female-specific genes and pathways that are probably implicated in sex-maintenance in this fish family. Our results contribute to the understanding of the complex processes behind the establishment of the functional sex, especially in hermaphrodite species and set the groundwork for future experiments by providing a gene toolkit that can improve efforts to control phenotypic sex in finfish in the ever-increasingly important field of aquaculture.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02620563/file/2019_Tsakogiannis_Front%20Gene_1.pdf BibTex
titre
Increasing Ascorbic Acid Content and Salinity Tolerance of Cherry Tomato Plants by Suppressed Expression of the Ascorbate Oxidase Gene
auteur
Karima F. Abdelgawad, Mohamed M. El-Mogy, Mohamed I. A. Mohamed, Cecile Garchery, Rebecca Stevens
article
Agronomy, 2019, 9 (2), pp.51. ⟨10.3390/agronomy9020051⟩
resume
Ascorbic acid is considered to be one of the most important antioxidants in plants and plays a vital role in the adaptation of plants to unfavorable conditions. In the present study, an ascorbate oxidase gene (Solyc04g054690) was over-expressed in cherry tomato cv. West Virginia 106 lines and compared with previously studied RNAi silenced ascorbate oxidase lines. Two lines with lower ascorbate oxidase activity (AO−15 and AO−42), two lines with elevated activity (AO+14 and AO+16), and the non-transgenic line (WVa106) were grown and irrigated with 75 mM and 150 mM NaCl in 2015 and 2016. Growth, yield, and chemical composition of the lines under salinity stress were evaluated. Lines with lower ascorbate oxidase activity resulted in higher plant growth parameters (plant height, leaf number, flower, and cluster number in 2015 and stem diameter and flower number in 2016), and improved fruit quality (firmness in 2016 and soluble solid content in 2015) and total yield per plant under salinity stress over both years. In addition, we show that ascorbic acid, lycopene, and carotene contents of fruits were higher in lines with lower ascorbate oxidase activity compared to lines with elevated activity and the non-transgenic line under conditions of moderate and high salinity in both years.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02620117/file/abdelgawad-agronomy-2019_1.pdf BibTex
titre
Get the Balance Right: ROS Homeostasis and Redox Signalling in Fruit
auteur
Guillaume Decros, Pierre Baldet, Bertrand Beauvoit, Rebecca Stevens, Amélie Flandin, Sophie Colombie, Yves Gibon, Pierre Pétriacq
article
Frontiers in Plant Science, 2019, 10, pp.1-16. ⟨10.3389/fpls.2019.01091⟩
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02619141/file/2019-Decros-Frontiers_in_Plant_Science_1.pdf BibTex
titre
Genetic analysis of cadmium accumulation in lettuce (Lactuca sativa)
auteur
Walid Zorrig, Jean-Yves Cornu, Brigitte Maisonneuve, Aida Rouached, Catherine Sarrobert, Zaigham Shahzad, Chedly Abdelly, Jean-Claude Davidian, Pierre Berthomieu
article
Plant Physiology and Biochemistry, 2019, 136, pp.67-75. ⟨10.1016/j.plaphy.2019.01.011⟩
resume
This work characterized mechanisms controlling cadmium (Cd) tolerance and accumulation in lettuce at both the physiological and genetic levels. These traits were evaluated in 18 Lactuca accessions representing a large genetic diversity. Cd tolerance and accumulation in roots and shoots as well as Cd translocation from roots to the shoot varied independently, and with a significant range of variation. Analyses of F1 progenies of crosses between cultivars with contrasted phenotypes showed that high tolerance to Cd, low Cd accumulation and low Cd root-shoot translocation were recessive traits. Results of analyses of F2 progenies of different crosses suggest that root Cd concentration and root-shoot Cd translocation were under a complex genetic determinism involving at least two loci. This work thus revealed that limiting both Cd accumulation and Cd root-shoot translocation in lettuce is possible and depends on recessive loci. Differences in the ability to accumulate Cd in roots in the long term could not be linked to differences in short-term 109Cd uptake into, or efflux from, roots. In contrast, the cultivar with the highest root-shoot Cd translocation was the same in the long term and in the short term, which suggests that this trait relies on processes that are implemented quickly (i.e. in less than three days) after the start of Cd exposure.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Root Architectural Trait Diversity in Aubergine (Solanum melongena L.) and Related Species and Correlations with Plant Biomass
auteur
Jérémy Salinier, Marie-Christine Daunay, Victor Talmot, Christophe Lecarpentier, Loïc Pagès, Amelie Bardel, Christine Fournier, Marie Torres, Rebecca Stevens
article
Genetics, Genomics and Breeding of Crop Plants, 2019, 1, 23 p. ⟨10.20900/cbgg20190011⟩
resume
Background: We investigated root architecture and plant biomass traits of 25 aubergine genepool accessions representative of 9 Solanum L. species, including S. melongena L., grown at two sites in South-East France in order to quantify the diversity of root phenotypes, identify correlations between traits and determine the influence of the environment on trait stability. Method: Aubergine seeds were sown in a mixture of sieved compost and vermiculite in 1m high PVC tubes of 10 cm diameter. Roots and aerial parts were harvested after 4–5 weeks growth. Measured root traits included: root depth and root growth rate, maximum apical diameter, minimum apical diameter, the ratio of daughter to mother root apical diameter, and root inter-lateral distance. Results: • Root maximum diameter and inter-lateral distance showed the largest phenotypic variability between the accessions of S. melongena as well as between the 9 Solanum species. • Most traits were significantly affected by the experimental site except root maximum diameter and shoot dry weight accumulation per day. For most traits there was an interaction between the genotype and the site. • Maximum root diameter and the ratio of daughter to mother root diameter are not correlated with other traits whereas root inter-lateral distance correlates with several traits including root fresh weight. Conclusions: Root architectural traits show diversity within S. melongena and between S. melongena and related species. We confirm that root maximum diameter one of the traits with the highest heritability, i.e., depends on the genotype and is stable in different environments and that root inter-lateral distance is a plastic trait affected by the environment. The study gives some indications on accessions that could be chosen as rootstocks.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02619315/file/CBGG2019-salinier-stevens_1.pdf BibTex
titre
Design and assessment of innovative Mediterranean vegetable cropping systems to manage root-knot nematodes Description of the subject.
auteur
Caroline Caporalino, Mireille Navarrete, Ariane Fazari, Marc Baily-Bechet, Nathalie Marteu, Arnaud Dufils, Marc Tchamitchian, Amélie Lefevre, Laure Pares, Thierry Mateille, Johannes Tavoillot, Alain Palloix, Anne-Marie Sage-Palloix, Hélène Védie, Claire Goillon, Philippe Castagnone-Sereno
article
Biotechnologie, Agronomie, Société et Environnement / Biotechnology, Agronomy, Society and Environment, 2019, 23 (1), pp.7-21. ⟨10.25518/1780-4507.17725⟩
resume
Design and assessment of innovative Mediterranean vegetable cropping systems to manage root-knot nematodes Description of the subject. A system approach based on co-design and experimental field evaluation of cropping systems (CSs), combining technical and varietal innovations, has been implemented for sustainable management of root-knot nematodes (RKN) in Mediterranean sheltered vegetable systems.Objectives. Cropping systems combining genetic resistance and cultural practices (crop rotations including susceptible, resistant, and non-host plants; intercropping management with nematicidal cover crops or soil solarization) were assessed over a period of 4 years (i) to reduce RKN populations and increase the durability of varietal resistances, (ii) to study the impact of these systems on soil ecology (plant-parasitic and free-living nematode communities), and (iii) to evaluate their acceptability by farmers.Method. Three CS prototypes, resulting from a co-design process with research and development stakeholders, were compared with CSs conventionally implemented in the Mediterranean region. The three prototypes were also evaluated using complementary methods: (i) system experiments in three commercial farms in Southern France; (ii) analytical experiments to decipher the mechanisms of action for some [agroecological??] levers; (iii) surveys to evaluate the acceptability of the prototypes by farmers.Results. All three CSs were found to be effective (90% RKN decrease, protection of partially resistant Solanaceae, no negative effect on non-phytoparasitic nematodes) and sustainable, when application conditions and soil biological equilibrium were favorable (global soil nematofauna diversified and abundant). The acceptability of the three systems depended on the type of farm where they were implemented and the attitude of the farmers towards innovation.Conclusions. These three CSs still need to be improved, in terms of their efficiency, in consultation with participating farmers, by introducing new agroecological levers, as well as innovation costs. Future research will also need to open up to a more comprehensive management of soil health.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02628239/file/djian.%20biotechnology_Agron_Soc_Environ2019_1.pdf BibTex
titre
Inheritance of Resistance to Cucurbit Powdery Mildew in Bitter Gourd
auteur
Narinder P.S. Dhillon, Supannika Sanguansil, Supornpun Srimat, Suwannee Laenoi, Roland Schafleitner, Michel Pitrat, James D. Mccreight
article
HortScience, 2019, 54 (6), pp.1013-1016. ⟨10.21273/HORTSCI13906-19⟩
resume
Cucurbit powdery mildew (CPM) caused by Podosphaera xanthii (Px) is an economically important disease of bitter gourd (BG; Momordica charantia) in Asia. High-level resistance to CPM is known in various BG accessions that have been used to develop BG breeding lines that originated in different countries. BG breeding lines THMC 113 (Belize), THMC 143 (India), THMC 153 (Thailand), THMC 167 (India), and THMC 170 (Taiwan) possess high-level resistance to BG Px race (BG-CPM), designated Mc-1 from a field at Kamphaeng Saen, Thailand, whereas THMC 144 (India) is susceptible. Our objective was to determine the inheritance of resistance to BG-CPM race Mc-1. To that end, THMC 144 (India) was crossed with the five resistant lines. The parents and their respective F1, F2, backcross progenies were evaluated for BG-CPM disease severity in inoculated field and growth chamber tests. Resistance to BG-CPM race Mc-1 in the five resistant lines was controlled by at least two independent, recessive genes. Intercrosses of the BG-CPM–resistant lines revealed allelic resistances in four of the breeding lines: THMC 113, THMC 153, THMC 167, and THMC 170. Resistance in THMC 143 was clearly non-allelic for resistance to BG-CPM with the other four BG-CPM–resistant lines.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Gone with the wind: Aerial dispersal of Parthenolecanium corni crawlers in a newly planted grapevine plot
auteur
Gerard Hommay, Louis Wiss, Joel Chadoeuf, Jean Le Maguet, Monique Beuve, Etienne Herrbach
article
Annals of Applied Biology, 2019, 174 (3), pp.372-387. ⟨10.1111/aab.12505⟩
resume
Soft scales nymphs are suspected to propagate grapevine leafroll viruses in the vineyard, while moving from vine to vine, but results of long distance dispersion, especially those due to wind, are poorly known. Thus, a net of sticky cylindrical traps was placed in a newly planted grapevine plot to evaluate aerial dispersal of Parthenolecanium corni (Hemiptera Coccidae) nymphs. The plot was surrounded by vine plots infested by this species. Number of crawlers collected on traps was generally higher on the trap side exposed downwind and depended on population density of neighbouring vines. Coloured glitters of size and weight similar to that of crawlers were used to simulate wind transport. The highest number of glitters was trapped at the prevailing wind sector. A majority of glitters was found on traps close to dispersion cups, and the most remote were collected up to 165 m away from glitter source. Wind dispersal of crawlers was confirmed by colonisation of the new vine plot by P. corni, 2 years after plantation. The settling of P. corni on the young plot displayed no significant structure, as expected from a wind dispersal. Although grapevine leafroll viruses and Grapevine virus A were detected by reverse transcription‐polymerase chain reaction in several batches of trapped nymphs, these viruses were not found in vines colonised by P. corni in the new plot within the 4 years following plantation.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor.
auteur
Jiantao Zhao, Christopher Sauvage, Jinghua Zhao, Frederique Bitton, Guillaume Bauchet, Dan Liu, Sanwen Huang, Denise M Tieman, Harry J Klee, Mathilde Causse
article
Nature Communications, 2019, 10 (1), pp.1534. ⟨10.1038/s41467-019-09462-w⟩
resume
Tomato flavor has changed over the course of long-term domestication and intensive breeding. To understand the genetic control of flavor, we report the meta-analysis of genome-wide association studies (GWAS) using 775 tomato accessions and 2,316,117 SNPs from three GWAS panels. We discover 305 significant associations for the contents of sugars, acids, amino acids, and flavor-related volatiles. We demonstrate that fruit citrate and malate contents have been impacted by selection during domestication and improvement, while sugar content has undergone less stringent selection. We suggest that it may be possible to significantly increase volatiles that positively contribute to consumer preferences while reducing unpleasant volatiles, by selection of the relevant allele combinations. Our results provide genetic insights into the influence of human selection on tomato flavor and demonstrate the benefits obtained from meta-analysis.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02628913/file/zhao-nature_communication-2019_1.pdf BibTex
titre
La laitue : Une large diversité enrichie par des espèces sauvages européennes
auteur
Brigitte Maisonneuve
article
Jardins de France, 2019, 654, pp.54-59
resume
Quoi de plus banal, dans nos assiettes, que quelques feuilles de salade ? La laitue, sa représentante la plus remarquable, est connue depuis l’Antiquité. Originaire d’Asie centrale, elle est aujourd’hui encore le légume-feuille le plus consommé en France. Derrière cette simplicité apparente se cachent cependant un genre riche, une culture complexe, des agents pathogènes et des ravageurs féroces. Vous en reprendrez bien quelques bonnes feuilles ?
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Efficient and transgene-free gene targeting using Agrobacterium-mediated delivery of the CRISPR/Cas9 system in tomato
auteur
Benoît Danilo, Laura Perrot, Kostlend Mara, Emmanuel Botton, Fabien Nogué, Marianne Mazier
article
Plant Cell Reports, 2019, 38 (4), pp.459-462. ⟨10.1007/s00299-019-02373-6⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis
auteur
Elisavet Kaitetzidou, Ioanna Katsiadaki, Jacques Lagnel, Efthimia Antonopoulou, Elena Sarropoulou
article
Scientific Reports, 2019, 9, ⟨10.1038/s41598-019-40127-2⟩
resume
Development requires the implementation of a plethora of molecular mechanisms, involving a large set of genes to ensure proper cell differentiation, morphogenesis of tissues and organs as well as the growth of the organism. Genome duplication and resulting paralogs are considered to provide the raw genetic materials important for new adaptation opportunities and boosting evolutionary innovation. The present study investigated paralogous genes, involved in three-spined stickleback (Gasterosteus aculeatus) development. Therefore, the transcriptomes of five early stages comprising developmental leaps were explored. Obtained expression profiles reflected the embryo's needs at different stages. Early stages, such as the morula stage comprised transcripts mainly involved in energy requirements while later stages were mostly associated with GO terms relevant to organ development and morphogenesis. The generated transcriptome profiles were further explored for differential expression of known and new paralogous genes. Special attention was given to hox genes, with hoxa13a being of particular interest and to pigmentation genes where itgb1, involved in the melanophore development, displayed a complementary expression pattern throughout studied stages. Knowledge obtained by untangling specific paralogous gene functions during development might not only significantly contribute to the understanding of teleost ontogenesis but might also shed light on paralogous gene evolution.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02627533/file/Kaitetzidou-scientific-reports2019_1.pdf BibTex
titre
Trait discovery and editing in tomato.
auteur
Christophe Rothan, Isidore Diouf, Mathilde Causse
article
The Plant Journal, 2019, 97 (1), pp.73-90. ⟨10.1111/tpj.14152⟩
resume
Tomato (Lycopersicum esculentum), which is used for both processing and fresh markets, is a major crop species that is ranked the first vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistances. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses and fruit sensorial and nutritional quality. New traits including resistance to various biotic and abiotic stresses and root architecture are increasingly being studied. Several major mutations and QTLs underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In the recent years, CRISPR/Cas9 gene editing already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement and precise base editing. Here, we give insights into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Further, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato. This article is protected by copyright. All rights reserved.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Limitation de l’usage des pesticides sur des cultures de laitue d’abri : bilan du projet DEPHY EXPE LILLA.
auteur
François Lecompte, Claire Goillon, Benjamin Gard, Christiane Raynal, Elise Vaud, Virginie Barrière, Brigitte Maisonneuve, Damien Rousselière, Justine Garnodier, Philippe C. Nicot
article
Innovations Agronomiques, 2019, 76, pp.35-50. ⟨10.15454/c1v2ph⟩
resume
Preventive chemical control is still today the main mean of managing pests in winter lettuce under shelter. Alternative strategies have been explored in the LILLA project, either to provide needed experimental results on non-chemical plant protection techniques, or to test cropping systems based on integrated protection strategies that reduce the use of pesticides. Innovative pest management levers, including increased genetic resistance to basal rots, or the use of drip instead of sprinkler-irrigation. Considering a set of 23 comparative crop management trials, halving the number of fungicide treatments in combination with alternative techniques does not show a statistical increase in the risk of crop failure. The biological control strategies tested against aphids remain to be improved. The cost of implementing alternative techniques is significant but remains moderate in most cases. The most effective of these techniques could be more easily implemented by farmers if uncertainties about crop income were lower.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02154669/file/2019_Lecompte_Innov-Agron.pdf BibTex
titre
Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker
auteur
Mariem Omrani, Morgane Roth, Guillaume Roch, Alain Blanc, Cindy E. Morris, Jean Marc Audergon
article
BMC Plant Biology, 2019, 19, pp.31. ⟨10.1186/s12870-019-1631-3⟩
resume
Background: Diseases caused by Pseudomonas syringae (Ps) are recognized as the most damaging factors in fruit trees with a significant economic and sanitary impact on crops. Among them, bacterial canker of apricot is exceedingly difficult to control due to a lack of efficient prophylactic measures. Several sources of partial resistance have been identified among genetic resources but the underlying genetic pattern has not been elucidated thus far. In this study, we phenotyped bacterial canker susceptibility in an apricot core-collection of 73 accessions over 4 years by measuring canker and superficial browning lengths issued from artificial inoculations in the orchard. In order to investigate the genetic architecture of partial resistance, we performed a genome-wide association study using best linear unbiased predictors on genetic (G) and genetic x year (G × Y) interaction effects extracted from linear mixed models. Using a set of 63,236 single-nucleotide polymorphism markers genotyped in the germplasm over the whole genome, multi-locus and multi-variate mixed models aimed at mapping the resistance while controlling for relatedness between individuals. Results: We detected 11 significant associations over 7 candidate loci linked to disease resistance under the two most severe years. Colocalizations between G and G × Y terms indicated a modulation on allelic effect depending on environmental conditions. Among the candidate loci, two loci on chromosomes 5 and 6 had a high impact on both canker length and superficial browning, explaining 41 and 26% of the total phenotypic variance, respectively. We found unexpected long-range linkage disequilibrium (LD) between these two markers revealing an inter-chromosomal LD block linking the two underlying genes. This result supports the hypothesis of a co-adaptation effect due to selection through population demography. Candidate genes annotations suggest a functional pathway involving abscisic acid, a hormone mainly known for mediating abiotic stress responses but also reported as a potential factor in plant-pathogen interactions. Conclusions: Our study contributed to the first detailed characterization of the genetic determinants of partial resistance to bacterial canker in a Rosaceae species. It provided tools for fruit tree breeding by identifying progenitors with favorable haplotypes and by providing major-effect markers for a marker-assisted selection strategy.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02621426/file/2019_Omrani_BMC%20Plant%20Biol_1.pdf BibTex

2018

Journal articles

titre
Impact of genetic drift, selection and accumulation level on virus adaptation to its host plants
auteur
Elsa Rousseau, Lucie Tamisier, Frédéric Fabre, Vincent Simon, Marion Szadkowski, Olivier Bouchez, Catherine Zanchetta, Gregory Girardot, Ludovic Mailleret, Frédéric Grognard, Alain Palloix, Benoît Moury
article
Molecular Plant Pathology, 2018, 19 (12), pp.2575-2589. ⟨10.1111/mpp.12730⟩
resume
The efficiency of plant major resistance genes is limited by the emergence and spread of resistance‐breaking mutants. Modulating the evolutionary forces acting on pathogen populations constitutes a promising way to increase the durability of these genes. We studied the effect of four plant traits affecting these evolutionary forces on the rate of resistance breakdown (RB) by a virus. Two of those traits correspond to virus effective population sizes (Ne), either at plant inoculation or during infection. The third trait corresponds to differential selection exerted by the plant on the virus population. Finally, the fourth trait corresponds to within‐plant virus accumulation (VA). These traits were measured experimentally on Potato virus Y (PVY) and a set of 84 pepper doubled‐haploid lines, all carrying the same pvr23 resistance gene but having contrasted genetic backgrounds. The lines showed extensive variation for the rate of pvr23 RB by PVY and for the four other traits of interest. A generalized linear model showed that three of these four traits, with the exception of Ne at inoculation, and several of pairwise interactions between them had significant effects on RB. RB increased when Ne during plant infection or VA increased. The effect of differential selection was more complex because of a strong interaction with VA. When VA was high, RB increased as the differential selection increased. An opposite relationship between RB and differential selection was observed when VA was low. This study provides a framework to select plants with appropriate virus‐evolution‐related traits to avoid or delay resistance breakdown.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://inria.hal.science/hal-01953902/file/Rousseau-MPP.pdf BibTex
titre
Interaction between a threatened endemic plant (Anchusa crispa) and the invasive Argentine ant (Linepithema humile)
auteur
Olivier Blight, Jérôme Orgeas, Aline Le Menn, Angélique Quilichini, Erick Provost
article
Arthropod-Plant Interactions, 2018, 12 (5), pp.725 - 731. ⟨10.1007/s11829-018-9619-8⟩
typdoc
Journal articles
Accès au texte intégral et bibtex
https://univ-avignon.hal.science/hal-01927139/file/Blight_et_al_Seed_dispersal_Lhumile_Acrispa_PREPRINT.pdf BibTex
titre
Characterization of the RMja resistance gene to root-knot nematodes from the ‘Alnem’ almond rootstock
auteur
Henri Duval, Cyril van Ghelder, Caroline Callot, Daniel Esmenjaud
article
Acta Horticulturae, 2018, 1219, pp.325-330. ⟨10.17660/ActaHortic.2018.1219.49⟩
resume
In Prunus spp., resistance (R) genes to RKNs with different spectra have been identified and mapped in plum (Ma), peach (RMia) and almond (RMja). The two genes Ma and RMia have been identified and located on the Linkage groups 7 and 2. In order to identify the RMja gene of the ‘Alnem’ rootstock released by Kochba and Spiegel-Roy (1976), we have created a population “‘Lauranne’ × ‘Alnem’” (LA) and we have done a fine mapping study on this “LA” population. Hybrids were tested in greenhouse for their resistance to Meloidogyne javanica and we could map the RMja resistance gene on the LG7 (linkage group) region between the two SSR markers CPPCT039 and CPPCT022. In a second step, the genome of the two parents ‘Lauranne’ and ‘Alnem’ were assembled by NGS sequencing and mapping on the V2 reference peach genome. We observed that the peach gene Prupe.7G065400 in this located RMja region was well aligned in ‘Alnem’ with a similar TNL gene which could be the RMja gene. We constructed an ‘Alnem’ BAC library in order to obtain the whole sequence of the RMja DNA region using PacBio technology and to validate if the candidate gene of RMja is really the orthologue of Prupe.7G065400. Finally, for using MAS (marker assisted selection) to screen this candidate RMja gene, we designed two Kasp® markers from a specific SNP between the resistant parent ‘Alnem’ and other susceptible almond cultivars.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Explore the best sugar factory: the fruit
auteur
Elsa Desnoues, Michel Génard, Bénédicte Quilot-Turion, Valentina Baldazzi
article
TheScienceBreaker, 2018, ⟨10.25250/thescbr.brk124⟩
resume
The taste of a fruit is largely determined by its sugar composition. Understanding the mechanisms responsible for the accumulation of different sugars will enable us to select fruits to increase their consumption. A model of sugar metabolism allowed the identification of a candidate mechanism to explain the difference in sugar composition observed in commercial and wild peach fruits.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://inria.hal.science/hal-01953091/file/Desnoues_TheScienceBreaker18.pdf BibTex
titre
Arthropods life cycle and temperature: beyond isomorphy hypothesis
auteur
Olivier Bonato, Joel Chadoeuf
article
Journal of Thermal Biology, 2018, 75, pp.1-6. ⟨10.1016/j.jtherbio.2018.05.004⟩
resume
In poikilotherms, developmental time and adult lifespan are biological traits driven by temperature although their underlying physiological mechanisms differ. The developmental theory of ageing predicts a positive correlation between these two traits without confirming a genetic or causal relationship. The developmental rate isomorphy hypothesis established that the proportionality in the duration of each pre-imaginal stage with respect to total developmental time does not vary with temperature. This may have important evolutionary implications. We conducted an analysis with arthropods of agronomic interest to study if the hypothesis could be extended to the total lifespan of poikilotherms, including adult lifespan. We showed that isomorphy could be acceptable for a global description of this relationship. However a general model of power law type is more appropriate for characterizing the relationship between developmental time and adult lifespan. In this model, the shape of the curve is a constant characteristic, but the parameters that control it depend on the functional type of the arthropod (phytophagous, predator or parasitoid). Presumably this power law could be extended to all arthropods of agricultural interest, and more generally to all arthropod.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02621643/file/bonato-arthropods-biology-2018_1.pdf BibTex
titre
A kinetic model of sugar metabolism in peach fruit reveals a functional hypothesis of markedly low fructose-to-glucose ratio phenotype
auteur
Elsa Desnoues, Michel Génard, Bénédicte Quilot-Turion, Valentina Baldazzi
article
The Plant Journal, 2018, 94 (4), pp.685-698. ⟨10.1111/tpj.13890⟩
resume
The concentrations of sugars in fruit vary with fruit development, environment, and genotype. In general, there were weak correlations between the variations in sugar concentrations and the activities of enzymes directly related with the synthesis or degradation of sugars. This finding suggests that the relationships between enzyme activities and metabolites are often non-linear and are difficult to assess. To simulate the concentrations of sucrose, glucose, fructose and sorbitol during the development of peach fruits, a kinetic model of sugar metabolism was developed by taking advantage of recent profiling data. Cell compartmentation (cytosol and vacuole) was described explicitly, and data-driven enzyme activities were used to parameterize equations. The model correctly accounts for both annual and genotypic variations, which were observed in ten genotypes derived from an interspecific cross. They provided important information on mechanisms underlying the specification of phenotypic differences. In particular, the model supports the hypothesis that a difference in fructokinase affinity could be responsible for a low fructose-to-glucose ratio phenotype, which was observed in the studied population.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://inria.hal.science/hal-01953042/file/Desnoues_et_al_ThePlantJournal_HAL.pdf BibTex
titre
Macro and Micronutrient Storage in Plants and Their Remobilization When Facing Scarcity: The Case of Drought
auteur
Philippe Etienne, Sylvain Diquelou, Marion Prudent, Christophe Salon, Anne Maillard, Alain A. Ourry
article
Agriculture, 2018, 8 (1), pp.14. ⟨10.3390/agriculture8010014⟩
resume
Human mineral malnutrition or hidden hunger is considered a global challenge, affecting a large proportion of the world's population. The reduction in the mineral content of edible plant products is frequently found in cultivars bred for higher yields, and is probably increased by intensive agricultural practices. The filling of grain with macro and micronutrients is partly the result of a direct allocation from root uptake and remobilization from vegetative tissues. The aim of this bibliographic review is to focus on recent knowledge obtained from ionomic analysis of plant tissues in order to build a global appraisal of the potential remobilization of all macro and micronutrients, and especially those from leaves. Nitrogen is always remobilized from leaves of all plant species, although with different efficiencies, while nutrients such as K, S, P, Mg, Cu, Mo, Fe and Zn can be mobilized to a certain extent when plants are facing deficiencies. On the opposite, there is few evidence for leaf mobilization of Ca, Mn, Ni and B. Mechanisms related to the remobilization process (remobilization of mineral forms from vacuolar and organic compounds associated with senescence, respectively) are also discussed in the context of drought, an abiotic stress that is thought to increase and known to modulate the ionic composition of grain in crops.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://normandie-univ.hal.science/hal-02183699/file/ETIENNE%202018-33_1.pdf BibTex
titre
Irrigation with salt water affects growth, yield, fruit quality, storability and marker-gene expression in cherry tomato
auteur
Mohamed Zaki Elmogy, Cecile Garchery, Rebecca Stevens
article
Acta Agriculturae Scandinavica, Section B - Soil and Plant Science, 2018, 68 (8), pp.727 - 737. ⟨10.1080/09064710.2018.1473482⟩
resume
The use of saline water for plant production will become increasingly necessary over future decades. In some cases, fruit quality such as in tomato, can be improved by irrigation with saline water. The influence of different salt concentrations on physiological responses and the expression of some selected genes of cherry tomato (Solanum lycopersicum L), cv. West Virginia 106, was examined. Tomato plants were grown in peatmoss substrate and irrigated with 0, 25, 50, 75, 100 or 150 mM sodium chloride (NaCl) in a glasshouse. The NaCl treatments of 75, 100 and 150 mM salt resulted in shorter plants, decreased stem width, a lower plant dry weight, fewer flowers, and smaller leaf area, while yield was reduced by treatment with concentrations of 50 mM NaCl and above. Average fruit weight and fruit number were also negatively affected by treatment with 50 mM salt and above. Salinity treatment led to increased fruit total soluble solids, titratable acidity and firmness and improved the taste index. Salt-responsive marker genes identified in Moneymaker were also induced in cherry tomato but not at the highest salt concentrations. Our results indicated that cherry tomato treated with 25 mM NaCl produced fruit with improved quality in comparison with non-salinized control plants without compromising yield, while at 50 and 75 mM the improved fruit quality was accompanied by a reduction in yield.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato
auteur
Elise Albert, Renaud Duboscq, Muriel Latreille, Sylvain Santoni, Matthieu Beukers, Jean-Paul Bouchet, Frederique Bitton, Justine Gricourt, Charles Poncet, Véronique Gautier, José Jimenez-Gomez, Guillem Rigaill, Mathilde Causse
article
The Plant Journal, 2018, 96 (3), pp.635-650. ⟨10.1111/tpj.14057⟩
resume
Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype by environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome-wide scale. We sequenced the transcriptome of growing leaves and fruit pericarps at cell expansion stage in a cherry and a large fruited accession and their F1 hybrid grown under two watering regimes. Gene expression levels were steadily affected by the genotype and the watering regime. Whereas phenotypes showed mostly additive inheritance, ~80% of the genes displayed non-additive inheritance. By comparing allele specific expression in the F1 hybrid to the allelic expression in both parental lines, respectively, 3,005 genes in leaf and 2,857 genes in fruit deviated from 1:1 ratio independently of the watering regime. Among these genes, ~55% were controlled by cis factors, ~25% by trans factors and ~20% by a combination of both types. A total of 328 genes in leaf and 113 in fruit exhibited significant allele specific expression by watering regime interaction, among which ~80% presented trans by watering regime interaction suggesting a response to water deficit mediated through a majority of trans acting loci in tomato. We cross-validated the expression levels of 274 transcripts in fruit and leaves of 124 RILs and identified 163 eQTLs mostly confirming the divergences identified by allele specific expression. Combining phenotypic and expression data, we observed a complex network of variation between genes encoding enzymes involved in the sugar metabolism.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02620940/file/Albert_he_Plant_Journal%282%29.2018pdf_1.pdf BibTex
titre
Atmosphere–soil carbon transfer as a function of soil depth
auteur
J. Balesdent, Isabelle Basile-Doelsch, Joel Chadoeuf, Sophie S. Cornu, Delphine Derrien, Zuzana Fekiacova, Christine Hatté
article
Nature, 2018, 559 (7715), pp.599-602. ⟨10.1038/s41586-018-0328-3⟩
resume
The exchange of carbon between soil organic carbon (SOC) and the atmosphere affects the climate1,2 and—because of the importance of organic matter to soil fertility—agricultural productivity3. The dynamics of topsoil carbon has been relatively well quantified4, but half of the soil carbon is located in deeper soil layers (below 30 centimetres)5,6,7, and many questions remain regarding the exchange of this deep carbon with the atmosphere8. This knowledge gap restricts soil carbon management policies and limits global carbon models1,9,10. Here we quantify the recent incorporation of atmosphere-derived carbon atoms into whole-soil profiles, through a meta-analysis of changes in stable carbon isotope signatures at 112 grassland, forest and cropland sites, across different climatic zones, from 1965 to 2015. We find, in agreement with previous work5,6, that soil at a depth of 30–100 centimetres beneath the surface (the subsoil) contains on average 47 per cent of the topmost metre’s SOC stocks. However, we show that this subsoil accounts for just 19 per cent of the SOC that has been recently incorporated (within the past 50 years) into the topmost metre. Globally, the median depth of recent carbon incorporation into mineral soil is 10 centimetres. Variations in the relative allocation of carbon to deep soil layers are better explained by the aridity index than by mean annual temperature. Land use for crops reduces the incorporation of carbon into the soil surface layer, but not into deeper layers. Our results suggest that SOC dynamics and its responses to climatic control or land use are strongly dependent on soil depth. We propose that using multilayer soil modules in global carbon models, tested with our data, could help to improve our understanding of soil–atmosphere carbon exchange.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02073138/file/Balesdent%20Nature%202018%20559%20599-602%20%20accepted%20manuscript%20postprint.pdf BibTex
titre
Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees
auteur
Courtney A. Hollender, Thierry Pascal, Amy Tabb, Toto Hadiarto, Chinnathambi Srinivasan, Wanpeng Wang, Zhongchi Liu, Ralph Scorza, Chris Dardick
article
Proceedings of the National Academy of Sciences of the United States of America, 2018, 115 (20), pp.E4690 - E4699. ⟨10.1073/pnas.1704515115⟩
resume
Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in Prunus persica (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90 degrees reorientation. The causative allele was found to be an uncharacterized gene, Ppa013325, having a 1.8-Kb deletion spanning the 5' end. This gene, dubbed WEEP, was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species Prunus domestica (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity perception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Seeking stable traits to characterize the root system architecture. Study on 60 species located at two sites in natura
auteur
Loïc Pagès, Jocelyne Kervella
article
Annals of Botany, 2018, 122 (1), pp.107-115. ⟨10.1093/aob/mcy061⟩
resume
Background and Aims: In several disciplines, identifying relevant root traits to characterize the root system architecture of species or genotypes is a crucial step. To address this question, we analysed the inter-specific variations of root architectural traits in two contrasting environments. Methods : We sampled 60 species in natura, at two sites, each presenting homogeneous soil conditions. We estimated for each species and site a set of five traits used for the modelling of the root system architecture: extreme tip diameters (Dmin and Dmax), relative diameter range (Drange), mean inter-branch distance (IBD) and dominance slope between the diameters of parent and lateral roots (DlDm). Key Results : The five traits presented a highly significant species effect, explaining between 77 and 98 % of the total variation. Dmin, Dmax and Drange were particularly determined by the species, while DlDm and IBD exhibited a higher percentage of environmental variations. These traits make it possible to confirm two main axes of variation: ‘fineness–density’ (defined by Dmin and IBD) and ‘dominance–heterorhizy’ (DlDm and Drange), that together accounted for 84 % of the variations observed. Conclusions : We confirmed the interest of these traits in the characterization of the root system architecture in ecology and genetics, and suggest using them to enrich the ‘root economic spectrum’.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The eggplant AG91-25 recognizes the Type III-secreted effector RipAX2 to trigger resistance to bacterial wilt (Ralstonia solanacearum species complex).
auteur
Arry Morel, Jérémy Guinard, Fabien Lonjon, Lakshmi Sujeeun, Patrick Barberis, Stéphane Genin, Fabienne Vailleau, Marie-Christine Daunay, Jacques Dintinger, Stéphane Poussier, Nemo Peeters, Emmanuel Wicker
article
Molecular Plant Pathology, 2018, 19 (11), pp.2459-2472. ⟨10.1111/mpp.12724⟩
resume
To deploy durable plant resistance, we must understand its underlying molecular mechanisms. Type III effectors (T3Es) and their recognition play a central role in the interaction between bacterial pathogens and crops. We demonstrate that the Ralstonia solanacearum species complex (RSSC) T3E ripAX2 triggers specific resistance in eggplant AG91-25, which carries the major resistance locus EBWR9. The eggplant accession AG91-25 is resistant to the wild-type R. pseudosolanacearum strain GMI1000, whereas a ripAX2 defective mutant of this strain can cause wilt. Notably, the addition of ripAX2 from GMI1000 to PSS4 suppresses wilt development, demonstrating that RipAX2 is an elicitor of AG91-25 resistance. RipAX2 has been shown previously to induce effector-triggered immunity (ETI) in the wild relative eggplant Solanum torvum, and its putative zinc (Zn)-binding motif (HELIH) is critical for ETI. We show that, in our model, the HELIH motif is not necessary for ETI on AG91-25 eggplant. The ripAX2 gene was present in 68.1% of 91 screened RSSC strains, but in only 31.1% of a 74-genome collection comprising R. solanacearum and R. syzygii strains. Overall, it is preferentially associated with R. pseudosolanacearum phylotype I. RipAX2(GMI1000) appears to be the dominant allele, prevalent in both R. pseudosolanacearum and R. solanacearum, suggesting that the deployment of AG91-25 resistance could control efficiently bacterial wilt in the Asian, African and American tropics. This study advances the understanding of the interaction between RipAX2 and the resistance genes at the EBWR9 locus, and paves the way for both functional genetics and evolutionary analyses.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02628790/file/Morel_MPP2018.pdf BibTex
titre
Water Deficit and Salinity Stress Reveal Many Specific QTL for Plant Growth and Fruit Quality Traits in Tomato.
auteur
Isidore Diouf, Laurent Derivot, Frederique Bitton, Laura Pascual, Mathilde Causse
article
Frontiers in Plant Science, 2018, 9, pp.1-13. ⟨10.3389/fpls.2018.00279⟩
resume
Quality is a key trait in plant breeding, especially for fruit and vegetables. Quality involves several polygenic components, often influenced by environmental conditions with variable levels of genotype × environment interaction that must be considered in breeding strategies aiming to improve quality. In order to assess the impact of water deficit and salinity on tomato fruit quality, we evaluated a multi-parent advanced generation intercross (MAGIC) tomato population in contrasted environmental conditions over 2 years, one year in control vs. drought condition and the other in control vs. salt condition. Overall 250 individual lines from the MAGIC population-derived from eight parental lines covering a large diversity in cultivated tomato-were used to identify QTL in both experiments for fruit quality and yield component traits (fruit weight, number of fruit, Soluble Solid Content, firmness), phenology traits (time to flower and ripe) and a vegetative trait, leaf length. All the traits showed a large genotype variation (33-86% of total phenotypic variation) in both experiments and high heritability whatever the year or treatment. Significant genotype × treatment interactions were detected for five of the seven traits over the 2 years of experiments. QTL were mapped using 1,345 SNP markers. A total of 54 QTL were found among which 15 revealed genotype × environment interactions and 65% (35 QTL) were treatment specific. Confidence intervals of the QTL were projected on the genome physical map and allowed identifying regions carrying QTL co-localizations, suggesting pleiotropic regulation. We then applied a strategy for candidate gene detection based on the high resolution mapping offered by the MAGIC population, the allelic effect of each parental line at the QTL and the sequence information of the eight parental lines.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02626981/file/2018_Diouf_Front%20Plant%20Sci_1.pdf BibTex
titre
Genotyping by Sequencing Highlights a Polygenic Resistance to Ralstonia pseudosolanacearum in Eggplant (Solanum melongena L.)
auteur
Sylvia Salgon, Morgane Raynal, Sylvain Lebon, Jean-Michel Baptiste, Marie-Christine Brand-Daunay, Jacques Dintinger, Cyril Jourda
article
International Journal of Molecular Sciences, 2018, 19 (2), pp.1-24. ⟨10.3390/ijms19020357⟩
resume
Eggplant cultivation is limited by numerous diseases, including the devastating bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC).Within the RSSC, Ralstonia pseudosolanacearum (including phylotypes I and III) causes severe damage to all solanaceous crops, including eggplant. Therefore, the creation of cultivars resistant to R. pseudosolanacearum strains is a major goal for breeders. An intraspecific eggplant population, segregating for resistance, was created from the cross between the susceptible MM738 and the resistant EG203 lines. The populationof 123 doubled haploid lines was challenged with two strains belonging to phylotypes I (PSS4) and III (R3598), which both bypass the published EBWR9 BW-resistance quantitative trait locus (QTL). Ten and three QTLs of resistance to PSS4 and to R3598, respectively, were detected and mapped. All were strongly influenced by environmental conditions. The most stable QTLs were found on chromosomes 3 and 6. Given their estimated physical position, these newly detected QTLs are putatively syntenic with BW-resistance QTLs in tomato. In particular, the QTLs’ position on chromosome 6 overlaps with that of the major broad-spectrum tomato resistance QTL Bwr-6. The present study is a first step towards understanding the complex polygenic system, which underlies the high level of BW resistance of the EG203 line.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02621157/file/2018_Salgon_International%20Journal%20of%20Molecular%20Sciences_1.pdf BibTex
titre
A systems biology study in tomato fruit reveals correlations between the ascorbate pool and genes involved in ribosome biogenesis, translation, and the heat-shock response
auteur
Rebecca Stevens, Pierre Baldet, Jean-Paul Bouchet, Mathilde Causse, Catherine Deborde, Claire Deschodt, Mireille Faurobert, Cecile Garchery, Virginie Garcia, Hélène Gautier, Barbara Gouble, Mickael Maucourt, Annick Moing, David Page, Johann Petit, Jean-Luc Poëssel, Vincent Truffault, Christophe Rothan
article
Frontiers in Plant Science, 2018, 9 (137), 16 p. ⟨10.3389/fpls.2018.00137⟩
resume
Changing the balance between ascorbate, monodehydroascorbate, and dehydroascorbate in plant cells by manipulating the activity of enzymes involved in ascorbate synthesis or recycling of oxidized and reduced forms leads to multiple phenotypes. A systems biology approach including network analysis of the transcriptome, proteome and metabolites of RNAi lines for ascorbate oxidase, monodehydroascorbate reductase and galactonolactone dehydrogenase has been carried out in orange fruit pericarp of tomato (Solanum lycopersicum). The transcriptome of the RNAi ascorbate oxidase lines is inversed compared to the monodehydroascorbate reductase and galactonolactone dehydrogenase lines. Differentially expressed genes are involved in ribosome biogenesis and translation. This transcriptome inversion is also seen in response to different stresses in Arabidopsis. The transcriptome response is not well correlated with the proteome which, with the metabolites, are correlated to the activity of the ascorbate redox enzymes—ascorbate oxidase and monodehydroascorbate reductase. Differentially accumulated proteins include metacaspase, protein disulphide isomerase, chaperone DnaK and carbonic anhydrase and the metabolites chlorogenic acid, dehydroascorbate and alanine. The hub genes identified from the network analysis are involved in signaling, the heat-shock response and ribosome biogenesis. The results from this study therefore reveal one or several putative signals from the ascorbate pool which modify the transcriptional response and elements downstream.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01721265/file/Stevens%20et%20al_ascorbate%20ribosome_Frontiers%202018.pdf BibTex
titre
The Crop Load Affects Brown Rot Progression in Fruit Orchards: High Fruit Densities Facilitate Fruit Exposure to Spores but Reduce the Infection Rate by Decreasing Fruit Growth and Cuticle Cracking
auteur
Michele Bellingeri, Bénédicte Quilot-Turion, Leandro Oliveira, Daniele Bevacqua
article
Frontiers in Ecology and Evolution, 2018, 5, ⟨10.3389/fevo.2017.00170⟩
resume
Brown rot, triggered by Monilinia spp., causes significant economic losses in fruit crop and it is mainly controlled by chemicals with inherent environmental costs. Controlling brown rot spreading by diminishing fruit susceptibility to the disease, via sustainable cultural practices, is a promising approach. In a 2 years experiment (2014–2015) on a peach (Prunus persica) orchard, we controlled fruit growth rates by varying the fruit load. Fruit thinning practices enhanced the fruit growth and laboratory analyses showed that, in both 2014 and 2015 samples, fast growing fruits weremore susceptible to infection when in contact with conidia suspension of Monilinia laxa. In the field, brown rot infection took place in 2014 and not in 2015. In 2014, trees subject to moderate thinning intensities had the highest brown rot incidence.We argue that this is due to the fact that, for null thinning, slow growing fruits are less susceptible to the infection while, for intense thinning, even if faster growing fruits are more susceptible to infection, the lower fruits density reduces per-contact probability of infection.We compared meteorological data of 2014 and 2015 and we argue that brown rot did not spread in 2015 due to an absence of favorable conditions, summarized as the number of rainy days with mean temperature between 22 and 26◦C, in the period of fruit susceptibility.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01684898/file/the%20crop.pdf BibTex
titre
The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish
auteur
A. Tsakogiannis, T. Manousaki, Jacques Lagnel, A. Sterioti, M. Pavlidis, N. Papandroulakis, C. C. Mylonas, C. S. Tsigenopoulos
article
Scientific Reports, 2018, 8 (1), pp.1-17. ⟨10.1038/s41598-018-21992-9⟩
resume
Sex differentiation is a puzzling problem in fish due to the variety of reproductive systems and the flexibility of their sex determination mechanisms. The Sparidae, a teleost family, reflects this remarkable diversity of sexual mechanisms found in fish. Our aim was to capture the transcriptomic signature of different sexes in two protogynous hermaphrodite sparids, the common pandora Pagellus erythrinus and the red porgy Pagrus pagrus in order to shed light on the molecular network contributing to either the female or the male phenotype in these organisms. Through RNA sequencing, we investigated sex-specific differences in gene expression in both species’ brains and gonads. The analysis revealed common male and female specific genes/pathways between these protogynous fish. Whereas limited sex differences found in the brain indicate a sexually plastic tissue, in contrast, the great amount of sex-biased genes observed in gonads reflects the functional divergence of the transformed tissue to either its male or female character. Α common “crew” of well-known molecular players is acting to preserve either sex identity of the gonad in these fish. Lastly, this study lays the ground for a deeper understanding of the complex process of sex differentiation in two species with an evolutionary significant reproductive system.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02620154/file/2018_Tsakogiannis_scientificReports_1.pdf BibTex
titre
Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance in plants
auteur
Anna Bastet, Baptiste Lederer, Nathalie Giovinazzo, Xavier Arnoux, Sylvie German-Retana, Catherine Reinbold, Véronique Brault, Damien Garcia, Samia Djennane, Sophie Gersch, Olivier Lemaire, Christophe Robaglia, Jean-Luc Gallois
article
Plant Biotechnology Journal, In press, 16 (9), pp.1569-1581. ⟨10.1111/pbi.12896⟩
resume
To infect plants, viruses rely heavily on their host's machinery. Plant genetic resistances based on host factor modifications can be found among existing natural variability and are widely used for some but not all crops. While biotechnology can supply for the lack of natural resistance alleles, new strategies need to be developed to increase resistance spectra and durability without impairing plant development. Here, we assess how the targeted allele modification of the Arabidopsis thaliana translation initiation factor eIF4E1 can lead to broad and efficient resistance to the major group of potyviruses. A synthetic Arabidopsis thaliana eIF4E1 allele was designed by introducing multiple amino acid changes associated with resistance to potyvirus in naturally occurring Pisum sativum alleles. This new allele encodes a functional protein while maintaining plant resistance to a potyvirus isolate that usually hijacks eIF4E1. Due to its biological functionality, this synthetic allele allows, at no developmental cost, the pyramiding of resistances to potyviruses that selectively use the two major translation initiation factors, eIF4E1 or its isoform eIFiso4E. Moreover, this combination extends the resistance spectrum to potyvirus isolates for which no efficient resistance has so far been found, including resistance‐breaking isolates and an unrelated virus belonging to the Luteoviridae family. This study is a proof‐of‐concept for the efficiency of gene engineering combined with knowledge of natural variation to generate trans‐species virus resistance at no developmental cost to the plant. This has implications for breeding of crops with broad‐spectrum and high durability resistance using recent genome editing techniques.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01852177/file/Bastet_et_al-2018-Plant_Biotechnology_Journal.pdf BibTex
titre
Fine mapping of the root-knot nematode resistance gene Me1 in pepper (Capsicum annuum L.) and development of markers tightly linked to Me1
auteur
Xueying Wang, Ariane Fazari, Yacong Cao, Zhenghai Zhang, Alain Palloix, Shengli Mao, Baoxi Zhang, Caroline Caporalino, Lihao Wang
article
Molecular Breeding, 2018, 38 (4), ⟨10.1007/s11032-018-0793-2⟩
resume
Root-knot nematodes (RKNs) can severely damage crops, including peppers, worldwide. The application of resistance genes identified in the Capsicum annuum genome may represent a safe and economically relevant strategy for controlling RKNs. Among the Me genes (Me1, Me3, Me7, and N) that have been mapped to a cluster on chromosome P9, Me1 confers a heat-stable and broad-spectrum resistance that is difficult for virulent RKNs to overcome. In this study, we developed several closely linked kompetitive allele-specific PCR (KASPar) markers, simple sequence repeat (SSR) markers, sequence characterized amplified region (SCAR) markers, and high-resolution melting (HRM) markers for the mapping of RKN-resistance genes. Analyses of 948 individuals (BC1 and F-2 progenies) revealed that Me1 was located between SCAR marker 16880-1-V2 and HRM marker 16830-H-V2, with 13 and 0 recombination events with Me1, respectively. These markers were localized to a 132-kb interval, which included six genes. The development of several PCR-based markers closely linked to Me1 will be useful for the marker-assisted selection of RKN resistance in pepper cultivars. Among these markers, 16830-H-V2 and 16830-CAPS are present in the CA09g16830 gene, which is predicted to be a putative late blight resistance protein homolog R1A-3 gene. This gene appears to be a suitable Me1 candidate gene.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Muscle and liver transcriptome characterization and genetic marker discovery in the farmed meagre, Argyrosomus regius
auteur
T. Manousaki, A. Tsakogiannis, Jacques Lagnel, D. Kyriakis, N. Duncan, A. Estevez, C.S. Tsigenopoulos
article
Marine Genomics, 2018, 39, pp.39-44. ⟨10.1016/j.margen.2018.01.002⟩
resume
Meagre (Argyrosomus regius), a teleost fish of the family Sciaenidae, is part of a group of marine fish species considered new for Mediterranean aquaculture representing the larger fish cultured in the region. Meagre aquaculture started ~ 25 years ago in West Mediterranean, and the supply of juveniles has been dominated by few hatcheries. This fact has raised concerns on possible inbreeding, urging the need for genetic information on the species and for an assessment of the polymorphisms found in the genome. To that end we characterized the muscle and liver transcriptome of a pool of meagre individuals, from different families and phenotypic size, to obtain a backbone that can support future studies regarding physiology, immunology and genetics of the species. The assembled transcripts were assigned to a wide range of biological processes including growth, reproduction, metabolism, development, stress and behavior. Then, to infer its genetic diversity and provide a catalogue of markers for future use, we scanned the reconstructed transcripts for polymorphic genetic markers. Our search revealed a total of 42,933 high quality SNP and 20,581 STR markers. We found a relatively low rate of polymorphism in the transcriptome that may indicate that inbreeding has taken place. This study has led to a catalogue of genetic markers at the expressed part of the genome and has set the ground for understanding growth and other traits of interest in meagre.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Role of the genetic background in resistance to plant viruses
auteur
Jean-Luc Gallois, Benoît Moury, Sylvie German-Retana
article
International Journal of Molecular Sciences, 2018, 19 (10), pp.2856. ⟨10.3390/ijms19102856⟩
resume
In view of major economic problems caused by viruses, the development of genetically resistant crops is critical for breeders but remains limited by the evolution of resistance-breaking virus mutants. During the plant breeding process, the introgression of traits from Crop Wild Relatives results in a dramatic change of the genetic background that can alter the resistance efficiency or durability. Here, we conducted a meta-analysis on 19 Quantitative Trait Locus (QTL) studies of resistance to viruses in plants. Frequent epistatic effects between resistance genes indicate that a large part of the resistance phenotype, conferred by a given QTL, depends on the genetic background. We next reviewed the different resistance mechanisms in plants to survey at which stage the genetic background could impact resistance or durability. We propose that the genetic background may impair effector-triggered dominant resistances at several stages by tinkering the NB-LRR (Nucleotide Binding-Leucine-Rich Repeats) response pathway. In contrast, effects on recessive resistances by loss-of-susceptibility-such as eIF4E-based resistances-are more likely to rely on gene redundancy among the multigene family of host susceptibility factors. Finally, we show how the genetic background is likely to shape the evolution of resistance-breaking isolates and propose how to take this into account in order to breed plants with increased resistance durability to viruses.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02629315/file/2018_Gallois_Int%20J%20Mol%20Sci_1.pdf BibTex
titre
Phenomics allows identification of genomic regions affecting maize stomatal conductance with conditional effects of water deficit and evaporative demand
auteur
Santiago Alvarez Prado, Llorenç Cabrera-Bosquet, Antonin Grau, Aude Coupel-Ledru, Emilie J Millet, Claude Welcker, Francois Tardieu
article
Plant, Cell and Environment, 2018, 41 (2), pp.314-326. ⟨10.1111/pce.13083⟩
resume
Stomatal conductance is central for the trades-off between hydraulics and photosynthesis. We aimed at deciphering its genetic control and that of its responses to evaporative demand and water deficit, a nearly impossible task with gas exchanges measurements. Whole-plant stomatal conductance was estimated via inversion of the Penman–Monteith equation from data of transpiration and plant architecture collected in a phenotyping platform. We have analysed jointly 4 experiments with contrasting environmental conditions imposed to a panel of 254 maize hybrids. Estimated whole-plant stomatal conductance closely correlated with gas-exchange measurements and biomass accumulation rate. Sixteen robust quantitative trait loci (QTLs) were identified by genome wide association studies and co-located with QTLs of transpiration and biomass. Light, vapour pressure deficit, or soil water potential largely accounted for the differences in allelic effects between experiments, thereby providing strong hypotheses for mechanisms of stomatal control and a way to select relevant candidate genes among the 1–19 genes harboured by QTLs. The combination of allelic effects, as affected by environmental conditions, accounted for the variability of stomatal conductance across a range of hybrids and environmental conditions. This approach may therefore contribute to genetic analysis and prediction of stomatal control in diverse environments.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Impact of canning and storage on apricot carotenoids and polyphenols
auteur
Carine Le Bourvellec, Barbara Gouble, Sylvie Bureau, Patrice Reling, Romain Bott, Albert Ribas, Jean Marc Audergon, Catherine M.G.C. Renard
article
Food Chemistry, 2018, 240, pp.615-625. ⟨10.1016/j.foodchem.2017.07.147⟩
resume
Apricot polyphenols and carotenoids were monitored after industrial and domestic cooking, and after 2 months of storage for industrial processing. The main apricot polyphenols were flavan-3-ols, flavan-3-ol monomers and oligomers, with an average degree of polymerization between 4.7 and 10.7 and caffeoylquinic acids. Flavonols and anthocyanins were minor phenolic compounds. Upon processing procyanidins were retained in apricot tissue. Hydroxycinnamic acids, flavan-3-ol monomers, flavonols and anthocyanins leached in the syrup. Flavonol concentrations on per-can basis were significantly increased after processing. Industrial processing effects were higher than domestic cooking probably due to higher temperature and longer duration. After 2 months of storage, among polyphenols only hydroxycinnamic acids, flavan-3-ol monomers and anthocyanins were reduced. Whichever the processing method, no significant reductions of total carotenoids were observed after processing. The cis-β-carotene isomer was significantly increased after processing but with a lower extent in domestic cooking. Significant decreased in total carotenoid compounds occurred during storage.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01607270/file/impactofcanning_1.pdf BibTex
titre
Cucurbit Powdery Mildew-resistant Bitter Gourd Breeding Lines Reveal Four Races of Podosphaera xanthii in Asia
auteur
Narinder P. S. Dhillon, Supannika Sanguansil, Supornpun Srimat, Roland Schafleitner, B. Manjunath, Parag Agarwal, Qu Xiang, Mohammed Abu Taher Masud, Thaingi Myint, - Ngo Thi Hanh, - Tran Kim Cuong, Conrado H. Balatero, Venus Salutan-Bautista, Michel Pitrat, Ales Lebeda, James D. Mccreight
article
HortScience, 2018, 53 (3), pp.337 - 341. ⟨10.21273/HORTSCI12545-17⟩
resume
Bitter gourd (Momordica charantia L.) is a commercially and nutritionally important market vegetable in Asia cultivated mainly by smallholder farmers. Cucurbit powdery mildew (CPM) caused by Podosphaera xanthii (Px) is a nearly ubiquitous and serious fungal disease of bitter gourd. Five bitter gourd breeding lines (THMC 113, THMC 143, THMC 153, THMC 167, and THMC 170) were selected at the World Vegetable Center for resistance to a local isolate of Px in Kamphaeng Saen, Thailand. We evaluated the resistance potential of these five inbred lines against local isolates of Px at 12 locations in five Asian countries. Plants were inoculated with the respective local Px isolate 15 and 30 days after transplanting and additional Px-infected plants of the inoculated control were interplanted throughout each test. Plants were rated 60 days after transplanting for CPM reaction using a 0 (no evidence of infection) to 5 (>75% infection evident on individual leaves) disease severity scale. THMC 153 and THMC 167 were resistant to the local race of Px in all locations, whereas THMC 143 was observed resistant in all test locations except one in China. THMC 113 was resistant in each location except one in India. THMC 170 was susceptible in three locations in India. The multilocation tests revealed four unique Px races on bitter gourd in different Asian countries and sources of resistance for breeding CPM-resistant bitter gourd cultivars. Six strains of Px isolated from other cucurbits (Cucumis and Cucurbita) and representing five melon CPM races were unable to infect the susceptible M. charantia accession THMC 144 and the five resistant breeding lines, indicating pathotype differences between them and an isolate of M. charantia origin typed as race 1 on melon. THMC 143 and THMC 167, which originated from India, exhibited good yield potential in trials conducted in Thailand, Myanmar, Vietnam, and Bangladesh.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A Model for Temporal Dynamics of Brown Rot Spreading in Fruit Orchards
auteur
Danièle Bevacqua, Bénédicte Quilot-Turion, Luca Bolzoni
article
Phytopathology, 2018, 108 (5), pp.595-601. ⟨10.1094/PHYTO-07-17-0250-R⟩
resume
Brown rot, caused by Monilinia spp., is a major disease of stone fruit and, in favorable environmental conditions and in the absence of fungicide treatments, it causes important economic losses. In the present work, we propose a modification of classical susceptible, exposed, infectious and removed compartmental models to grasp the peculiarities of the progression of brown rot epidemics in stone fruit orchards in the last stage of the fruit growth (i.e., from the end of the pit hardening to harvest time). Namely, we took into account (i) the lifespan of airborne spores; (ii) the dependence of the latent period on the cuticle crack surface area, which itself varies in time with fruit growth; (iii) the impossibility of recovery in infectious fruit; and (iv) the abrupt interruption of disease development by the elimination of the host fruit at harvest time. We parametrized the model by using field data from a peach Prunus persica orchard infected by Monilinia laxa and M. fructicola in Avignon (southern France). The basic reproduction number indicates that the environmental conditions met in the field were extremely favorable to disease development and the model closely fitted the temporal evolution of the fruit abundance in the different epidemiological compartments. The model permits us to highlight crucial mechanisms undergoing brown rot build up and to evaluate the consequences of different agricultural practices on the quantity and quality of the yield. We found that winter sanitation practices (which decrease the initial infection incidence) and the control of the fruit load (which affects the host fruit density and the single fruit growth trajectory) can be effective in controlling brown rot in conjunction with or in place of fungicide treatments.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The DFR locus: A smart landing pad for targeted transgene insertion in tomato.
auteur
Benoît Danilo, Laura Perrot, Emmanuel Botton, Fabien Nogué, Marianne Mazier
article
PLoS ONE, 2018, 13 (12), pp.e0208395. ⟨10.1371/journal.pone.0208395⟩
resume
Targeted insertion of transgenes in plants is still challenging and requires further technical innovation. In the present study, we chose the tomato DFR gene involved in anthocyanin biosynthesis as a landing pad for targeted transgene insertion using CRISPR-Cas9 in a two-step strategy. First, a 1013 bp was deleted in the endogenous DFR gene. Hypocotyls and callus of in vitro regenerated plantlets homozygous for the deletion were green instead of the usual anthocyanin produced purple colour. Next, standard Agrobacterium-mediated transformation was used to target transgene insertion at the DFR landing pad in the dfr deletion line. The single binary vector carried two sgRNAs, a donor template containing two homology arms of 400 bp, the previously deleted DFR sequence, and a NptII expression cassette. Regenerating plantlets were screened for a purple-colour phenotype indicating that DFR function had been restored. Targeted insertions were identified in 1.29% of the transformed explants. Thus, we established an efficient method for selecting HDR-mediated transgene insertion using the CRISPR-Cas9 system in tomato. The visual screen used here facilitates selection of these rare gene targeting events, does not necessitate the systematic PCR screening of all the regenerating material and can be potentially applied to other crops.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02621940/file/2018_Danilo_Plos%20One_1.pdf BibTex
titre
Ma Orthologous Genes in Prunus spp. Shed Light on a Noteworthy NBS-LRR Cluster Conferring Differential Resistance to Root-Knot Nematodes
auteur
Cyril van Ghelder, Daniel Esmenjaud, Caroline Callot, Emeric Dubois, Marianne Mazier, Henri Duval
article
Frontiers in Plant Science, 2018, 9, ⟨10.3389/fpls.2018.01269⟩
resume
Root-knot nematodes (RKNs) are considerable polyphagous pests that severely challenge plants worldwide and especially perennials. The specific genetic resistance of plants mainly relies on the NBS-LRR genes that are pivotal factors for pathogens control. In Prunus spp., the Ma plum and RMja almond genes possess different spectra for resistance to RKNs. While previous works based on the Ma gene allowed to clone it and to decipher its peculiar TIR-NBS-LRR (TNL) structure, we only knew that the RMja gene mapped on the same chromosome as Ma. We carried out a high-resolution mapping using an almond segregating F2 progeny of 1448 seedlings from resistant (R) and susceptible (S) parental accessions, to locate precisely RMja on the peach genome, the reference sequence for Prunus species. We showed that the RMja gene maps in the Ma resistance cluster and that the Ma ortholog is the best candidate for RMja. This co-localization is a crucial step that opens the way to unravel the molecular determinants involved in the resistance to RKNs. Then we sequenced both almond parental NGS genomes and aligned them onto the RKN susceptible reference peach genome. We produced a BAC library of the R parental accession and, from two overlapping BAC clones, we obtained a 336-kb sequence encompassing the RMja candidate region. Thus, we could benefit from three Ma orthologous regions to investigate their sequence polymorphism, respectively, within plum (complete R spectrum), almond (incomplete R spectrum) and peach (null R spectrum). We showed that the Ma TNL cluster has evolved orthologs with a unique conserved structure comprised of five repeated postLRR (PL) domains, which contain most polymorphism. In addition to support the Ma and RMja orthologous relationship, our results suggest that the polymorphism contained in the PL sequences might underlie differential resistance interactions with RKNs and an original immune mechanism in woody perennials. Besides, our study illustrates how PL exon duplications and losses shape TNL structure and give rise to atypical PL domain repeats of yet unknown role.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02621840/file/Van%20Ghelder-frontiers-in-plant-science-2018_1.pdf BibTex
titre
The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
auteur
Mathieu Gautier, Junichi Yamaguchi, Julien Foucaud, Anne Loiseau, Aurélien Ausset, Benoit Facon, Bernhard Gschloessl, Jacques Lagnel, Etienne Loire, Hugues Parrinello, Dany Severac, Celine Lopez-Roques, Cecile Donnadieu, Maxime Manno, Helene Berges, Karim Gharbi, Lori Lawson-Handley, Lian-Sheng Zang, Heiko Vogel, Arnaud Estoup, Benjamin Prud’homme
article
Current Biology, 2018, 28 (20), pp.1-7. ⟨10.1016/j.cub.2018.08.023⟩
resume
Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1, 2, 3, 4, 5, 6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [7, 8]. In the harlequin ladybird, Harmonia axyridis, more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [9, 10]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H. axyridis. We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H. axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of ∼170 kb in the cis-regulatory regions of pannier, with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that highly variable discrete color forms can arise in natural populations through cis-regulatory allelic variation of a single gene.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01864435/file/gautier.current.biology.2018.pdf BibTex
titre
PUX10 is a CDC48A Adaptor Protein that Regulates the Extraction of Ubiquitinated Oleosins from Seed Lipid Droplets in Arabidopsis
auteur
Carine Deruyffelaere, Zita Purkrtova, Isabelle Bouchez, Boris Collet, Jean-Luc Cacas, Thierry T. Chardot, Jean-Luc Gallois, Sabine d'Andrea
article
The Plant cell, 2018, 30 (9), pp.2116-2136. ⟨10.1105/tpc.18.00275⟩
resume
Post-germinative mobilization of neutral lipids stored in seed lipid droplets (LDs) is preceded by the degradation of oleosins, the major structural LD proteins that stabilize LDs in dry seeds. We previously showed that Arabidopsis thaliana oleosins are marked for degradation by ubiquitination, and extracted from LDs before proteolysis. However, the mechanisms underlying the dislocation of these LD-anchored proteins from the LD monolayer are yet unknown. Here, we report that PUX10, a member of the plant UBX-domain containing (PUX) protein family, is an integral LD protein that associates with a subpopulation of LDs during seed germination. In pux10 mutant seedlings, PUX10 deficiency impaired the degradation of ubiquitinated oleosins, and prevented the extraction of ubiquitinated oleosins from LDs. We also showed that PUX10 interacts with ubiquitin and CDC48A, the AAA ATPase Cell Division Cycle 48, through its UBA and UBX domains, respectively. Collectively, these results strongly suggest that PUX10 is an adaptor recruiting CDC48A to ubiquitinated oleosins, thus facilitating the dislocation of oleosins from LDs by the segregase activity of CDC48A. We propose that PUX10 and CDC48A are core components of a LD-associated degradation machinery, which we named the LD-associated degradation (LDAD) system. Importantly, PUX10 is also the first determinant of a LD subpopulation described in plants, suggesting functional differentiation of LDs in Arabidopsis seedlings.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://agroparistech.hal.science/hal-02126918/file/TPC2018-RA-00275R1_DAndrea-Final-Merged.pdf BibTex
titre
Growth stage-dependent resistance to the potyviruses lettuce Italian necrotic virus and Lettuce mosaic virus displayed by Lactuca sativa introgression lines carrying the Mo3 locus from L. virosa
auteur
Brigitte Maisonneuve, Michel Pitrat, Patrick Gognalons, Benoît Moury
article
Plant Pathology, 2018, 67 (9), pp.2013-2018. ⟨10.1111/ppa.12909⟩
resume
The single dominant gene Mo3 from accession PIVT1398 of Lactuca virosa was shown previously to confer resistance to all tested isolates of Lettuce mosaic virus (LMV; genus Potyvirus), including mo1‐resistance‐breaking isolates. Because accession PIVT1398 is also resistant to the recently described potyvirus lettuce Italian necrotic virus (LINV), this study checked whether the Mo3 resistance locus could be involved in resistance to LINV. Introgression lines of Mo3 into two different L. sativa genetic backgrounds (Girelle and Mantilia) were resistant to isolates LMV‐9, LMV‐13 and LINV‐Fr (a French isolate of LINV), whereas Girelle and Mantilia were susceptible to these virus isolates. The resistance reaction in inoculated leaves of the introgression lines varied from absence of symptoms and absence of virus detection for LMV‐9, to hypersensitive‐like necrotic lesions and low virus titres for LINV‐Fr and large necrotic lesions and relatively abundant virus detection for LMV‐13. At the systemic level, the resistance phenotype was growth stage‐dependent for LINV‐Fr and LMV‐13. Inoculation of ≥28‐days‐old plants led to absence of symptoms and no virus with the three tested potyvirus isolates in almost all plants. Inoculation of younger plants (≤22‐days‐old) led to chlorotic/necrotic lesions on some apical leaves with low virus titre in a varying proportion of plants with LINV‐Fr and on all plants with efficient virus detection with LMV‐13. These results show that the Mo3 gene, or a tightly linked locus, in L. virosa PIVT1398 controls resistance to LINV in addition to LMV and could be used to breed L. sativa cultivars with broad‐spectrum potyvirus resistance.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02625006/file/Maisonneuve_HAL-INRAE.pdf BibTex
titre
Deletion of the miR172 target site in a TOE-type gene is a strong candidate variant for dominant double-flower trait in Rosaceae
auteur
Stefano Gattolin, Marco Cirilli, Igor Pacheco, Angelo Ciacciulli, Cassia da Silva Linge, Jehan-Baptiste Mauroux, Patrick Lambert, Elia Cammarata, Daniele Bassi, Thierry Pascal, Laura Rossini
article
The Plant Journal, 2018, 96 (2), pp.358-371. ⟨10.1111/tpj.14036⟩
resume
Double‐flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants including peach, a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double‐flower phenotype in peach, we focused on the dominant Di2 locus. High‐resolution linkage mapping in 5 segregating progenies delimited Di2 to an interval spanning 150,858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic re‐sequencing data from single‐ and double‐flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double‐flower trait and showed transcript expression for both wild‐type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical times for floral development. The indelDi2 molecular marker designed on this sequence variant co‐segregated with the phenotype in 621 progenies accounting for the dominant inheritance of the Di2 locus. Further corroborating results in peach, we identified a distinct but similar mutation in the ortholog of Prupe.6G242400 in double‐flower roses. Phylogenetic analysis showed that these two genes belong to a TOE‐type clade not represented in Arabidopsis, indicating divergence of gene functions between AP2‐type and TOE‐type factors in Arabidopsis and other species. Identification of orthologous candidate genes for the double‐flower phenotype in two important Rosaceae species provides valuable information to understand the genetic control of this trait in other major ornamental plants.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Comparison of the responses to NaCl stress of three tomato introgression lines
auteur
Fedia Rebah, Chayma Ouhibi, K. H. Alamer, Najoua Msilini, Mouhiba Ben Nasri, Rebecca Stevens, Houneida Attia
article
Acta Biologica Hungarica, 2018, 69 (4), pp.464-480. ⟨10.1556/018.69.2018.4.8⟩
resume
We aimed to examine the response of three tomato introgression lines (IL925.3, IL925.5 and IL925.6) to NaCl stress. These lines originated from a cross between M82 (Solanum lycopersicum) and the wild salttolerant tomato Solanum pennellii, each line containing a different fragment of the S.pennellii genome. Salt-sensitive phenotypes related to plant growth and physiology, and the response of antioxidants, pigments and antioxidant enzymes were measured. In general, salt stress decreased the fresh weight of leaves, leaf area and leaf number and an increase of Na+ accumulation in aerial parts was observed, which caused a reduction in the absorption of K+ and Ca2+. Salt stress also induced a decrease in chlorophyll, carotenoids and lipid peroxidation (MDA) and an increase in anthocyanins and reduced ascorbate, although some differences were seen between the lines, for example for carotenoid levels. Guaiacol peroxidase, catalase and glutathione reductase activity enhanced in aerial parts of the lines, but again some differences were seen between the three lines. It is concluded that IL925.5 might be the most sensitive line to salt stress as its dry weight loss was the greatest in response to salt and this line showed the highest Na+ ion accumulation in leaves.
typdoc
Journal articles
Accès au bibtex
BibTex

2017

Journal articles

titre
Ecological and sanitary impacts of bacterial communities associated to biological invasions in African commensal rodent communities
auteur
C. Lippens, Christophe Diagne, Maxime Galan, Lucie Tamisier, Jonathan D’ambrosio, Ambroise Dalecky, Khalilou Bâ, Youssoupha Niang, Mamoudou Diallo, Aliou Sow, Philippe Gauthier, Caroline Tatard, Anne Loiseau, Sylvain S. Piry, Mbacké Sembene, Jean-François Cosson, Nathalie Charbonnel, Carine Brouat, Mamadou Kane
article
Scientific Reports, 2017, 7 (1), art. 14995 [11 p.]. ⟨10.1038/s41598-017-14880-1⟩
resume
Changes in host-parasite ecological interactions during biological invasion events may affect both the outcome of invasions and the dynamics of exotic and/or endemic infections. We tested these hypotheses, by investigating ongoing house mouse (Mus musculus domesticus) and black rat (Rattus rattus) invasions in Senegal (West Africa). We used a 16S gene rRNA amplicon sequencing approach to study potentially zoonotic bacterial communities in invasive and native rodents sampled along two well-defined independent invasion routes. We found that individual host factors (body mass and sex) were important drivers of these bacterial infections in rodents. We observed that the bacterial communities varied along invasion routes and differed between invasive and native rodents, with native rodents displaying higher overall bacterial diversity than invasive rodents. Differences in prevalence levels for some bacterial Operational Taxonomic Units (OTUs) provided support for ecological processes connecting parasitism and invasion success. Finally, our results indicated that rodent invasions may lead to the introduction of exotic bacterial genera and/or to changes in the prevalence of endemic ones. This study illustrates the difficulty of predicting the relationship between biodiversity and disease risks, and advocate for public health prevention strategies based on global pathogen surveillance followed by accurate characterization of potential zoonotic agents.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01792669/file/Diagne_etal_2017_ecological_sanitary_1.pdf BibTex
titre
Estimating virus effective population size and selection without neutral markers
auteur
Elsa Rousseau, Benoît Moury, Ludovic Mailleret, Rachid Senoussi, Alain Palloix, Vincent Simon, Sophie Valière, Frédéric Grognard, Frédéric Fabre
article
PLoS Pathogens, 2017, 13 (11), pp.e1006702. ⟨10.1371/journal.ppat.1006702⟩
resume
By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and, variant frequencies were determined by HTS in eight plants of each pepper line, at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes N e at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (N e 2 [10, 2000]) and selection (|s| 2 [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of N e were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://inria.hal.science/hal-01658535/file/journal.ppat.1006702.pdf BibTex
titre
Juvenile coffee leaves acclimated to low light are unable to cope with a moderate light increase
auteur
Claudine Campa, Laurent Urban, Laurence Mondolot, Sandrine Roques, Yves Lizzi, Jawad Aarrouf, Sylvie Doulbeau, Jean-Christophe Breitler, Céline Letrez, Lucile Toniutti, Philippe La Fisca, Luc P. R. Bidel, Hervé Etienne, Denis Fabre, Benoît Bertrand
article
Frontiers in Plant Science, 2017, 8, pp.1126. ⟨10.3389/fpls.2017.01126⟩
resume
The understorey origin of coffee trees and the strong plasticity of Coffea arabica leaves in relation to contrasting light environments have been largely shown. The adaptability of coffee leaves to changes in light was tested under controlled conditions by increasing the illumination rate on C. arabica var. Naryelis seedlings acclimated to low light conditions and observing leaf responses at three different developmental stages (juvenile, growing and mature). Only mature leaves proved capable of adapting to new light conditions. In these leaves, different major mechanisms were found to contribute to maintaining a good photosynthetic level. With increased illumination, a high photosynthetic response was conserved thanks to fast nitrogen remobilization, as indicated by SPAD values and the photorespiration rate. Efficient photoprotection was accompanied by a great ability to export sucrose, which prevented excessive inhibition of the Calvin cycle by hexose accumulation. In contrast, in younger leaves, increased illumination caused photodamage, observable even after 9 days of treatment. One major finding was that young coffee leaves rely on the accumulation of chlorogenic acids, powerful antioxidant phenolic compounds, to deal with the accumulation of reactive oxygen species rather than on antioxidant enzymes. Due to a lack of efficient photoprotection, a poor ability to export sucrose and inadequate antioxidant protection, younger leaves seemed to be unable to cope with increased illumination. In these leaves, an absence of induced antioxidant enzyme activity was accompanied, in growing leaves, by an absence of antioxidant synthesis or, in juvenile leaves, inefficient synthesis of flavonoids because located in some epidermis cells. These observations showed that coffee leaves, at the beginning of their development, are not equipped to withstand quick switches to higher light levels. Our results confirm that coffee trees, even selected for full sunlight conditions, remain shade plants possessing leaves able to adapt to higher light levels only when mature.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://ird.hal.science/ird-01599877/file/Juvenile_coffee_leaves.pdf BibTex
titre
Quantitative trait loci in pepper control the effective population size of two RNA viruses at inoculation
auteur
Lucie Tamisier, Elsa Rousseau, Sebastien Barraillé, Ghislaine Nemouchi, Marion Szadkowski, Ludovic Mailleret, Frédéric Grognard, Frederic Fabre, Benoît Moury, Alain Palloix
article
Journal of General Virology, 2017, 98 (7), pp.1923 - 1931. ⟨10.1099/jgv.0.000835⟩
resume
Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne. We aimed to (i) identify the plant genetic factors controlling Ne during inoculation, (ii) understand the mechanisms used by the plant to control Ne and (iii) compare these genetic factors with the genes controlling plant resistance to viruses. Ne was measured in a doubled-haploid population of Capsicum annuum. Plants were inoculated with either a Potato virus Y (PVY) construct expressing the green fluorescent protein or a necrotic variant of Cucumber mosaic virus (CMV). Newas assessed by counting the number of primary infection foci on cotyledons for PVY or the number of necrotic local lesions on leaves for CMV. The number of foci and lesions was correlated (r=0.57) and showed a high heritability (h2=0.93 for PVY and h2=0.98 for CMV). The Ne of the two viruses was controlled by both common quantitative trait loci (QTLs) and virus-specific QTLs, indicating the contribution of general and specific mechanisms. The PVY-specific QTL colocalizes with a QTL that reduces PVY accumulation and the capacity to break down a major-effect resistance gene.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo
auteur
David Latrasse, Natalia Rodriguez Granados, Alaguraj Veluchamy, Kiruthiga Gayathri Mariappan, Claudia Bevilacqua, Nicolas Crapart, Céline Camps, Vivien Sommard, Cécile Raynaud, Catherine Dogimont, Adnane Boualem, Moussa Benhamed, Abdelhafid Bendahmane
article
Epigenetics and Chromatin, 2017, 10 (22), pp.1-17. ⟨10.1186/s13072-017-0132-6⟩
resume
Background Melon (Cucumis melo) is an important vegetable crop from the Cucurbitaceae family and a reference model specie for sex determination, fruit ripening and vascular fluxes studies. Nevertheless, the nature and role of its epigenome in gene expression regulation and more specifically in sex determination remains largely unknown. Results We have investigated genome wide H3K27me3 and H3K9ac histone modifications and gene expression dynamics, in five melon organs. H3K9ac and H3K27me3 were mainly distributed along gene-rich regions and constrained to gene bodies. H3K9ac was preferentially located at the TSS, whereas H3K27me3 distributed uniformly from TSS to TES. As observed in other species, H3K9ac and H3K27me3 correlated with high and low gene expression levels, respectively. Comparative analyses of unisexual flowers pointed out sex-specific epigenetic states of TFs involved in ethylene response and flower development. Chip-qPCR analysis of laser dissected carpel and stamina primordia, revealed sex-specific histone modification of MADS-box genes. Using sex transition mutants, we demonstrated that the female promoting gene, CmACS11, represses the expression of the male promoting gene CmWIP1 via deposition of H3K27me3. Conclusions Our findings reveal the organ-specific landscapes of H3K9ac and H3K27me3 in melon. Our results also provide evidence that the sex determination genes recruit histone modifiers to orchestrate unisexual flower development in monoecious species. Natalia Y. Rodriguez-Granados and Alaguraj Veluchamy contributed equally to this work
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01594682/file/the%20quest_%7B523A892C-9D23-470E-B3BA-889643B46DF9%7D.pdf BibTex
titre
A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives
auteur
Gautier Sarah, Félix Homa, Stéphanie Pointet, Sandy Contreras, François Sabot, Benoit Nabholz, Sylvain S. Santoni, Laure Sauné, Morgane Ardisson, Nathalie N. Chantret, Christopher Sauvage, James Tregear, Cyril Jourda, David Pot, Yves Vigouroux, Hana Chair, Nora Scarcelli, Claire Billot, Nabila Yahiaoui, Roberto Bacilieri, Bouchaib Khadari, Michel Boccara, Adeline Barnaud, Jean-Pierre Péros, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin, Manuel Ruiz
article
Molecular Ecology Resources, 2017, 17 (3), pp.565-580. ⟨10.1111/1755-0998.12587⟩
resume
A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives The International Center for Tropical Agriculture (CIAT) believes that open access contributes to its mission of reducing hunger and poverty, and improving human nutrition in the tropics through research aimed at increasing the eco-efficiency of agriculture. CIAT is committed to creating and sharing knowledge and information openly and globally. We do this through collaborative research as well as through the open sharing of our data, tools, and publications.. 2016. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01930391/file/A%20large%20set%20of%2026%20new%20reference%20transcriptomes%20dedicated%20to%20comparative%20population%20genomics%20in%20crops%20and%20wild%20relatives-MANUSCRIPT.pdf BibTex
titre
Nucleotide diversity in the two co-resident genomes of allopolyploid cotton
auteur
Corrinne E. Grover, Joseph P. Gallagher, Emmanuel Szadkowski, Justin T. Page, Michael A. Gore, Joshua A. Udall, Jonathan F. Wendel
article
Plant Systematics and Evolution, 2017, 303 (8), pp.1-22. ⟨10.1007/s00606-017-1411-1⟩
resume
Genetic diversity within and among populations lies at the heart of evolution. Unraveling the extent to which each intrinsic or extrinsic factor determines levels of diversity among genes, populations, and species is challenging, given the difficulty of isolating any single potentially important variable from all others. Allopolyploid species provide an opportunity to disentangle external and intrinsic factors, as the two (or more) homoeologous genomes co-occur in the same nucleus, often exhibiting high collinearity along homoeologous chromosomes. Here we evaluate the pace of molecular evolution and intraspecific, intragenomic diversity in two species of allopolyploid Gossypium, G. hirsutum and G. barbadense, using several hundred genes sequenced from multiple accessions of each species. Genic diversity in both species is low, having been influenced both by the polyploid bottleneck and a domestication bottleneck (for cultivated accessions), but with a directional bias in homoeolog diversity favoring the same genome in both allopolyploids. Total diversity is remarkably similar for the two homoeologous genomes overall, but the two copies of many gene pairs have accumulated statistically different diversity levels, and in a biased fashion with respect to genome. Domesticated accessions show reduced diversity in both genomes, as expected, but with a much greater reduction in one of the two homoeologous genomes. Furthermore, this biased reduction affects opposite homoeologous genomes in the two species. Interspecific introgression has played a role in shaping diversity within each species. Introgression was only detected for certain accessions, and only from G. barbadense into G. hirsutum in one of the two co-resident genomes.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Molecular and biological characterization of two potyviruses infecting lettuce in southeastern France
auteur
Cecile Desbiez, Alexandra Schoeny, Brigitte Maisonneuve, Karine Berthier, Isabelle Bornard, Charlotte Chandeysson, Frédéric Fabre, Gregory Girardot, Patrick Gognalons, Hervé Lecoq, Hervé Lot, Pauline Millot, Karine Nozeran, Vincent Simon, Mark Tepfer, Eric Verdin, Catherine Wipf-Scheibel, Benoît Moury
article
Plant Pathology, 2017, 66 (6), pp.970-979. ⟨10.1111/ppa.12651⟩
resume
Several potyviruses affect lettuce (Lactuca sativa) and chicory (Cichorium spp.) crops worldwide and are important constraints for production because of the direct losses that they induce and/or because of their seed transmission. Here, the molecular and biological properties are described of two potyviruses that were recently isolated from lettuce plants showing mosaic or strong necrotic symptoms in an experimental field in southeastern France. The first potyvirus belongs to the species Endive necrotic mosaic virus and is present in a large number of wild plant species, especially Tragopogon pratensis. It is unable to infect lettuce cultivars with a resistance to Turnip mosaic virus that is present in many European cultivars and probably conferred by the Tu gene. The second potyvirus belongs to the tentative species lettuce Italian necrotic virus and was not observed in wild plants. It infected all tested lettuce cultivars. Wild accessions of Lactuca serriola, Lactuca saligna, Lactuca virosa and Lactuca perennis were identified as resistant to one or the other potyvirus and could be used for resistance breeding in lettuce. No resistance against these two potyviruses was observed in the tested Cichorium endivia cultivars. In contrast, all tested Cichorium intybus cultivars or accessions were resistant.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01533923/file/A%20d%C3%A9poser%20sous%20HAL.pdf BibTex
titre
Evolutionary forces affecting synonymous variations in plant genomes
auteur
Yves Clément, Sarah Gallien, Yan Holtz, Félix Homa, Stéphanie Pointet, Sandy Contreras, Benoit Nabholz, François Sabot, Laure Saune, Morgane Ardisson, Roberto Bacilieri, Guillaume Besnard, Angélique Berger, Céline Cardi, Fabien de Bellis, Olivier Fouet, Cyril Jourda, Bouchaib Khadari, Claire Lanaud, Thierry Leroy, David Pot, Christopher Sauvage, Nora Scarcelli, James Tregear, Yves Vigouroux, Nabila Yahiaoui, Manuel Ruiz, Sylvain Santoni, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin
article
PLoS Genetics, 2017, 13 (5), pp.e1006799. ⟨10.1371/journal.pgen.1006799⟩
resume
Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01608613/file/pgen.1006799.pdf BibTex
titre
Spatial and temporal pattern analyses of Esca grapevine disease in vineyards in France
auteur
Shuxian Li, Florent Bonneu, Joel Chadoeuf, Delphine Deshors-Picart, Anne Gégout Petit, Lucia Guérin-Dubrana
article
Phytopathology, 2017, 107 (1), pp.59-69. ⟨10.1094/PHYTO-07-15-0154-R⟩
resume
To assess the capacity of esca to spread within vineyards of the Bordeaux region, over 8 years of annual records, containing between 1,200 and 2,300 contiguous Cabernet Sauvignon vines from 15 mature vineyards, were used for spatial statistical analyses. A group of non-parametric tests, based on join count statistics and on permutation methods, was developed to characterize the spatial structure of esca-symptomatic vines in terms of spread in any direction or within-row only. Among vineyards, a large range of spatial patterns, from random to strongly structured, associated with various prevalence rates that increased over time, were observed. In four vineyards, the complex esca distribution pattern indicated different levels of clustering. By contrast, in other vineyards, only small clusters of two adjacent symptomatic vines were observed, and they were localized along rows, without enlargement over time, except in one vineyard. An analysis of spatial dependence between previously- and newly-symptomatic vines within k-order neighborhoods (k = 1 to 5), showed, for 5 of the 15 vineyards, that the newly-symptomatic vines were located close to previously-infected vines, without a favored orientation or neighbor order. All the results together suggested a limited potential for secondary local spread from neighboring symptomatic vine.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Towards the Use of Biochemical Indicators in the Raw Fruit for Improved Texture of Pasteurized Apricots
auteur
Albert Ribas, Barbara Gouble, Sylvie Bureau, Jean Francois Maingonnat, Jean Marc Audergon, Catherine M.G.C. Renard
article
Food and Bioprocess Technology, 2017, 10 (4), pp.1-12. ⟨10.1007/s11947-016-1850-7⟩
resume
Quality of canned apricots is seriously compromised by the loss of their flesh firmness during pasteurization. This work conducted a comprehensive characterization of the biochemical properties of raw apricots, as well as of the tissue softening during pasteurization using a multimethodology approach. Biochemical and textural results were analyzed to seek possible correlations, with the aim to elucidate which properties could be used as indicators in raw fruit for obtaining pasteurized products with better texture. There were large effects of cultivar, ripening stage, and intra-fruit zone on the biochemical and textural properties of apricots. The titratable acidity, amongst ethylene production, soluble solid content, and pectinolytic enzyme activities, was the biochemical property that correlated more robustly to the loss of texture. It had significant correlation coefficients of −0.9 and 0.5 with firmness of pasteurized fruit and loss of firmness, respectively. We propose titratable acidity to be used as indicator for raw material selection and/or to be modulated during apricot food processing.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01424786/file/1-166%20FABT%20%282017%29_%7BAB885B1F-6D33-43CD-AAB8-BA27137F53E0%7D.pdf BibTex
titre
Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study
auteur
Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Julien Bonnet, Laurent Grivet, Mathilde Causse
article
TAG Theoretical and Applied Genetics, 2017, 130 (5), pp.875-889. ⟨10.1007/s00122-017-2857-9⟩
resume
A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A kinetic model of sugar metabolism in peach fruit allows the exploration of genetic variability
auteur
Elsa Desnoues, Michel Génard, Bénédicte Quilot-Turion, Valentina Baldazzi
article
Acta Horticulturae, 2017, 1182, pp.169-176. ⟨10.17660/ActaHortic.2017.1182.20⟩
resume
The organoleptic properties of peach, as fruit in general, largely depend on the accumulated sugars and acids. From sucrose, glucose and fructose, main sugars found in peach, fructose is the sweetest one. While commercial peach has equivalent fructose and glucose concentration, some wild or ornamental accessions display an imbalanced fructose-to-glucose ratio with a very low fructose concentration. In addition to genetic control, sugar metabolism is driven by fruit development and environment. The relative role of biochemical strengths and gene regulation in the elaboration of fruit sugar content at maturity is not well known. As the complex interplay between synthesis, degradation, transport and storage held in the cell is difficult to formulate, mathematical modelling appears to be an effective tool to challenge the issue. Thus, on the basis of profiling data, we developed a kinetic model of sugar metabolism in peach fruit. It simulates the evolution of sucrose, glucose, fructose and sorbitol concentrations during fruit development. A particular attention has been given to represent cellular compartmentation (cytosol and vacuole) in order to modulate the availability of the metabolites for the enzymatic reactions. The model was parameterized for different peach genotypes including a particular phenotype with low fructose-to-glucose ratio. It described well genetic variability. It was then used to further explore the system including the mechanisms driving genotypic differences.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01662057/file/Desnoues_Genard_Acta_Hortimodel_revised.pdf BibTex
titre
Is monodehydroascorbate reductase activity in leaf tissue critical for the maintenance of yield in tomato?
auteur
Vincent Truffault, Gisele Riqueau, Cecile Garchery, Hélène Gautier, Rebecca Stevens
article
Journal of Plant Physiology, 2017, 222, pp.1-28. ⟨10.1016/j.jplph.2017.12.012⟩
resume
Ascorbate redox metabolism and growth have been shown to be linked and related to the activity of enzymes that produce or remove the radical monodehydroascorbate, the semi-oxidized form of ascorbate (ascorbate oxidase or peroxidase and monodehydroascorbate reductase respectively). Previous work in cherry tomato has revealed correlations between monodehydroascorbate reductase and ascorbate oxidase activity and fruit yield: decreased whole plant MDHAR activity decreases yield while decreased whole plant ascorbate oxidase activity increases yield under unfavourable environmental conditions. We aimed to investigate if similar effects on yield are obtained in a large-fruited variety of tomato, Moneymaker. Furthermore we wished to establish whether previously observed effects on yield in cherry tomato following changes in whole plant enzyme activity could be reproduced by reducing MDHAR activity in fruit only by using a fruit-specific promoter in cherry tomato (West Virginia 106). In Moneymaker, RNAi lines for monodehydroascorbate reductase did not show significant yield decrease compared to control lines when plants were grown under optimal or non-optimal conditions of carbon stress generated by mature leaf removal. In addition, we show that a decrease in monodehydroascorbate reductase activity in fruit of cherry tomato had no effect on yield compared to a reduction in whole-plant monodehydroascorbate reductase activity: we therefore show that whole plant MDHAR activity is necessary to maintain yield in cherry tomato, suggesting that the carbon source in autotrophic tissue is more important than fruit sink activity. The present data also revealed differences between cherry and large fruited tomato that could be linked to a source of genetic variability in the response to monodehydroascorbate metabolism in tomato: maybe the domestication of tomato towards large-fruited lines could have affected the importance of MDHAR in yield maintenance.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01669403/file/truffault-_1.pdf BibTex
titre
A kinetic model of sugar metabolism allows the simulation of sugar concentrations and their genetic variability during peach fruit growth
auteur
Elsa Desnoues, Michel Génard, Bénédicte Quilot-Turion, Valentina Baldazzi
article
Acta Horticulturae, 2017, 1160, pp.361-366. ⟨10.17660/ActaHortic.2017.1160.52⟩
resume
Fruit taste is largely affected by the concentration of soluble sugars. Moreover sugar metabolism is central because it feeds respiration and acid metabolism via glycolysis and provides carbon for synthesis of structural compounds (cell wall). Concentrations of sugars in fruit vary according to fruit development, environment and genotype. In general, weak correlations were found between the variations of sugar concentrations and the capacities of enzymes directly related to the synthesis or degradation of sugars. This suggests that the relationships between enzyme capacities and metabolites are not direct and difficult to assess with conventional statistics. Thus a kinetic model of sugar metabolism has been developed to simulate the concentrations of sugars (sucrose, glucose, fructose and sorbitol) during fruit development in peach, taking advantage of recent profiling data. Cellular compartmentation (cytosol and vacuole) is explicitly described and data-driven enzyme capacities are used to parameterize the equations. The model correctly accounts for genotypic variability observed in four genotypes derived from an interspecific cross. The novelty of the present model is the representation of the mechanisms at the molecular level, which provides important information on sugar metabolism functioning and cues on the determinants of phenotypic differences.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Ascorbate degradation in tomato leads to accumulation of oxalate, threonate and oxalyl threonate
auteur
Vincent Truffault, Stephen C. Fry, Rebecca Stevens, Hélène Gautier
article
The Plant Journal, 2017, 89 (5), pp.996 - 1008. ⟨10.1111/tpj.13439⟩
resume
Ascorbate content in plants is controlled by its synthesis from carbohydrates, recycling of the oxidized forms and degradation. Of these pathways, ascorbate degradation is the least studied and represents a lack of knowledge that could impair improvement of ascorbate content in fruits and vegetables as degradation is non-reversible and leads to a depletion of the ascorbate pool. The present study revealed the nature of degradation products using [C-14] ascorbate labelling in tomato, a model plant for fleshy fruits; oxalate and threonate are accumulated in leaves, as is oxalyl threonate. Carboxypentonates coming from diketogulonate degradation were detected in relatively insoluble (cell wall-rich) leaf material. No [C-14] tartaric acid was found in tomato leaves. Ascorbate degradation was stimulated by darkness, and the degradation rate was evaluated at 63% of the ascorbate pool per day, a percentage that was constant and independent of the initial ascorbate or dehydroascorbic acid concentration over periods of 24 h or more. Furthermore, degradation could be partially affected by the ascorbate recycling pathway, as lines under-expressing monodehydroascorbate reductase showed a slight decrease in degradation product accumulation.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Integrated QTL detection for key breeding traits in multiple peach progenies
auteur
José R. Hernández Mora, Diego Micheletti, Marco Bink, Eric van de Weg, Celia Cantín, Nelson Nazzicari, Andrea Caprera, Maria Teresa Dettori, Sabrina Micali, Elisa Banchi, José Antonio Campoy-Corbalan, Elisabeth Dirlewanger, Patrick Lambert, Thierry Pascal, Michela Troggio, Daniele Bassi, Laura Rossini, Ignazio Verde, Bénédicte Quilot-Turion, Francois Laurens, Pere Arus, Maria José Aranzana
article
BMC Genomics, 2017, 18 (1), ⟨10.1186/s12864-017-3783-6⟩
resume
Background: Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. Results: Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value. Conclusions: The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01533858/file/integrated_%7B185EA729-19D4-4999-ABED-6EDC8FC83FEA%7D.pdf BibTex
titre
Eggplant Resistance to the Ralstonia solanacearum Species Complex Involves Both Broad-Spectrum and Strain-Specific Quantitative Trait Loci
auteur
Sylvia Salgon, Cyril Jourda, Christopher Sauvage, Marie-Christine Brand-Daunay, Bernard Reynaud, Emmanuel Wicker, Jacques Dintinger
article
Frontiers in Plant Science, 2017, 8, ⟨10.3389/fpls.2017.00828⟩
resume
Bacterial wilt (BW) is a major disease of solanaceous crops caused by the Ralstonia solanacearum species complex (RSSC). Strains are grouped into five phylotypes (I, IIA, IIB, III, and IV). Varietal resistance is the most sustainable strategy for managing BW. Nevertheless, breeding to improve cultivar resistance has been limited by the pathogen's extensive genetic diversity. Identifying the genetic bases of specific and non-specific resistance is a prerequisite to breed improvement. A major gene (ERs1) was previously mapped in eggplant (Solanum melongena L.) using an intraspecific population of recombinant inbred lines derived from the cross of susceptible MM738 (S) x resistant AG91-25 (R). ERs1 was originally found to control three strains from phylotype I, while being totally ineffective against a virulent strain from the same phylotype. We tested this population against four additional RSSC strains, representing phylotypes I, IIA, IIB, and III in order to clarify the action spectrum of ERs1. We recorded wilting symptoms and bacterial stem colonization under controlled artificial inoculation. We constructed a high-density genetic map of the population using single nucleotide polymorphisms (SNPs) developed from genotyping-by-sequencing and added 168 molecular markers [amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and sequence-related amplified polymorphisms (SRAPs)] developed previously. The new linkage map based on a total of 1,035 markers was anchored on eggplant, tomato, and potato genomes. Quantitative trait locus (QTL) mapping for resistance against a total of eight RSSC strains resulted in the detection of one major phylotype-specific QTL and two broad-spectrum QTLs. The major QTL, which specifically controls three phylotype I strains, was located at the bottom of chromosome 9 and corresponded to the previously identified major gene ERs1. Five candidate R-genes were underlying this QTL, with different alleles between the parents. The two other QTLs detected on chromosomes 2 and 5 were found to be associated with partial resistance to strains of phylotypes I, IIA, III and strains of phylotypes IIA and III, respectively. Markers closely linked to these three QTLs will be crucial for breeding eggplant with broad-spectrum resistance to BW. Furthermore, our study provides an important contribution to the molecular characterization of ERs1, which was initially considered to be a major resistance gene.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01595097/file/eggplant_%7B1A48BBAE-5477-4DA9-8A5B-17E48E966AFE%7D.pdf BibTex
titre
Réalités et perspectives de l’écologisation en arboriculture fruitière - Pour une approche intégrée à partir du cas des vergers de pêchers et d’abricotiers en Rhône-Alpes
auteur
Claire Lamine, Sylvaine Simon, Jean Marc Audergon, Servane Penvern, Guy Clauzel, Lucile Garçon, Samuel Buis, Jean Pluvinage
article
Innovations Agronomiques, 2017, 59, pp.103-118. ⟨10.15454/1.5138445077696033E12⟩
resume
The Prunus project has explored the issue of sustainable orchards (re)design, through an integrative approach articulating the different dimensions of varietal choice, pest management strategies, and larger evolutions within the agrifood system (including not only the economic actors but also extension, research, public policies and consumers). It brought together sociologists, economists, agronomists and geneticists, as well as diverse stakeholders in a socio-historical analysis, farm surveys, and multi-actors workshops for the co-construction of varietal ideotypes. Our analyses show the impact of the constraints set by retailers and intermediaries, in a context of production calendar extension, on the innovation model (fruit ability to be transported and stored and fruit visual aspect), to the expense of environmental and farm viability criteria. Farm surveys show a large variability of practices observed in orchards producing similar levels of yield and suggest that a substantive reduction in pesticide use can be achieved in apricot production. New techniques but also references and exchange arenas should be developed to achieve this. Regarding varietal innovation and cultivars conception, we show that we need to develop multi-criteria approaches. Finally we how how multi-actors approaches help discussing the constraints and criteria of the diverse components of the agrifood system in an ecolologisation perspective
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01675819/file/2017_Lamine_Innovations%20Agronomiques.pdf BibTex
titre
Résistance et agroécologie, des fleurs pour ‘Margot’ le melon
auteur
Alexandra Schoeny, Nathalie Boissot
article
Jardins de France, 2017, 647, pp.71-73
resume
L’agroécologie a le vent en poupe et ses principes perfusent dans toutes les strates de notre société : agriculture, espaces verts de nos villes et villages, jardins des particuliers, et même industrie agroalimentaire où elle devient un argument marketing. Le melon charentais bénéficie de cette démarche.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
eIF4E Resistance: Natural Variation Should Guide Gene Editing
auteur
Anna Bastet, Christophe Robaglia, Jean-Luc Gallois
article
Trends in Plant Science, 2017, 22 (5), pp.411-419. ⟨10.1016/j.tplants.2017.01.008⟩
resume
eIF4E translation initiation factors have emerged as major susceptibility factors for RNA viruses. Natural eIF4E-based resistance alleles are found in many species and are mostly variants that maintain the translation function of the protein. eIF4E genes represent major targets for engineering viral resistance, and gene-editing technologies can be used to make up for the lack of natural resistance alleles in some crops, often by knocking out eIF4E susceptibility factors. However, we report here how redundancy among eIF4E genes can restrict the efficient use of knockout alleles in breeding. We therefore discuss how gene-editing technologies can be used to design de novo functional alleles, using knowledge about the natural evolution of eIF4E genes in different species, to drive resistance to viruses without affecting plant physiology.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies
auteur
Filippo Biscarini, Nelson Nazzicari, Marco Bink, Pere Arús, Maria José Aranzana, Ignazio Verde, Sabrina Micali, Thierry Pascal, Bénédicte Quilot-Turion, Patrick Lambert, Cassia da Silva Linge, Igor Pacheco, Daniele Bassi, Alessandra Stella, Laura Rossini
article
BMC Genomics, 2017, 18 (1), ⟨10.1186/s12864-017-3781-8⟩
resume
BACKGROUND: Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and highly reliable genotyping, preparing the ground for GS in peach. RESULTS: A repeatability model (multiple records per individual plant) for genome-enabled predictions in eleven European peach populations is presented. The analysis included 1147 individuals derived from both commercial and non-commercial peach or peach-related accessions. Considered traits were average fruit weight (FW), sugar content (SC) and titratable acidity (TA). Plants were genotyped with the 9K IPSC array, grown in three countries (France, Italy, Spain) and phenotyped for 3-5 years. An analysis of imputation accuracy of missing genotypic data was conducted using the software Beagle, showing that two of the eleven populations were highly sensitive to increasing levels of missing data. The regression model produced, for each trait and each population, estimates of heritability (FW:0.35, SC:0.48, TA:0.53, on average) and repeatability (FW:0.56, SC:0.63, TA:0.62, on average). Predictive ability was estimated in a five-fold cross validation scheme within population as the correlation of true and predicted phenotypes. Results differed by populations and traits, but predictive abilities were in general high (FW:0.60, SC:0.72, TA:0.65, on average). CONCLUSIONS: This study assessed the feasibility of Genomic Selection in peach for highly polygenic traits linked to yield and fruit quality. The accuracy of imputing missing genotypes was as high as 96%, and the genomic predictive ability was on average 0.65, but could be as high as 0.84 for fruit weight or 0.83 for titratable acidity. The estimated repeatability may prove very useful in the management of the typical long cycles involved in peach productions. All together, these results are very promising for the application of genomic selection to peach breeding programmes.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01602738/file/genome_1.pdf BibTex
titre
The timeline of corona formation around silica nanocarriers highlights the role of the protein interactome
auteur
Cedric Pisani, Jean-Charles Gaillard, Michaël Odorico, Jeff Nyalosaso, Clarence Charnay, Yannick Guari, Joel Chopineau, Jean-Marie Devoisselle, J. Armengaud, Odette Prat
article
Nanoscale, 2017, 9 (5), pp.1840-1851. ⟨10.1039/C6NR04765C⟩
resume
Magnetic mesoporous silica nanoparticles (M-MSNs) represent promising targeting tools for theranostics. Engineering the interaction of nanoparticles (NPs) with biological systems requires an understanding of protein corona formation around the nanoparticles as this drives the biological fate of nanocarriers. We investigated the behavior of proteins in contact with M-MSNs by high-throughput comparative proteomics, using human and bovine sera as biological fluids, in order to assess the adsorption dynamics of proteins in these media. Using system biology tools, and especially protein-protein interaction databases, we demonstrated how the protein network builds up within the corona over the course of the experiment. Based on these results, we introduce and discuss the role of the "corona interactome" as an important factor influencing protein corona evolution. The concept of the "corona interactome" is an original methodology which could be generalized to all NP candidates. Based on this, pre-coating nanocarriers with specific proteins presenting minimal interactions with opsonins might provide them with properties such as stealth.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Impact of Vat resistance in melon on viral epidemics and genetic structure of virus populations
auteur
Alexandra Schoeny, Cecile Desbiez, Pauline Millot, Catherine Wipf-Scheibel, Karine Nozeran, Patrick Gognalons, Hervé Lecoq, Nathalie Boissot
article
Virus Research, 2017, 241, pp.105-115. ⟨10.1016/j.virusres.2017.05.024⟩
resume
Cultivar choice is at the heart of cropping systems and resistant cultivars should be at the heart of disease management strategies whenever available. They are the easiest, most efficient and environmentally friendly way of combating viral diseases at the farm level. Among the melon genetic resources, Vat is a unique gene conferring resistance to both the melon aphid Aphis gossypii and the viruses it carries. The ‘virus side’ of this pleiotropic phenotype is seldom regarded as an asset for virus control. Indeed, the effect of Vat on virus epidemics in the field is expected to vary according to the composition of aphid populations in the environment and long-term studies are needed to draw a correct trend. Therefore, the first objective of the study was to re-evaluate the potential of Vat to reduce viral diseases in melon crops. The second objective was to investigate the potential of Vat to exert a selection pressure on virus populations. We monitored the epidemics of Cucurbit aphid-borne yellows virus (CABYV), Cucumber mosaic virus (CMV), Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV) in two melon lines having a common genetic background, a resistant line (R) and a susceptible line (S), in eight field trials conducted in southeastern France between 2011 and 2015. Vat had limited impact if any on WMV epidemics probably because A. gossypii is not the main vector of WMV in the field, but a favorable impact on CMV, yet of variable intensity probably related to the importance of A. gossypii in the total aphid population. Vat had a significant impact on CABYV epidemics with mean incidence reduction exceeding 50% in some trials. There was no effect of Vat on the structure of virus populations, both for the non-persistent WMV transmitted by numerous aphid species and for the persistent CABYV transmitted predominantly by A. gossypii.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01535203/file/2017_Schoeny_Virus%20Research_postprint_2.pdf BibTex
titre
Mapping of new resistance (Vr2, Rm1) and ornamental (Di2, pl) Mendelian trait loci in peach
auteur
Thierry Pascal, Romain Aberlenc, Carole Confolent, Mathilde Hoerter, Elodie Lecerf, Christophe Tuero, Patrick Lambert
article
Euphytica, 2017, 213 (6), ⟨10.1007/s10681-017-1921-5⟩
resume
Peach powdery mildew is one of the major diseases of the peach. Various sources of resistance to PPM have thus been identified, including the single dominant locus Vr2 carried by the peach rootstock 'Pamirskij 5'. To map Vr2, a linkage map based on microsatellite markers was constructed from the F2 progeny (WP2) derived from the cross 'Weeping Flower Peach' 9 'Pamirskij 5'. Self-pollinations of the parents were also performed. Under greenhouse conditions, all progenies were scored after artificial inoculations in two classes of reactions to PPM (resistant/susceptible). In addition to Vr2, WP2 segregated for three other traits from 'Weeping Flower Peach': Rm1 for green peach aphid resistance, Di2 for double-flower and pl for weeping-growth habit. With their genomic locations unknown or under-documented, all were phenotyped as Mendelian characters and mapped: Vr2 mapped at the top of LG8, at 3.3 cM, close to the CPSCT018 marker; Rm1 mapped at the bottom of LG1, at a position of 116.5 cM, cosegregating with the UDAp-467 marker and in the same region as Rm2 from 'Rubira'(R); Di2 mapped at 28.8 cM on LG6, close to the MA027a marker; and pl mapped at 44.1 cM on LG3 between the MA039a and SSRLG3_16m46 markers. Furthermore, this study revealed, for the first time, a pseudo-linkage between two traits of the peach: Vr2 and the Gr locus, which controls the red/green color of foliage. The present work therefore constitutes a significant preliminary step for implementing marker-assisted selection for the four major traits targeted in this study.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement
auteur
Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Vincent Segura, Aniko Kende, Jules Beekwilder, Katarina Cankar, Jean-Luc Gallois, Justine Gricourt, Julien Bonnet, Charles Baxter, Laurent Grivet, Mathilde Causse
article
New Phytologist, 2017, 215 (2), pp.624-641. ⟨10.1111/nph.14615⟩
resume
Plant metabolites are important to world food security due to their roles in crop yield and nutritional quality. Here we report the metabolic profile of 300 tomato accessions (Solanum lycopersicum and related wild species) by quantifying 60 primary and secondary metabolites, including volatile organic compounds, over a period of 2 yr. Metabolite content and genetic inheritance of metabolites varied broadly, both within and between different genetic groups. Using genotype information gained from 10 000 single nucleotide polymorphism markers, we performed a metabolite genome-wide association mapping (GWAS) study. We identified 79 associations influencing 13 primary and 19 secondary metabolites with large effects at high resolution. Four genome regions were detected, highlighting clusters of associations controlling the variation of several metabolites. Local linkage disequilibrium analysis and allele mining identified possible candidate genes which may modulate the content of metabolites that are of significant importance for human diet and fruit consumption. We precisely characterized two associations involved in fruit acidity and phenylpropanoid volatile production. Taken together, this study reveals complex and distinct metabolite regulation in tomato subspecies and demonstrates that GWAS is a powerful tool for gene-metabolite annotation and identification, pathways elucidation, and further crop improvement.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Impact of cooking on apricot texture as a function of cultivar and maturity
auteur
Jamal Ayour, Barbara Gouble, Patrice Reling, Albert Ribas, Jean Marc Audergon, Jean Francois Maingonnat, Mohamed Benichou, Catherine M.G.C. Renard
article
LWT - Food Science and Technology, 2017, 85 (Part B), pp.385-389. ⟨10.1016/j.lwt.2016.10.040⟩
resume
The rapid loss of fruit firmness is a qualitative decisive factor for characterizing apricot (Prunus armeniaca L.) use (fresh or processed) and commercialization pathways (short or storage). To better understand the texture variability in apricot, we studied the impact of a heat treatment as a function of fruit harvest stage on a large range of cultivars. Eighteen apricot cultivars were characterized at two maturity stages before and after cooking (85 °C in light syrup). A compression test allowed sorting the fruits to obtain homogeneous batches. Kramer shear tests provided global firmness of cooked fruits and puncture tests were performed on the median equatorial area of apricot flesh for fresh and cooked fruits. Among the registered variables, the apricot texture expressed by the “Work to limit” integrates the global evolution and allows a good discrimination of the ripening effect. The texture data was used to classify the varieties according to their firmness and suitability for industrial processing. Thus Vertige, Candide and Gaterie, followed by Orangered and Bergarouge, have been found as the most suitable cultivars for industrial processes
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01608395/file/Audergon%20Food%20Science%20and%20Technology%202016%20in%20press_1.pdf BibTex
titre
Loss of AvrSr50 by somatic exchange in stem rust leads to virulence for Sr50 resistance in wheat
auteur
Jiapeng Chen, Narayana Upadhyaya, Diana Ortiz-Vallejo, Jana Sperschneider, Feng Li, Clement Bouton, Susan Breen, Chongmei Dong, Bo Xu, Xiaoxiao Zhang, Rohit Mago, Kim Newell, Xiaodi Xia, Maud Bernoux, Jennifer Taylor, Brian Steffenson, Yue Jin, Peng Zhang, Kostya Kanyuka, Melania Figueroa, Jeffrey Ellis, Robert Park, Peter Dodds
article
Science, 2017, 358 (6370), pp.1607-1610. ⟨10.1126/science.aao4810⟩
resume
The fungal pathogen Ug99 (named for its identification in Uganda in 1999) threatens wheat crops worldwide. Ug99 can kill entire fields of wheat and is undeterred by many of the disease-resistance genes that otherwise protect wheat crops. Two papers describe two peptides secreted by the fungus as it attacks the wheat (see the Perspective by Moscou and van Esse). Chen et al. show that fungal AvrSr50 binds to the plant's immune receptor Sr50, and Salcedo et al. show that fungal AvrSr35 binds to Sr35. Successful binding activates the plant's immune defenses. Removing or inactivating these Avr effectors leaves the plant defenseless and susceptible to disease.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04717695/file/Chen%20et%20al%202017.%20Loss%20of%20AvrSr50%20by%20somatic%20exchange%20in%20stem%20rust%20leads%20to%20virulence%20for%20Sr50%20resistance%20in%20wheat.%20Final%20version.pdf BibTex
titre
Population structure and core collection construction of apricot (Prunus armeniaca L.) in north Africa based on microsatellite markers
auteur
Hedia Bourguiba, Mohamed-Amine Batnini, Lamia Krichen, Neila Trifi-Farah, Jean Marc Audergon
article
Plant Genetic Resources, 2017, 15 (1), pp.21-28. ⟨10.1017/S1479262115000313⟩
resume
North Africa enclosed original apricot genetic resources with the cohabitation of grafting and seed-propagated accessions. In this study, we assessed the genetic diversity and population structure of 183 apricot accessions using 24 microsatellite markers distributed evenly in the Prunus genome. A total of 192 alleles and a high level of gene diversity (0.593) were detected among the whole panel. Genetic structure analysis revealed the presence of four genetic clusters. We also found that both geographical origin and mode of propagation are important factors structuring genetic diversity in apricot species. Results confirmed the presence of gene exchange between the northern and southern countries of the Mediterranean Basin. Subsequently, a core collection of 98 accessions based on M (maximization) strategy showing 99.47% of allele retention ratio was constructed. No significant differences for Shannon’s information index and Nei’s diversity index were observed between the core and entire collections. Our results provide an effective aid for future germplasm preservation and conservation strategies as well as genetic association studies development in relation to phenotypic data
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Domestication rewired gene expression and nucleotide diversity patterns in tomato
auteur
Christopher Sauvage, Andrea Rau, Charlotte Aichholz, Joel Chadoeuf, Gautier Sarah, Manuel Ruiz, Sylvain Santoni, Mathilde Causse, Jacques David, Sylvain Glémin
article
The Plant Journal, 2017, 91 (4), pp.631-645. ⟨10.1111/tpj.13592⟩
resume
Plant domestication has led to considerable phenotypic modifications from wild species to modern varieties. However, although changes in key traits have been well documented, less is known about the underlying molecular mechanisms, such as the reduction of molecular diversity or global gene co-expression patterns. In this study, we used a combination of gene expression and population genetics in wild and crop tomato to decipher the footprints of domestication. We found a set of 1,729 differentially expressed genes (DEG) between the two genetic groups, belonging to 17 clusters of co-expressed DEG, suggesting that domestication affected not only individual genes but also regulatory networks. Five co-expression clusters were enriched in functional terms involving carbohydrate metabolism or epigenetic regulation of gene expression. We detected differences in nucleotide diversity between the crop and wild groups specific to DEG. Our study provides an extensive profiling of the rewiring of gene co-expression induced by the domestication syndrome in one of the main crop species.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01594937/file/domestication_1.pdf BibTex
titre
Effectiveness of quantitative resistance conferred by the genetic background of pepper in the control of root-knot nematodes and influence onto durability of Me1 and Me3 resistant genes in greenhouse conditions
auteur
Fulgencio Sanchez-Solana, Caridad Ros, María del Mar Guerrero, Victoriano Martínez, Carmen María Lacasa, Ana Hernández, Alain Palloix, Alfredo Lacasa
article
Plant Breeding, 2017, 136 (5), pp.759-766. ⟨10.1111/pbr.12517⟩
resume
n pepper (Capsicum annuum), the major genes (R-genes) Me1 and Me3 confer resistance against root-knot nematodes (Meloidogyne spp.). The combination of R-genes and quantitative resistance factors in the same genotype is considered a good breeding strategy for increasing the durability of R-genes. To ascertain this hypothesis, five pepper inbred lines, differing in their quantitative resistance level, were combined with Me1 or Me3 genes in F 1 hybrids. The resistance of inbred lines and F1 hybrids was evaluated in a greenhouse with soil naturally infected by M. incognita in two successive growing years. In both years, lines carrying Me3 were less infected by the nematode when combined with quantitative resistance. An increase in nematode infection was observed in the second growing year in lines carrying Me1 or Me3, independently of quantitative resistance. The infection level recorded in inbred lines without R-genes was similar in both years. The effectiveness of quantitative resistance controlling M. incognita is confirmed in greenhouse conditions,although the durability of Me1 and Me3 when combined with quantitative resistancefactors was not seen to increase.
typdoc
Journal articles
Accès au bibtex
BibTex

2016

Journal articles

titre
La diversité génétique des plantes cultivées à l'heure de l'informatique génétique à haut débit: génomique comparative de la domestication
auteur
Jacques David, Sylvain Glémin, Gautier Sarah, Benoit Nabholz, Francois Sabot, Yan Holtz, Félix Homa, Stéphanie Pointet, Sandy Contreras, Laure Sauné, Morgane Ardisson, Roberto Bacilieri, Bouchaib Khadari, Claire Lanaud, David Pot, Christopher Sauvage, Nora Scarcelli, James Tregear, Yves Vigouroux, Nabila Yahiaoui, Manuel Ruiz, Sylvain Santoni, Jean-Pierre Labouisse, Jean-Louis Pham
article
Sélectionneur Français, 2016, 67, pp.3-13
resume
La diversité génétique des plantes cultivées à l'heure de l'informatique génétique à haut débit: génomique comparative de la domestication
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01607736/file/LSF-2016.pdf BibTex
titre
The battle for survival between viruses and their host plants
auteur
Adnane Boualem, Catherine Dogimont, Abdelhafid Bendahmane
article
Current Opinion in Virology, 2016, 17, pp.32-38. ⟨10.1016/j.coviro.2015.12.001⟩
resume
Evolution has equipped plants with defense mechanisms to counterattack virus infections. However, some viruses have acquired the capacity to escape these defense barriers. In their combats, plants use mechanisms such as antiviral RNA silencing that viruses fight against using silencing-repressors. Plants could also resist by mutating a host factor required by the virus to complete a particular step of its infectious cycle. Another successful mechanism of resistance is the hypersensitive response, where plants engineer R genes that recognize specifically their assailants. The recognition is followed by the triggering of a broad spectrum resistance. New understanding of such resistance mechanisms will probably helps to propose new means to enhance plant resistance against viruses.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02889521/file/Revue.Virus.pdf BibTex
titre
Characterisation of Shigella Spa33 and Thermotoga FliM/N reveals a new model for C-ring assembly in T3SS
auteur
Melanie Mcdowell, Julien Marcoux, Gareth Mcvicker, Steven Johnson, Yu Hang Fong, Rebecca Stevens, Lesley Bowman, Matteo Degiacomi, Jun Yan, Adam Wise, Miriam Friede, Justin Benesch, Janet Deane, Christoph Tang, Carol Robinson, Susan Lea
article
Molecular Microbiology, 2016, 99 (4), pp.749-766. ⟨10.1111/mmi.13267⟩
resume
Flagellar type III secretion systems (T3SS) contain an essential cytoplasmic-ring (C-ring) largely composed of two proteins FliM and FliN, whereas an analogous substructure for the closely related non-flagellar (NF) T3SS has not been observed in situ. We show that the spa33 gene encoding the putative NF-T3SS C-ring component in Shigella flexneri is alternatively translated to produce both full-length (Spa33-FL) and a short variant (Spa33-C), with both required for secretion. They associate in a 1:2 complex (Spa33-FL/C 2) that further oligomerises into elongated arrays in vitro. The structure of Spa33-C 2 and identification of an unexpected intramolecular pseudodimer in Spa33-FL reveal a molecular model for their higher order assembly within NF-T3SS. Spa33-FL and Spa33-C are identified as functional counterparts of a FliM-FliN fusion and free FliN respectively. Furthermore, we show that Thermotoga maritima FliM and FliN form a 1:3 complex structurally equivalent to Spa33-FL/C 2, allowing us to propose a unified model for C-ring assembly by NF-T3SS and flagellar-T3SS.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02335543/file/MMI-99-749.pdf BibTex
titre
Production et purification rapide d'une Taq polymérase pour les applications routinières de biologie moléculaire
auteur
Jerome Olivares, Bernard Caromel
article
Cahier des Techniques de l'INRA, 2016, 87, 9 p
resume
Cet article présente un protocole simple, rapide et économique de production et de purification d'une enzyme thermostable de type ADN polymérase (Taq polymérase) à destination des manipulations routinières de biologie moléculaire comme la PCR et ses diverses applications.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01605626/file/CT87-Art3-Olivares-Taq_1.pdf BibTex
titre
Sensibilité des variétés de laitue aux pourritures du collet
auteur
François Lecompte, Brigitte Maisonneuve, Philippe C. Nicot
article
Phytoma , 2016, 699, pp.43-47
resume
Contexte - La protection des cultures de laitue contre les maladies fongiques fait appel à des fongicides, même si la sélection variétale prend en compte la principale maladie qu’est le mildiou dû à Bremia lactucae. En revanche, les schémas de sélection n’intègrent pas les pourritures du collet dues à Botrytis cinerea et Sclerotinia spp. (S. sclerotiorum, S. minor), cible d’une part des traitements fongicides. Travail - Dans ce contexte, on a voulu savoir si la sensibilité des variétés actuelles avait évolué par rapport à celles anciennement sur le marché. Une cinquantaine de variétés (surtout de batavia) actuellement disponibles ainsi que trois variétés anciennes ont été testées vis-à-vis de deux souches de B. cinerea et deux souches de S. sclerotiorum, par inoculation artificielle sur feuilles détachées. Résultats - Les résultats ont permis de classer les variétés. Il en ressort que : – la sensibilité à B. cinerea a légèrement (mais significativement) augmenté ; – la sensibilité à S. sclerotiorum a plus fortement augmenté ; – chez les deux variétés anciennes les moins sensibles à S. sclerotiorum, il y a aussi une faible sensibilité à B. cinerea. Ces résultats, à confirmer sur le terrain, montrent une érosion globale de la résistance aux agents de pourriture du collet, mais aussi l’existence des sources de résistances chez la laitue cultivée. Les implications pour la sélection et la protection des laitues sont présentées.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Verticillium chez l'aubergine à travers le projet Vasculeg. Recherche de nouveaux moyens de protection (2ième partie)
auteur
Marie-Christine Brand-Daunay, François Villeneuve, F. Latour, Théophile Théry, Christine Fournier, Patricia Erard
article
Infos CTIFL, 2016, 325, pp.45-59
resume
Aubergine (Solanum melongena L.) is par- ticularly sensitive to soilborne pests and diseases, especially verticillium wilt (Verticil- lium sp.) and gall nematodes (Meloidogyne spp.) in temperate climates. Used by growers for decades, grafting is a solution but there are new problems with it. Therefore new resistances and alternative rootstocks need to be identified, as well as new protective measures to accompany them. From 2011 to 2015, the VASCUleg project had this objec- tive thanks to collaboration between the Ctifl, INRA, regional experimental stations and seed companies. This has resulted in finding new sources of resistance to Verticillium sp., but also combinations with Solanum spp., giving positive results and possible future alternative protection techniques.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01603029/file/Daunay%20Infos-ctifl%202016%2045-59_1.pdf BibTex
titre
Efficiency of genomic selection for tomato fruit quality
auteur
Janejira Duangjit, Mathilde Causse, Christopher Sauvage
article
Molecular Breeding, 2016, 36 (3), pp.on-line. ⟨10.1007/s11032-016-0453-3⟩
resume
Fruit quality is polygenic; each component has variable heritability and is difficult to assess. Genomic selection, which allows the prediction of phenotypes based on the whole-genome genotype, could vastly help to improve fruit quality. The goal of this study is to evaluate the accuracy of genomic selection for several metabolomic and quality traits by cross-validation and to estimate the impact of different factors on its accuracy. We analyzed data from 45 phenotypic traits and genotypic data obtained from a previous study of genetic association on a collection of 163 tomato accessions. We tested the influence of (1) the size of training population, (2) the number and density of molecular markers and (3) individual relatedness on the accuracy of prediction. The prediction accuracy of phenotypic values was largely related to the heritability of the traits. The size of training population increased the accuracy of predictions. Using 122 accessions and 5995 single nucleotide polymorphisms (SNPs) was the optimal condition. The density of markers and their numbers also affected the accuracy of the prediction. Using 2313 SNP markers distributed 0.1 cM or more apart from each other reduced the accuracy of prediction, and no gain in prediction accuracy was found when more markers were used in the model. Additionally, the more accessions were related, the more accurate were the predictions. Finally, the structure of the population negatively affected the prediction accuracy. In conclusion, the results obtained by cross-validation illustrated the effect of several parameters on the accuracy of prediction and revealed the potential of genomic selection in tomato breeding programs.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01285248/file/Duangjit%20et%20al%20Mol%20Breeding%202016_%7B6ABD7090-CF16-4A60-B4A5-A5776C021873%7D.pdf BibTex
titre
L'apport des marqueurs moléculaires et de la génomique pour l'utilisation des ressources génétiques chez la tomate
auteur
Christopher Sauvage, Guillaume Bauchet, Mathilde Causse
article
Sélectionneur Français, 2016, 67, pp.29-40
resume
La tomate est l'un des légumes les plus produits dans le monde et cette espèce est également un ,modèle dans le domaine scientifique pour l'étude du développement du fruit. Au cours des 60 dernières années, de nombreuses campagnes de collecte en Amérique Centrale et du Sud (zone d'origine), mais aussi dans le monde entier, ont permis de conserver plus de 83.000 accessions chez cette espèce. En parallèle, l'apport de la biologie moléculaire au travers du développement de marqueurs moléculaires a permis de cartographier de nombreux QTL pour des caractères d'intérêt tels que la qualité du fruit ou la résistance à des stress biotiques et abiotiques. Depuis 2012, date de la publication du génome séquencé de la tomate, la combinaison de ces importantes ressources génétiques et de la génomique haut-débit permet d'étendre les travaux à l'échelle du génome afin de mieux comprendre sa nature, d'identifier un grand nombre de sites polymorphes mais aussi de revisiter des questions scientifiques, telles que l'histoire évolutive de cette espèce et l'étude de l'architecture génétique de caractères quantitatifs par le biais de nouvelles approches comme la génétique d'association ou la sélection génomique. Les ressources génétiques disponibles chez cette espèce sont primordiales pour la recherche scientifique fondamentale mais aussi pour l'amélioration génétique de cette espèce.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Guara et Tuono: deux noms pour une variété
auteur
Henri Duval, Federico Dicenta
article
Réussir Fruits et Légumes, 2016, 362, pp.44-45
resume
Amande : Une étude par marqueurs moléculaires démontre que Guara, variété autofertile la plus plantée en Espagne, est en fait la variété Tuono originaire des Pouilles en Italie et diffusée depuis 1830.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Abeille domestique: un dépérissement aux multiples causes
auteur
Yves Le Conte, Michel Pitrat
article
Jardins de France, 2016, 643, pp.23-25
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Curcubitacées: une sexualité complexe et variée
auteur
Michel Pitrat
article
Jardins de France, 2016, 642, pp.22-25
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Mais pourquoi tailler les légumes ?
auteur
Michel Javoy, Michel Pitrat, Jean-Daniel Arnaud
article
Jardins de France, 2016, 641, pp.19-21
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The andromonoecious sex determination gene predates the separation of cucumis and citrullus genera
auteur
Adnane Boualem, Afef Lemhamdi, Marie-Agnès Sari, Sarah Pignoly, Christelle Troadec, Fadi Abou Choucha, Ilkour Solmaz, Nebahat Sari, Catherine Dogimont, Abdelhafid Bendahmane
article
PLoS ONE, 2016, 11 (5), pp.e0155444. ⟨10.1371/journal.pone.0155444⟩
resume
Understanding the evolution of sex determination in plants requires the cloning and the characterization of sex determination genes. Monoecy is characterized by the presence of both male and female flowers on the same plant. Andromonoecy is characterized by plants carrying both male and bisexual flowers. In watermelon, the transition between these two sexual forms is controlled by the identity of the alleles at the A locus. We previously showed, in two Cucumis species, melon and cucumber, that the transition from monoecy to andromonoecy results from mutations in 1-aminocyclopropane-1-carboxylic acid synthase (ACS) gene, ACS-7/ACS2. To test whether the ACS-7/ACS2 function is conserved in cucurbits, we cloned and characterized ClACS7 in watermelon. We demonstrated co-segregation of ClACS7, the homolog of CmACS-7/CsACS2, with the A locus. Sequence analysis of ClACS7 in watermelon accessions identified three ClACS7 isoforms, two in andromonoecious and one in monoecious lines. To determine whether the andromonoecious phenotype is due to a loss of ACS enzymatic activity, we expressed and assayed the activity of the three protein isoforms. Like in melon and cucumber, the isoforms from the andromonoecious lines showed reduced to no enzymatic activity and the isoform from the monoecious line was active. Consistent with this, the mutations leading andromonoecy were clustered in the active site of the enzyme. Based on this, we concluded that active ClACS7 enzyme leads to the development of female flowers in monoecious lines, whereas a reduction of enzymatic activity yields hermaphrodite flowers. ClACS7, like CmACS-7/CsACS2 in melon and cucumber, is highly expressed in carpel primordia of buds determined to develop carpels and not in male flowers. Based on this finding and previous investigations, we concluded that the monoecy gene, ACS7, likely predated the separation of the cucumis and citrullus genera.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02637987/file/Dogimont%20PlosOne%202016%20e0155444_1.pdf BibTex
titre
Resistance to root-knot nematodes [i]Meloidogyne[/i] spp. in woody plants
auteur
Simon Bernard Saucet, Cyril van Ghelder, Pierre Abad, Henri Duval, Daniel Esmenjaud
article
New Phytologist, 2016, 211 (1), pp.41-56. ⟨10.1111/nph.13933⟩
resume
Root-knot nematodes (RKNs) [i]Meloidogyne[/i] spp. cause major damage to cultivated woody plants. Among them, Prunus, grapevine and coffee are the crops most infested by worldwide polyphagous species and species with a more limited distribution and/or narrower host range. The identification and characterization of natural sources of resistance are important steps to develop RKN control strategies. In woody crops, resistant rootstocks genetically different from the scion of agronomical interest may be engineered. We describe herein the interactions between RKNs and different woody crops, and highlight the plant species in which resistance and corresponding resistance (R) genes have been discovered. Even though grapevine and, to a lesser extent, coffee have a history of rootstock selection for RKN resistance, few cases of resistance have been documented. By contrast, in [i]Prunus[/i], R genes with different spectra have been mapped in plums, peach and almond and can be pyramided for durable resistance in interspecific rootstocks. We particularly discuss here the Ma Toll/interleukin-1 receptor-like-nucleotide binding-leucine-rich repeat gene from Myrobalan plum, one of the longest plant R genes cloned to date, due to its unique biological and structural properties. RKN R genes in Prunus will enable us to carry out molecular studies aimed at improving our knowledge of plant immunity in woody plants.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Vat, an amazing gene conferring resistance to aphids and viruses they carry: from molecular structure to field effects
auteur
Nathalie Boissot, Alexandra Schoeny, Flavie Vanlerberghe-Masutti
article
Frontiers in Plant Science, 2016, 7, pp.1420. ⟨10.3389/fpls.2016.01420⟩
resume
We review half a century of research on Cucumis melo resistance to Aphis gossypii from molecular to field levels. The Vat gene is unique in conferring resistance to both A. gossypii and the viruses it transmits. This double phenotype is aphid clone-dependent and has been observed in 25 melon accessions, mostly from Asia. It is controlled by a cluster of genes including CC-NLR, which has been characterized in detail. Copy-number polymorphisms (for the whole gene and for a domain that stands out in the LLR region) and single-nucleotide polymorphisms have been identified in the Vat cluster. The role of these polymorphisms in plant/aphid interactions remains unclear. The Vat gene structure suggests a functioning with separate recognition and response phases. During the recognition phase, the VAT protein is thought to interact (likely indirectly) with an aphid effector introduced during cell puncture by the aphid. A few hours later, several miRNAs are upregulated in Vat plants. Peroxidase activity increases, and callose and lignin are deposited in the walls of the cells adjacent to the stylet path, disturbing aphid behavior. In aphids feeding on Vat plants, Piwi-interacting RNA-like sequences are abundant and the levels of other miRNAs are modified. At the plant level, resistance to aphids is quantitative (aphids escape the plant and display low rates of reproduction). Resistance to viruses is qualitative and local. Durability of NLR genes is highly variable. A. gossypii clones are adapted to Vat resistance, either by introducing a new effector that interferes with the deployment of plant defenses, or by adapting to the defenses it triggered. Viruses transmitted in a non-persistent manner cannot adapt to Vat resistance. At population level, Vat reduces aphid density and genetic diversity. The durability of Vat resistance to A. gossypii populations depends strongly on the agro-ecosystem, including, in particular, the presence of other cucurbit crops serving as alternative hosts for adapted clones in fall and winter. At the crop level, Vat resistance decreases the intensity of virus epidemics when A. gossypii is the main aphid vector in the crop environment.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01512038/file/Boissot%20Frontiers%20in%20Plant%20Science%202016%201-18_%7BC6845359-1AF1-437B-9291-46217B944035%7D.pdf BibTex
titre
Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits
auteur
Elise Albert, Vincent Segura, Justine Gricourt, Julien Bonnefoi, Laurent Derivot, Mathilde Causse
article
Journal of Experimental Botany, 2016, 67 (22), pp.6413-6430. ⟨10.1093/jxb/erw411⟩
resume
Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01403394/file/Albert_Causse%20J.%20Exp.%20Bot.%202016%206413-6430_%7BEB4FD2FD-E873-4412-A11F-4A26343D6EA5%7D.pdf BibTex
titre
Premières cartes d’abondance relative de six mustélidés en France
auteur
Clément Calenge, Michel Albaret, François Leger, Jean-Michel Vandel, Joel J. Chadoeuf, Christophe Giraud, Sylvie Huet, Romain Julliard, Pascal P. Monestiez, Jeremy Piffady, David Pinaud, Sandrine Ruette
article
Faune Sauvage, 2016, 130 (1er. trimestre), pp.17
resume
Depuis 2001, un système de « carnets de bord petits carnivores » a été mis en place par l’ONCFS, afin de relever en continu toutes les observations d’espèces de ce groupe faites par les agents des services départementaux au cours de leurs déplacements. Jusqu’à présent, ces données avaient permis d’élaborer des cartes de répartition nationale. Mais grâce à un modèle statistique innovant, l’effort d’observa- tion et les différences de probabilité de détection ont pu être pris en compte, permettant d’estimer pour la première fois des indices de densité. Cet article présente ainsi les premières cartes d’abondance relative de six mustélidés à l'échelle des petites régions agricoles de la France.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Alain Palloix died on 8 March 2016 IN MEMORIAM
auteur
Véronique Lefebvre
article
Fruits, 2016, 71 (3), pp.195. ⟨10.1051/fruits/2016009⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A resistant pepper used as a trap cover crop in vegetable production strongly decreases root-knot nematode infestation in soil
auteur
Mireille Navarrete, Caroline Djian-Caporalino, Thierry Mateille, Alain Palloix, Anne-Marie Sage-Palloix, Amélie Lefevre, Ariane Fazari, Nathalie Marteu, Johannes Tavoillot, Arnaud Dufils, Claudine Furnion, Laure Pares, Isabelle Forest
article
Agronomy for Sustainable Development, 2016, 36 (4), 11 p. ⟨10.1007/s13593-016-0401-y⟩
resume
Root-knot nematodes are causing serious economic losses of vegetable production. Actual agroecological control solutions are not effective enough to control this pest or are difficult to implement in farms. There is little knowledge on the use of crops to trap nematodes in protected cultivation systems. Therefore, we tested a resistant pepper as a trap crop for root-knot nematodes over 4 years in a commercial farm and an experimental station in Southern France. The effects of pepper trap crop on plant damages and soil infestation were compared with a sorghum cover crop. We also surveyed 28 local vegetable farmers for their interest concerning the possible use of the pepper trap crop. Our results show that nematode infestation of the soil decreased by 99 and 80%after the first and second implementation of the trap crop. The gall index measured on Swiss chard decreased from 2.5 to less than 1 after 4 years. Respectively, 21 and 36 % of farmers found the cropping system completely and partially acceptable. The most interested farmers were those having sufficient labor and available land in summer. Farmer criticisms were higher nursery costs and planting duration, versus sorghum. Overall, this is the first design of a cropping system using a resistant cultivar as a dead-end trap crop for root-knot nematodes. The process used, moving from a genetic construct to agronomic innovation through an interdisciplinary and participatory approach, holds promise for scientists seeking new integrated pest management approaches to increase the sustainability of agriculture.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01512079/file/Palloix_Sage-Palloix%20Agron.%20Sustain.%20Dev.%202016%20in%20press_%7BD3B12097-B202-4937-ACC0-B35CBF2DED74%7D.pdf BibTex
titre
Tomates sous serre et l'envol des bourdons
auteur
Rene Damidaux, Michel Pitrat, Bernard Vaissière
article
Jardins de France, 2016, 643, pp.6
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Reduction of MDHAR activity in cherry tomato suppresses growth and yield and MDHAR activity is correlated with sugar levels under high light
auteur
Vincent Truffault, Noé Gest, Cecile Garchery, Alexandra Florian, Alisdair R Fernie, Hélène Gautier, Rebecca Stevens
article
Plant, Cell and Environment, 2016, 39 (6), pp.1279-1292. ⟨10.1111/pce.12663⟩
resume
Ascorbate is oxidized into the radical monodehydroascorbate (MDHA) through ascorbate oxidase or peroxidase activity or non-enzymatically by reactive oxygen species. Regeneration of ascorbate from MDHA is ensured by the enzyme monodehydroascorbate reductase (MDHAR). Previous work has shown that growth processes and yield can be altered by modifying the activity of enzymes that recycle ascorbate, therefore we have studied similar processes in cherry tomato (Solanum lycopersium L.) under- or overexpressing MDHAR. Physiological and metabolic characterization of these lines was carried out under different light conditions or by manipulating the source-sink ratio. Independently of the light regime, slower early growth of all organs was observed in MDHAR silenced lines, decreasing final fruit yield. Stomatal conductance and photosynthesis were altered as was the accumulation of hexoses and sucrose in a light-dependent manner in plantlets. Sucrose accumulation was also repressed in young fruits and final yield of MDHAR silenced lines showed a stronger decrease under carbon limitation. Ascorbate and monodehydroascorbate appear to be involved in control of growth and sugar metabolism in cherry tomato and these enzymes could be potential targets for yield improvement
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Identifying SNP markers tightly associated with six major genes in peach [Prunus persica (L.) Batsch] using a high-density SNP array with an objective of marker-assisted selection (MAS)
auteur
Patrick Lambert, José Antonio Campoy-Corbalan, Igor Pacheco, Jehan-Baptiste Mauroux, Cassia da Silva Linge, Diego Micheletti, Danièle Bassi, Laura Rossini, Elisabeth Dirlewanger, Thierry Pascal, Michela Troggio, Maria José Aranzana, Andrea Patocchi, Pere Arús
article
Tree Genetics and Genomes, 2016, 12 (61), pp.1-21. ⟨10.1007/s11295-016-1080-1⟩
resume
One of the applications of genomics is to identify genetic markers linked to loci responsible for variation in phenotypic traits, which could be used in breeding programs to select individuals with favorable alleles, particularly at the seedling stage. With this aim, in the framework of the European project FruitBreedomics, we selected five main peach fruit characters and a resistance trait, controlled by major genes with Mendelian inheritance: fruit flesh color Y, fruit skin pubescence G, fruit shape S, sub-acid fruit D, stone adhesion-flesh texture F-M, and resistance to green peach aphid Rm2. They were all previously mapped in Prunus. We then selected three F1 and three F2 progenies segregating for these characters and developed genetic maps of the linkage groups including the major genes, using the single nucleotide polymorphism (SNP) genome-wide scans obtained with the International Peach SNP Consortium (IPSC) 9K SNP array v1. We identified SNPs co-segregating with the characters in all cases. Their positions were in agreement with the known positions of the major genes. The number of SNPs linked to each of these, as well as the size of the physical regions encompassing them, varied depending on the maps. As a result, the number of useful SNPs for marker-assisted selection varied accordingly. As a whole, this study establishes a sound basis for further development of MAS on these characters. Additionally, we also discussed some limitations that were observed regarding the SNP array efficiency.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Les saveurs au potager
auteur
Pierre Vaysse, Amélie Devillepoix, Mathilde Causse, Michel Pitrat
article
Jardins de France, 2016, 640, pp.1-6
resume
Le bon goût est à la mode dans le potager. Les consommateurs sont de plus en plus exigeants sur la qualité gustative des légumes ou des fruits. Les sélectionneurs en tiennent compte. Voici quatre exemples avec la fraise, la framboise, la tomate et le melon.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01313373/file/2016_vaysse_jardinsdefrance_1.pdf BibTex
titre
Guide des sensibilités variétales aux bio-agresseurs
auteur
Laurent Brun, Vincent Mercier, Armand Guillermin, Charlotte Arbona, Guy Clauzel, Vincent Delaunay, Magalie Léon-Chapoux, Jean-Marc Audergon, Claude-Eric Parveaud, Christelle Gomez, Jean-Marc Broquaire, Gilles Libourel, Lionel Romet, François Warlop, Simon Sylvaine, Didier Pouzoulet, Alain Delebecq, Sandrine Oste, Ludovic Tournant, François Laurens, Eva Laget, Christophe Gros, Luciana Parisi, Frédérique Didelot, Mehdi Al-Rifaï, Marie-Noëlle Bellanger, Caroline Denancé, Charles-Eric Durel, Pascale Expert, Elisa Ravon, Valérie Caffier, Gilles Orain, Philippe Billy, Christophe Brouard, Arnaud Lemarquand, Annabelle Hubert
article
Arboriculture Fruitière, 2016, Supplément n°698
resume
Ce guide utile au choix et aux préconisations variétales compte 12 fiches techniques pour l'abricotier, le pêcher et le pommier. Par couple espèce bio-agresseur, des éléments sur la biologie et l'épidémiologie du bioagresseur, sur la méthodologie expérimentale et sur les principaux résultats sont présentés.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-04903219/file/GRAB_guide_varietal_sensibilites_aux_bioagresseurs_2016.pdf BibTex
titre
Fighting sharka in peach: current limitations and future perspectives
auteur
Marco Cirilli, Filippo Geuna, Anna-Rosa Babini, Valentina Bozhkova, Luigi Catalano, Beniamino Cavagna, Sylvie Dallot, Véronique Decroocq, Luca Dondini, Stefano Foschi, Vincenza Ilardi, Alessandro Liverani, Bruno Mezzetti, Angelantonio Minafra, Marco Pancaldi, Tiziana Pandolfini, Thierry Pascal, Vito Nicolas Savino, Ralph Scorza, Ignazio Verde, Danièle Bassi
article
Frontiers in Plant Science, 2016, 7, ⟨10.3389/fpls.2016.01290⟩
resume
Sharka, caused by Plum Pox Virus (PPV), is by far the most important infectious disease of peach [P. persica (L.) Batsch] and other Prunus species. The progressive spread of the virus in many important growing areas throughout Europe poses serious issues to the economic sustainability of stone fruit crops, peach in particular. The adoption of internationally agreed-upon rules for diagnostic tests, strain-specific monitoring schemes and spatial-temporal modeling of virus spread, are all essential for a more effective sharka containment. The EU regulations on nursery activity should be modified based on the zone delimitation of PPV presence, limiting open-field production of propagation materials only to virus-free areas. Increasing the efficiency of preventive measures should be augmented by the short-term development of resistant cultivars. Putative sources of resistance/tolerance have been recently identified in peach germplasm, although the majority of novel resistant sources to PPV-M have been found in almond. However, the complexity of introgression from related-species imposes the search for alternative strategies. The use of genetic engineering, particularly RNAi-based approaches, appears as one of the most promising perspectives to introduce a durable resistance to PPV in peach germplasm, notwithstanding the well-known difficulties of in vitro plant regeneration in this species. In this regard, rootstock transformation to induce RNAi-mediated systemic resistance to PPV would avoid the transformation of numerous commercial cultivars, and may alleviate consumer resistance to the use of GM plants.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01512030/file/Pascal%20Frontiers%202016%20in%20press_%7B09021C18-B95F-487B-AD47-27F489555152%7D.pdf BibTex
titre
Which QTL associations for efficient and durable resistances to the potato cyst nematode Globodera pallida?
auteur
Marie-Claire Kerlan, Jean-Paul Dantec, Lionel Renault, D. Ruer, Catherine Souchet, Marie Ange Dantec, François Monot, Josiane Quéré, Bernard Caromel, Laura Chauvin, Josselin Montarry, Sylvain Fournet
article
Innovations Agronomiques, 2016, 50, pp.87-100. ⟨10.15454/1.472109676217473E12⟩
resume
Actuellement, les variétés de pomme de terre résistantes au nématode à kyste Globodera pallida inscrites au catalogue français sont peu nombreuses et proviennent toutes de l a source Solanum vernei . Il existe deux autres sources , S. sparsipilum et S. spegazzinii qui ont en commun avec S. vernei un QTL à effet fort ( GpaV ) cartographié sur le chromosome V. La source S. sparsipilum se distingue des deux autres par la présence d’un QTL à effet faible ( GpaXI spl ) qui quand, il est associé à GpaV sp l transforme la réaction de masculinisation en un blocage des larves dans les racines. Cette combinaison procure, aux clones qui la possèdent, une efficacité et une durabilité plus important e. L’INRA, en collaboration avec les sélectionneurs français, et la Coopérative de Noirmoutier a développé et testé des constructions génétiques innovantes, associant le QTL à effet faible GpaXI spl aux QTL GpaV issus des deux autres espèces. Dans la majori té des cas et quelque soient les sources de résistance, l’association du QTL GpaXI spl et du QTL GpaV conduit à un blocage précoce des nématodes. Cette association permet également de contrôler des populations virulentes au QTL GpaV vrn qu’elles soient obtenues expérimentalement ou d’origine naturelle . Ces résultats donnent des bases pour construire de nouvelles combinaisons génétiques qui permettront d’élargir le spectre d’efficacité des variétés, dans le temps et dans l’espace.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02637067/file/2016_Caromel_Innovations%20Agronomiques_1.pdf BibTex
titre
Human management of a wild plant modulates the evolutionary dynamics of a gene determining recessive resistance to virus infection.
auteur
Nils Poulicard, Luis Fernández Pacios, Jean-Luc Gallois, Daniel Piñero, Fernando García-Arenal
article
PLoS Genetics, 2016, 12 (8), 31 p. ⟨10.1371/journal.pgen.1006214⟩
resume
This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA) host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin). Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in home gardens started about 25 years ago. Potyvirus infection of Capsicum plants requires the physical interaction of the viral VPg with the pvr2 product, the translation initiation factor eIF4E1. Mutations impairing this interaction result in resistance, according to the MA model. The diversity of pvr2/eIF4E1 in wild and cultivated chiltepin populations from six biogeographical provinces in Mexico was analysed in 109 full-length coding sequences from 97 plants. Eleven alleles were found, and their interaction with potyvirus VPg in yeast-two-hybrid assays, plus infection assays of plants, identified six resistance alleles. Mapping resistance mutations on a pvr2/eIF4E1 model structure showed that most were around the cap-binding pocket and strongly altered its surface electrostatic potential, suggesting resistance-associated costs due to functional constraints. The pvr2/eIF4E1 phylogeny established that susceptibility was ancestral and resistance was derived. The spatial structure of pvr2/eIF4E1 diversity differed from that of neutral markers, but no evidence of selection for resistance was found in wild populations. In contrast, the resistance alleles were much more frequent, and positive selection stronger, in cultivated chiltepin populations, where diversification of pvr2/eIF4E1 was higher. This analysis of the genetic variation of a recessive resistance gene involved in MA host-pathogen interactions in populations of a wild plant show that evolutionary patterns differ according to the plant habitat, wild or cultivated. It also demonstrates that human management of the plant population has profound effects on the diversity and the evolution of the resistance gene, resulting in the selection of resistance alleles.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01374695/file/journal-pgen-1006214.pdf BibTex
titre
Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression
auteur
Elise Albert, Justine Gricourt, Nadia Bertin, Julien Bonnefoi, Stephanie Pateyron, Jean-Philippe Tamby, Frederique Bitton, Mathilde Causse
article
TAG Theoretical and Applied Genetics, 2016, 129 (2), pp.395-418. ⟨10.1007/s00122-015-2635-5⟩
resume
In tomato, genotype by watering interaction resulted from genotype re-ranking more than scale changes. Interactive QTLs according to watering regime were detected. Differentially expressed genes were identified in some intervals. As a result of climate change, drought will increasingly limit crop production in the future. Studying genotype by watering regime interactions is necessary to improve plant adaptation to low water availability. In cultivated tomato [i](Solanum lycopersicum[/i] L.), extensively grown in dry areas, well-mastered water deficits can stimulate metabolite production, increasing plant defenses and concentration of compounds involved in fruit quality, at the same time. However, few tomato Quantitative Trait Loci (QTLs) and genes involved in response to drought are identified or only in wild species. In this study, we phenotyped a population of 119 recombinant inbred lines derived from a cross between a cherry tomato and a large fruit tomato, grown in greenhouse under two watering regimes, in two locations. A large genetic variability was measured for 19 plant and fruit traits, under the two watering treatments. Highly significant genotype by watering regime interactions were detected and resulted from re-ranking more than scale changes. The population was genotyped for 679 SNP markers to develop a genetic map. In total, 56 QTLs were identified among which 11 were interactive between watering regimes. These later mainly exhibited antagonist effects according to watering treatment. Variation in gene expression in leaves of parental accessions revealed 2259 differentially expressed genes, among which candidate genes presenting sequence polymorphisms were identified under two main interactive QTLs. Our results provide knowledge about the genetic control of genotype by watering regime interactions in cultivated tomato and the possible use of deficit irrigation to improve tomato quality
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca)
auteur
Stéphanie Mariette, Fabienne Wong Jun Tai, Guillaume Roch, Aurélien Barré, Aurélie Chague, Stéphane Decroocq, Alexis Groppi, Yec’han Laizet, Patrick Lambert, David Tricon, Macha Nikolski, Jean-Marc Audergon, Albert G. Abbott, Véronique Decroocq
article
New Phytologist, 2016, 209 (2), DOI: 10.1111/nph.13627. ⟨10.1111/nph.13627⟩
resume
Summary In fruit tree species, many important traits have been characterized genetically by using single-family descent mapping in progenies segregating for the traits. However, most mapped loci have not been sufficiently resolved to the individual genes due to insufficient progeny sizes for high resolution mapping and the previous lack of whole-genome sequence resources of the study species. To address this problem for Plum Pox Virus (PPV) candidate resistance gene identification in Prunus species, we implemented a genome-wide association (GWA) approach in apricot. This study exploited the broad genetic diversity of the apricot (Prunus armeniaca) germplasm containing resistance to PPV, next-generation sequence-based genotyping, and the high-quality peach (Prunus persica) genome reference sequence for single nucleotide polymorphism (SNP) identification. The results of this GWA study validated previously reported PPV resistance quantitative trait loci (QTL) intervals, highlighted other potential resistance loci, and resolved each to a limited set of candidate genes for further study. This work substantiates the association genetics approach for resolution of QTL to candidate genes in apricot and suggests that this approach could simplify identification of other candidate genes for other marked trait intervals in this germplasm.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A TILLING approach to generate broad-spectrum resistance to potyviruses in tomato is hampered by eIF4E gene redundancy
auteur
Camille Gauffier, Caroline Lebaron, André Moretti, Carole Constant, Frédéric Moquet, Grégori Bonnet, Carole Caranta, Jean-Luc Gallois
article
The Plant Journal, 2016, 85 (6), pp.717-729. ⟨10.1111/tpj.13136⟩
resume
Genetic resistance to pathogens is important for sustainable maintenance of crop yields. Recent biotechnologies offer alternative approaches to generate resistant plants by compensating for the lack of natural resistance. Tomato ([i]Solanum lycopersicum[/i]) and related species offer a model in which natural and TILLING-induced potyvirus resistance alleles may be compared. For resistance based on translation initiation factor eIF4E1, we confirm that the natural allele Sh-eIF4E1(PI24)-pot1, isolated from the wild tomato species [i]Solanum habrochaites[/i], is associated with a wide spectrum of resistance to both potato virus Y and tobacco etch virus isolates. In contrast, a null allele of the same gene, isolated through a TILLING strategy in cultivated tomato[i] S.lycopersicum[/i], is associated with a much narrower resistance spectrum. Introgressing the null allele into [i]S.habrochaites[/i] did not extend its resistance spectrum, indicating that the genetic background is not responsible for the broad resistance. Instead, the different types of eIF4E1 mutations affect the levels of eIF4E2 differently, suggesting that eIF4E2 is also involved in potyvirus resistance. Indeed, combining two null mutations affecting eIF4E1 and eIF4E2 re-establishes a wide resistance spectrum in cultivated tomato, but to the detriment of plant development. These results highlight redundancy effects within the eIF4E gene family, where regulation of expression alters susceptibility or resistance to potyviruses. For crop improvement, using loss-of-function alleles to generate resistance may be counter-productive if they narrow the resistance spectrum and limit growth. It may be more effective to use alleles encoding functional variants similar to those found in natural diversity. Significance Statement New resistance traits are important targets for plant breeding. Here we compared a functional natural eIF4E allele in a wild tomato species, which broadly conferred resistance to Potato virus Y and Tobacco etch virus, to TILLING-generated null alleles in cultivated tomato. Due to gene redundancy, the TILLING alleles were not as effective unless null mutations in two genes were combined, and the double mutant had impaired plant growth. These results indicate that null alleles are not necessarily suitable for generating broad spectrum resistance in crops.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Optimization of Allelic Combinations Controlling Parameters of a Peach Quality Model
auteur
Bénédicte Quilot-Turion, Michel Génard, Pierre Valsesia, Mohamed-Mahmoud Memmah
article
Frontiers in Plant Science, 2016, 20 (7), ⟨10.3389/fpls.2016.01873⟩
resume
Process-based models are effective tools to predict the phenotype of an individual in different growing conditions. Combined with a quantitative trait locus (QTL) mapping approach, it is then possible to predict the behavior of individuals with any combinations of alleles. However the number of simulations to explore the realm of possibilities may become infinite. Therefore, the use of an efficient optimization algorithm to intelligently explore the search space becomes imperative. The optimization algorithm has to solve a multi-objective problem, since the phenotypes of interest are usually a complex of traits, to identify the individuals with best tradeoffs between those traits. In this study we proposed to unroll such a combined approach in the case of peach fruit quality described through three targeted traits, using a process-based model with seven parameters controlled by QTL. We compared a current approach based on the optimization of the values of the parameters with a more evolved way to proceed which consists in the direct optimization of the alleles controlling the parameters. The optimization algorithm has been adapted to deal with both continuous and combinatorial problems. We compared the spaces of parameters obtained with different tactics and the phenotype of the individuals resulting from random simulations and optimization in these spaces. The use of a genetic model enabled the restriction of the dimension of the parameter space toward more feasible combinations of parameter values, reproducing relationships between parameters as observed in a real progeny. The results of this study demonstrated the potential of such an approach to refine the solutions toward more realistic ideotypes. Perspectives of improvement are discussed.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01441597/file/Quilot%20Frontiers%20in%20plant%20sci.%202016%20in%20press_%7BEDF22F1D-E27F-4867-8A1C-A2196B0E625A%7D.pdf BibTex
titre
Le piment : des goûts et des couleurs pour tous les amateurs d’épices
auteur
Anne-Marie Sage-Palloix, Alain Palloix
article
Jardins de France, 2016, 639, pp.11-14
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Maladies et ravageurs. La génétique au service des résistances
auteur
Michel Pitrat
article
Jardins de France, 2016, 642, pp.29-31
resume
Les résistances génétiques sont l’un des éléments dans les stratégies de contrôle les bioagresseurs tels des champignons, des insectes ou des nématodes dans une perspective de réduction de la gamme des produits phytosanitaires. Mais si les variétés résistantes sont l’un des facteurs les plus faciles à employer pour limiter l’incidence des maladies des plantes, cela ne signifie pas qu’elles suffisent à résoudre tous les problèmes.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Crop wild relatives of the brinjal eggplant ([i]Solanum melongena):[/i] Poorly represented in genebanks and many species at risk of extinction
auteur
Mindy M. Syfert, Nora P. Castaneda-Alvarez, Colin K. Khoury, Tiina Särkinen, Chrystian C. Sosa, Harold A. Achicanoy, Vivian Bernau, Jaime Prohens, Marie-Christine Brand-Daunay, Sandra Knapp
article
American Journal of Botany, 2016, 103 (4), pp.635-651. ⟨10.3732/ajb.1500539⟩
resume
Crop wild relatives (CWR) provide important traits for plant breeding, including pest, pathogen, and abiotic stress resistance. Therefore, their conservation and future availability are essential for food security. Despite this need, the world's genebanks are currently thought to conserve only a small fraction of the total diversity of CWR. We define the eggplant genepool using the results of recent taxonomic and phylogenetic studies. We identify the gaps in germplasm accessions for eggplant (Solanum melongena L.) CWR by comparing georeferenced herbarium records and germplasm accessions using a gap analysis methodology implementing species distribution models (SDM). Preliminary conservation assessments using IUCN criteria were done for all species and were combined with the gap analysis to pinpoint where under-collected and threatened CWR species coincide with high human disturbance and occur outside of protected areas. We show that many eggplant CWR are poorly represented in genebanks compared to their native ranges. Priority areas for future collecting are concentrated in Africa, especially along the Kenya-Tanzania border. Fourteen species of eggplant CWR are assessed as threatened or near-threatened; these are also concentrated in eastern Africa. The knowledge base upon which conservation of wild relative germplasm depends must take into account both taxonomic and phylogenetic advances. Beyond traditional research focus on close relatives of crops, we emphasize the benefits of defining a broad CWR genepool, and the importance of assessing threats to wild species when targeting localities for future collection of CWR to improve crop breeding in the face of environmental change.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01315233/file/ajb.1500539.full-1_%7BA9854ED1-F285-4212-97BD-E220AF4C735C%7D.pdf BibTex
titre
A new eIF4E1 allele characterized by RNAseq data mining is associated with resistance to PVY in tomato albeit with a low durability
auteur
Caroline Lebaron, Aurélie Rosado, Christopher Sauvage, Camille Gauffier, Sylvie S. German-Retana, Benoît Moury, Jean-Luc J.-L. Gallois
article
Journal of General Virology, 2016, 97 (11), pp.3063-3072. ⟨10.1099/jgv.0.000609⟩
resume
Allele mining on susceptibility factors offers opportunities to find new sources of resistance among crop wild relatives for breeding purposes. As a proof of concept, we used available RNAseq data to investigate polymorphisms among the four tomato genes encoding translation initiation factors (eIF4E1 and eIF4E2, eIFiso4E and the related gene New Cap-binding Protein -nCBP) to look for new potential resistance alleles to potyviruses. By analyzing polymorphism among RNAseq data obtained for 20 tomato accessions, ten belonging to the cultivated type Solanum lycopersicum and 10 belonging to the closest related wild species Solanum pimpinellifolium, we isolated one new eIF4E1 allele, in the Solanum pimpinellifolium LA0411 accession, which encodes a potential new resistance allele, mainly due to a polymorphism associated with an amino acid change within eIF4E1 region II. We confirmed that this new allele, pot1², is indeed associated with resistance to PVY, although with a restricted resistance spectrum and a very low durability potential. This suggests that mutations occurring in eIF4E region II only may not be sufficient to provide efficient and durable resistance in plants. However, our study emphasizes the opportunity brought by RNAseq data to mine for new resistance alleles. Moreover, this approach could be extended to seek for putative new resistance alleles by screening for variant forms of susceptibility genes encoding plant host proteins known to interact with viral proteins
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02639858/file/2016_Lebaron_J%20Gen%20Virol_postprint_1.pdf BibTex
titre
Viruses carried to soil by irrigation can be aerosolized later during windy spells
auteur
Guillaume G. Girardin, Pierre P. Renault, Fabienne Bon, Line Capowiez, Joel Chadoeuf, Camille Krawczyk, Dominique Courault
article
Agronomy for Sustainable Development, 2016, 36, pp.on-line. ⟨10.1007/s13593-016-0393-7⟩
resume
Reclaiming domestic wastewaters for irrigation helps to meet increasing water needs, to reduce discharge to conventional waters, and to fertilize soils. Unfortunately, it also contaminates crop and soil with human enteric pathogens. However, partial aerosolization of pathogens deposited on soil surface during windy periods has never been studied. Here, we investigated this putative aerosolization of pathogens from soil surface during windy periods by using murine mengoviruses, a surrogate of human enteric viruses, and assess the impact of environmental conditions on this phenomenon. Wind tunnel experiments were carried out on viruscontaminated plots submitted to various wind, soil surface moisture, and water types. Aerosolized viruses were trapped by impingers for RT-qPCR quantification. Virus concentrations were corrected for partial virus trapping efficiency and reaerosolization. A mathematical model was devised for one or more virus groups, characterized by their number of viruses and their kinetic aerosolization coefficient. The model was fitted to real trial data and used to generate numerical experiments to study the model estimators. We showed that 1 to 15 % of viruses carried to soil were aerosolized, of which 11 to 89%during the first 0.5 h. The viruses fell into two groups: a group that get aerosolized near instantaneously and a group that get aerosolized gradually. The range of kinetic coefficients of aerosolization of the gradually aerosolized group accounted for 90 % of viruses of this group aerosolized after 0.5–10.6 days. The size of this group increased with wind speed, decreased with soil warming, and increased with organic content of spray water. This first study on virus aerosolization shows that aerosolization cannot be neglected both in terms of quantities and speeds. Combined with virus stability in air, we anticipate our model to help policymakers refine regulations and standards governing wastewater reuse in irrigation.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02637699/file/Chadoeuf%20Agron.%20Sustain.%20Dev.%202016%201-10_1.pdf BibTex
titre
Model-Assisted Estimation of the Genetic Variability in Physiological Parameters Related to Tomato Fruit Growth under Contrasted Water Conditions
auteur
Dario Constantinescu, Mohamed Memmah, Gilles Vercambre, Michel Génard, Valentina Baldazzi, Mathilde Causse, Elise Albert, Beatrice Brunel, Pierre Valsesia, Nadia Bertin
article
Frontiers in Plant Science, 2016, 7, ⟨10.3389/fpls.2016.01841⟩
resume
Drought stress is a major abiotic stress threatening plant and crop productivity. In case of fleshy fruits, understanding mechanisms governing water and carbon accumulations and identifying genes, QTLs and phenotypes, that will enable trade-offs between fruit growth and quality under Water Deficit (WD) condition is a crucial challenge for breeders and growers. In the present work, 117 recombinant inbred lines of a population of Solanum lycopersicum were phenotyped under control and WD conditions. Plant water status, fruit growth and composition were measured and data were used to calibrate a process-based model describing water and carbon fluxes in a growing fruit as a function of plant and environment. Eight genotype-dependent model parameters were estimated using a multiobjective evolutionary algorithm in order to minimize the prediction errors of fruit dry and fresh mass throughout fruit development. WD increased the fruit dry matter content (up to 85%) and decreased its fresh weight (up to 60%), big fruit size genotypes being the most sensitive. The mean normalized root mean squared errors of the predictions ranged between 16–18% in the population. Variability in model genotypic parameters allowed us to explore diverse genetic strategies in response to WD. An interesting group of genotypes could be discriminated in which (i) the low loss of fresh mass under WD was associated with high active uptake of sugars and low value of the maximum cell wall extensibility, and (ii) the high dry matter content in control treatment (C) was associated with a slow decrease of mass flow. Using 501 SNP markers genotyped across the genome, a QTL analysis of model parameters allowed to detect three main QTLs related to xylem and phloem conductivities, on chromosomes 2, 4, and 8. The model was then applied to design ideotypes with high dry matter content in C condition and low fresh mass loss in WD condition. The ideotypes outperformed the RILs especially for large and medium fruit-size genotypes, by combining high pedicel conductance and high active uptake of sugars. Interestingly, five small fruit-size RILs were close to the selected ideotypes, and likely bear interesting traits and alleles for adaptation to WD. Drought stress is a major abiotic stress threatening plant and crop productivity. In case of fleshy fruits, understanding mechanisms governing water and carbon accumulations and identifying genes, QTLs and phenotypes, that will enable trade-offs between fruit growth and quality under Water Deficit (WD) condition is a crucial challenge for breeders and growers. In the present work, 117 recombinant inbred lines of a population of Solanum lycopersicum were phenotyped under control and WD conditions. Plant water status, fruit growth and composition were measured and data were used to calibrate a process-based model describing water and carbon fluxes in a growing fruit as a function of plant and environment. Eight genotype-dependent model parameters were estimated using a multiobjective evolutionary algorithm in order to minimize the prediction errors of fruit dry and fresh mass throughout fruit development. WD increased the fruit dry matter content (up to 85%) and decreased its fresh weight (up to 60%), big fruit size genotypes being the most sensitive. The mean normalized root mean squared errors of the predictions ranged between 16–18% in the population. Variability in model genotypic parameters allowed us to explore diverse genetic strategies in response to WD. An interesting group of genotypes could be discriminated in which (i) the low loss of fresh mass under WD was associated with high active uptake of sugars and low value of the maximum cell wall extensibility, and (ii) the high dry matter content in control treatment (C) was associated with a slow decrease of mass flow. Using 501 SNP markers genotyped across the genome, a QTL analysis of model parameters allowed to detect three main QTLs related to xylem and phloem conductivities, on chromosomes 2, 4, and 8. The model was then applied to design ideotypes with high dry matter content in C condition and low fresh mass loss in WD condition. The ideotypes outperformed the RILs especially for large and medium fruit-size genotypes, by combining high pedicel conductance and high active uptake of sugars. Interestingly, five small fruit-size RILs were close to the selected ideotypes, and likely bear interesting traits and alleles for adaptation to WD.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01475599/file/2016_Constantinescu_Frontiers%20in%20Plant%20Science_1.pdf BibTex
titre
Pollinisations contrôlées au cours de la création variétale
auteur
Michel Pitrat, Yves Lespinasse
article
Jardins de France, 2016, 643, pp.39-42
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Nematode quantitative resistance conferred by the pepper genetic background presents additive effects and is stable against different isolates of [i]Meloidogyne incognita[/i]
auteur
Fulgencio Sanchez-Solana, Caridad Ros, Carmen María Lacasa, Alain Palloix, Alfredo Lacasa
article
Plant Pathology, 2016, 65 (4), pp.673-681. ⟨10.1111/ppa.12459⟩
resume
Root-knot nematodes (RKNs), [i]Meloidogyne[/i] spp., are a major disease problem in solanaceous crops worldwide, including pepper (Capsicum spp.). Genetic control provides an economically and environmentally sustainable protection alternative to soil fumigants. In pepper, resistance to the main RKN species ([i]M.incognita[/i],[i] M.javanica[/i] and [i]M.arenaria[/i]) is conferred by the major genes (R genes) Me1, Me3 and N. However, RKNs are able to develop virulence, thus endangering the efficiency of R genes. Quantitative resistance (QR) against [i]Meloidogyne[/i] spp. is expected to provide an alternative to R genes, or to be combined with R genes, to increase the resistance efficiency and durability in pepper. In order to explore the ability of QR to protect pepper against RKNs, five pepper inbred lines, differing in their QR level, were tested directly, or after combination with the Me1 and Me3 genes, for their resistance to a panel of[i] M.arenaria, M.javanica[/i] and [i]M.incognita[/i] isolates. The[i] M.arenaria[/i] and [i]M.javanica[/i] isolates showed low pathogenicity to pepper, unlike the [i]M.incognita[/i] isolates. The QR, controlled by the pepper genetic background, displayed a high resistance level with a broad spectrum of action, protecting pepper against Me3-virulent as well as avirulent [i]M.incognita[/i] isolates. The QR was also expressed when combined with the Me1 and Me3 genes, but presented additive genetic effects so that heterozygous F-1 hybrids proved less resistant than homozygous inbred lines. The discovery of this QR is expected to provide promising applications for preserving the efficiency and durability of nematode resistance.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic diversity of pepper ([i]Capsicum[/i] spp.) germplasm resources in China reflects selection for cultivar types and spacial distribution
auteur
Xiao-Min Zhang, Zheng-Hai Zhang, Xiao-Zhen Gu, Sheng-Li Mao, Xi-Xiang Li, Joël Chadoeuf, Alain Palloix, Li-Hao Wang, Bao-Xi Zhang
article
Journal of Integrative Agriculture , 2016, 15 (9), pp.1991-2001. ⟨10.1016/S2095-3119(16)61364-3⟩
resume
Pepper ([i]Capsicum[/i] spp.) is an important vegetable crop in the world. Now the pepper in China contributes one-third of the world's peppers production. Genetic diversity of the pepper germplasm of China is expected interesting to know. To explore the structure of genetic diversity in Chinese pepper germplasm resources and possible relationship with cultivar types or geographic origin, we sampled and compared 372 GenBank pepper accessions (local cultivars and landraces) from 31 provinces, autonomous regions and municipalities of China and 31 additional accessions from other countries. These accessions were genotyped using 28 simple sequence repeat (SSR) markers spanning the entire pepper genome. We then investigated the genetic structure of the sampled collection using model-based analysis in STRUCTURE v2.3.4 and examined genetic relationships by the unweighted pair-group method of mathematical averages (UPGMA) in MEGA. In addition to geographic origin, we evaluated eight plant and fruit traits. In total, 363 alleles were amplified using the 28 SSR primers. Gene diversity, polymorphism information content and heterozygosity of the 28 SSR loci were estimated as 0.09-0.92, 0.08-0.92 and 0.01-0.34, respectively. The UPGMA cluster analysis clearly distinguished Capsicum annuum L. from other cultivated pepper species. Population structure analysis of the 368 C. annuum accessions uncovered three genetic groups which also corresponded to distinct cultivar types with respect to the plant and fruit descriptors. The genetic structure was also related to the geographic origin of the landraces. Overall results indicate that genetic diversity of Chinese pepper landraces were structured by migration of genotypes followed by human selection for cultivar types in agreement with consumption modes and adaptation to the highly diversified agro-climatic conditions.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Brown rot strikes Prunus fruit: an ancient fight almost always lost
auteur
Leandro de Oliveira-Lino, Igor Pacheco, Vincent Mercier, Franco Faoro, Daniele Bassi, Isabelle Bornard, Bénédicte Quilot-Turion
article
Journal of Agricultural and Food Chemistry, 2016, 64 (20), pp.4029-4047. ⟨10.1021/acs.jafc.6b00104⟩
resume
Brown rot (BR) caused by Monilinia spp., has been an economic problem for the stone fruit market due to the dramatic losses, with the biggest losses mainly during the postharvest period. There is much literature about basic aspects of Monilinia spp. infection, which indicates that environment significantly influences its occurrence in the orchard. However, progress is needed to sustainably limit this disease: the pathogen is able to develop resistance to pesticides and most of BR resistance research programs in plant models perish. Solving this problem becomes important due to the need to decrease chemical treatments and reduce residues on fruit. Thus, research has recently increased, exploring a wide range of disease control strategies (e.g. genetic, chemical, physical). Summarizing this information is difficult, as studies evaluate different Monilinia and Prunus model species, with diverse strategies and protocols. Thus, the purpose of this review is to present the diversity and distribution of agents causing BR, focusing on the biochemical mechanisms of Monilinia spp. infection both of the fungi and of the fruit, and report on the resistance sources in Prunus germplasm. In this review, we comprehensively compile the information currently available to better understand mechanisms related to BR resistance.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01594477/file/acs.jafc.6b00104_%7BDE6FE245-92E2-4082-A970-1F6511A90758%7D.pdf BibTex
titre
Plant genetic background increasing the efficiency and durability of major resistance genes to root-knot nematodes can be resolved into a few resistance QTLs
auteur
Arnaud Barbary, Caroline Djian-Caporalino, Nathalie Marteu, Ariane Fazari, Bernard Caromel, Philippe Castagnone-Sereno, Alain Palloix
article
Frontiers in Plant Science, 2016, 7, 9 p. ⟨10.3389/fpls.2016.00632⟩
resume
With the banning of most chemical nematicides, the control of root-knot nematodes (RKNs) in vegetable crops is now based essentially on the deployment of single, major resistance genes (R-genes). However, these genes are rare and their efficacy is threatened by the capacity of RKNs to adapt. In pepper, several dominant R-genes are effective against RKNs, and their efficacy and durability have been shown to be greater in a partially resistant genetic background. However, the genetic determinants of this partial resistance were unknown. Here, a quantitative trait loci (QTL) analysis was performed on the F-2:3 population from the cross between Yolo Wonder, an accession considered partially resistant or resistant, depending on the RKN species, and Doux Long des Landes, a susceptible cultivar. A genetic linkage map was constructed from 130 F2 individuals, and the 130 F-3 families were tested for resistance to the three main RKN species, Meloidogyne incognita, M. arenaria, and M. javanica. For the first time in the pepper-RKN pathosystem, four major QTLs were identified and mapped to two clusters. The cluster on chromosome P1 includes three tightly linked QTLs with specific effects against individual RKN species. The fourth QTL, providing specific resistance to M. javanica, mapped to pepper chromosome P9, which is known to carry multiple NBS-LRR repeats, together with major R-genes for resistance to nematodes and other pathogens. The newly discovered cluster on chromosome P1 has a broad spectrum of action with major additive effects on resistance. These data highlight the role of host QTLs involved in plant-RKN interactions and provide innovative potential for the breeding of new pepper cultivars or rootstocks combining quantitative resistance and major R-genes, to increase both the efficacy and durability of RKN control by resistance genes.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02639203/file/barbary_2016_frontiersinplantscience_1.pdf BibTex
titre
Verticillium on eggplant via the vasculeg project : presence and characterisation of bioagressors (part 1)
auteur
François Villeneuve, François Latour, Théophile Théry, Christine Fournier, Patricia Erard, Véronique Edel-Hermann, Nadine Gautheron, Christian Steinberg, Marie-Christine Daunay
article
Infos CTIFL, 2016, 322, pp.40-48
resume
Vascular wilt diseases of vegetable crops remain a major problem for eggplant growers in particular. After having used genetic resistance to Verticillium for several years, they are again confronted with the same problems. The VASCUleg project has led to a precise evaluation of the current situation on farms. Apart from the fungus that causes vascular disease, other pathogens are also present creating a whole range of bioagressors in different zones of production. The characterisation of isolated strains is quite complicated due to the complexity of Verticllium: new classification of Verticillium species, difficult identification of races and low aggressiveness of strains. V. dahliae is only one of the components of the parasite complex that provokes symptoms on grafted plants.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Dissecting quantitative trait variation in the resequencing era: Complementarity of bi-parental, multi-parental and association panels
auteur
Laura Pascual, Elise Albert, Christopher Sauvage, Janejira Duangjit, Jean-Paul Bouchet, Frederique Bitton, Nelly Desplat, Dominique D. Brunel, Marie-Christine Le Paslier, Nicolas N. Ranc, Laure Bruguier, Betty Chauchard, Philippe Verschave, Mathilde M. Causse
article
Plant Science, 2016, 242, pp.120-130. ⟨10.1016/j.plantsci.2015.06.017⟩
resume
Quantitative trait loci (QTL) have been identified using traditional linkage mapping and positional cloningidentified several QTL. However linkage mapping is limited to the analysis of traits differing betweentwo lines and the impact of the genetic background on QTL effect has been underlined. Genome-wideassociation studies (GWAs) were proposed to circumvent these limitations. In tomato, we have shownthat GWAs is possible, using the admixed nature of cherry tomato genomes that reduces the impactof population structure. Nevertheless, GWAs success might be limited due to the low decay of linkagedisequilibrium, which varies along the genome in this species.Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditionallinkage and GWAs by increasing the precision of QTL mapping. We have developed a MAGIC popula-tion by crossing eight tomato lines whose genomes were resequenced. We showed the potential of theMAGIC population when coupled with whole genome sequencing to detect candidate single nucleotidepolymorphisms (SNPs) underlying the QTL. QTL for fruit quality traits were mapped and related to thevariations detected at the genome sequence and expression levels. The advantages and limitations of thethree types of population, in the context of the available genome sequence and resequencing facilities,are discussed
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02635859/file/dissepanel.pdf BibTex
titre
Diversity of genetic backgrounds modulating the durability of a major resistance gene. Analysis of a core collection of pepper landraces resistant to Potato virus Y
auteur
Julie Quenouille, Ludovic Saint-Félix, Benoît Moury, Alain Palloix
article
Molecular Plant Pathology, 2016, 17 (2), pp.296-302. ⟨10.1111/mpp.12277⟩
resume
The evolution of resistance-breaking capacity in pathogen populations has been shown to depend on the plant genetic background surrounding the resistance genes. We evaluated a core collection of pepper (Capsicum annuum) landraces, representing the worldwide genetic diversity, for its ability to modulate the breakdown frequency by Potato virus Y of major resistance alleles at the pvr2 locus encoding the eukaryotic initiation factor 4E (eIF4E). Depending on the pepper landrace, the breakdown frequency of a given resistance allele varied from 0% to 52.5%, attesting to their diversity and the availability of genetic backgrounds favourable to resistance durability in the plant germplasm. The mutations in the virus genome involved in resistance breakdown also differed between plant genotypes, indicating differential selection effects exerted on the virus population by the different genetic backgrounds. The breakdown frequency was positively correlated with the level of virus accumulation, confirming the impact of quantitative resistance loci on resistance durability. Among these loci, pvr6, encoding an isoform of eIF4E, was associated with a major effect on virus accumulation and on the breakdown frequency of the pvr2-mediated resistance. This exploration of plant genetic diversity delivered new resources for the control of pathogen evolution and the increase in resistance durability.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02640439/file/2016_Quenouille_MPP_postprint_2.pdf BibTex
titre
Dossier Melon - Préserver le gène Vat
auteur
Véronique Bargain, Alexandra Schoeny, Nathalie Boissot
article
Réussir Fruits et Légumes, 2016, 367, pp.64-66
resume
Dossier Melon - Préserver le gène Vat
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Two tomato GDP-D-mannose epimerase isoforms involved in ascorbate biosynthesis play specific roles in cell wall biosynthesis and development
auteur
Louise Mounet-Gilbert, Marie Dumont, Carine Ferrand, Celine Bournonville, Antoine Monier, Joana Jorly, Martine Lemaire Lemaire-Chamley, Kentaro Mori, Isabelle Atienza, Michel Hernould, Rebecca Stevens, Arnaud Lehner, Jean Claude Mollet, Christophe Rothan, Patrice Lerouge, Pierre Baldet
article
Journal of Experimental Botany, 2016, 67 (15), pp.4767-4777. ⟨10.1093/jxb/erw260⟩
resume
GDP-D-mannose epimerase (GME, EC 5.1.3.18) converts GDP-D-mannose to GDP-L-galactose, and is considered to be a central enzyme connecting the major ascorbate biosynthesis pathway to primary cell wall metabolism in higher plants. Our previous work demonstrated that GME is crucial for both ascorbate and cell wall biosynthesis in tomato. The aim of the present study was to investigate the respective role in ascorbate and cell wall biosynthesis of the two SlGME genes present in tomato by targeting each of them through an RNAi-silencing approach. Taken individually SlGME1 and SlGME2 allowed normal ascorbate accumulation in the leaf and fruits, thus suggesting the same function regarding ascorbate. However, SlGME1 and SlGME2 were shown to play distinct roles in cell wall biosynthesis, depending on the tissue considered. The RNAi-SlGME1 plants harbored small and poorly seeded fruits resulting from alterations of pollen development and of pollination process. In contrast, the RNAi-SlGME2 plants exhibited vegetative growth delay while fruits remained unaffected. Analysis of SlGME1-and SlGME2-silenced seeds and seedlings further showed that the dimerization state of pectin rhamnogalacturonan-II (RG-II) was altered only in the RNAi-SlGME2 lines. Taken together with the preferential expression of each SlGME gene in different tomato tissues, these results suggest sub-functionalization of SlGME1 and SlGME2 and their specialization for cell wall biosynthesis in specific tomato tissues.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01775273/file/2016-Mounet-Gilbert%20et%20al-J%20Exp%20Bot.pdf BibTex
titre
Stratégie de résistance durable aux nématodes à galles chez les porte-greffe de [i]Prunus[/i] par pyramidage : marquage à haute résolution d’un gène du pêcher et localisation fine d’un gène de l’amandier
auteur
Henri Duval, Cyril van Ghelder, Martin Masse, G. Roch, Hugo Hussie, Daniel Esmenjaud
article
Innovations Agronomiques, 2016, 50, pp.59-68. ⟨10.15454/1.4721091038488276E12⟩
resume
Les nématodes à galles ([i]Meloidogyne[/i] spp.) sont de ravageurs extrêmement polyphages des racines et dont l’impact est très important à l’échelle globale. La stratégie de résistance aux espèces prédominantes [i]M. arenaria[/i], [i]M. incognita[/i] et[i] M. javanica[/i], est une alternative prioritaire chez de nombreuses plantes cultivées confrontées au retrait des nématicides et notamment chez les arbres fruitiers du genre Prunus. Trois gènes majeurs dominants de résistance, Ma (prunier), RMia (pêcher) et RMja (amandier), ont été identifiés et cartographiés dans cet objectif. Le pyramidagede ces trois gènes, par exemple dans des hybrides 3-voies, ouvre la voie à la création de porte-greffe protégés par au moins deux gènes vis-à-vis de chacune des espèces de nématodes précitées. Du fait de l’interaction durable entre ces plantes pérenneset les nématodes, ce pyramidagegarantit la création de matériels dotés d’une durabilité de résistance sans précédent au niveau mondial. La sélection assistée par marqueurs (SAM) du gène Ma,à spectre complet et cloné (famille desTIR-NB-LRRs(TNLs)), est possible grâce à des marqueurs SCAR intragéniques chez la source P.2175. Nous présentons donc ici les résultats des travaux sur les gènes RMia et RMja conduits dans le cadre d’un projet soutenu par le Ministère de l’Agriculture. Une cartographie à haute résolution du gène RMia chez la source Nemared, par marqueurs SSR (simple sequence repeat) et SNP (single nucleotide polymorphism), a été entreprise notamment dans une descendance F2 [Montclar (sensible) x Nemared]. Des marqueurs SNP ont permis de localiser le gène dans un intervalle physique de 92 kb du génome de référence du pêcher Lovell contenant 3 gènes candidats de type TNL. Le gène RMja porté par l’amandier Alnem, dont le marquage fin est en cours à partir de 800 individus de la population F2 [Lauranne (sensible) x Alnem]), a été situé dans un intervalle d’environ 2 Mb contenant également l’orthologue de Ma. L’obtention prochaine de la séquence NGS des parents Lauranne et Alnem permettra d’assurer un marquage à haute résolution de RMja et ainsi de disposer des outils de SAM pour les trois gènes de résistance
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01323663/file/2016_Duval_Innovations%20Agronomiques%2050.pdf BibTex
titre
Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development
auteur
Elsa Desnoues, Valentina Baldazzi, Michel Génard, Jehan-Baptiste Mauroux, Patrick Lambert, Carole Confolent, Bénédicte Quilot-Turion
article
Journal of Experimental Botany, 2016, 67 (11), pp.3419-3431. ⟨10.1093/jxb/erw169⟩
resume
Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and promote fruit consumption. The sugar content and composition of fruits varies with species, cultivar and stage of development, and is controlled by multiple enzymes. A QTL (quantitative trait locus) study was performed on peach fruit [Prunus persica (L.) Batsch], the model species for Prunus Progeny derived from an interspecific cross between P. persica cultivars and P. davidiana was used. Dynamic QTLs for fresh weight, sugars, acids, and enzyme activities related to sugar metabolism were detected at different stages during fruit development. Changing effects of alleles during fruit growth were observed, including inversions close to maturity. This QTL analysis was supplemented by the identification of genes annotated on the peach genome as enzymes linked to sugar metabolism or sugar transporters. Several cases of co-locations between annotated genes, QTLs for enzyme activities and QTLs controlling metabolite concentrations were observed and discussed. These co-locations raise hypotheses regarding the functional regulation of sugar metabolism and pave the way for further analyses to enable the identification of the underlying genes. In conclusion, we identified the potential impact on fruit breeding of the modification of QTL effect close to maturity.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Differential effect of resistance inducers on the susceptibility of lettuce varieties to Sclerotinia sclerotiorum and Botrytis cinerea
auteur
Asti Irawanti Azis, Magali Duffaud, Claire Troulet, Brigitte B. Maisonneuve, Efi Toding Tondok, Suryo Wiyono, Marc Bardin, Philippe C. Nicot
article
IOBC WPRS Bulletin, 2016, 115, pp.191-195
resume
The preventive use of resistance inducers has been shown to be an interesting method to reduce dependency on pesticides for plant protection. However, little is known on possible differences in the protective effects of such methods for different varieties of a given crop. In the present study, we assessed the effect of three compounds (acibenzolar-S-méthyl, a calcium-based mineral compound and a yeast extract) for the protection of six varieties of lettuce against two major pathogens, Sclerotinia sclerotiorum and Botrytis cinerea. The compounds were sprayed on the plants three days before inoculation. A water spray was used as a control. The protective effect of the compounds was then assessed by comparing the size of lesions developing on inoculated leaves. For both pathogens, none of the compounds fully inhibited disease development. However, reduction in lesion size was observed on some of the leaves. The effect of the three compounds was different for the two pathogens. For tests with B. cinerea, effects of plant treatment were not statistically significant. In contrast, significant effects were found for five of the varieties inoculated with S. sclerotiorum. Overall, the yeast extract provided the highest level of protection against that pathogen. However, for all compounds, the extent of the protective effect depended on the variety. Furthermore, in some cases the effect of the compound was opposite to that desired and disease was more severe on treated plants than on the water control. Possible consequences for field application of such methods will be discussed.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02640024/file/2016_Azis_IOBC_115.pdf BibTex
titre
Insight into the durability of plant resistance to aphids from a demo-genetic study of Aphis gossypii in melon crops
auteur
Sophie Thomas, Flavie Vanlerberghe-Masutti, Pascale Mistral, Anne Loiseau, Nathalie Boissot
article
Evolutionary Applications, 2016, 9 (6), pp.756-768. ⟨10.1111/eva.12382⟩
resume
Resistance breakdown has been observed following the deployment of plant cultivars resistant to pests. Assessing the durability of a resistance requires long-term experiments at least at a regional scale. We collected such data for melon resistance conferred by the Vat gene cluster to melon aphids. We examined landscape- level populations of Aphis gossypii collected in 2004–2015, from melonproducing regions with and without the deployment of Vat resistance and with different climates. We conducted demo-genetic analyses of the aphid populations on Vat and non-Vat plants during the cropping seasons. The Vat resistance decreased the density of aphid populations in all areas and changed the genetic structure and composition of these populations. Two bottlenecks were identified in the dynamics of adapted clones, due to the low levels of production of dispersal morphs and winter extinction. Our results suggest that (i) Vat resistance will not be durable in the Lesser Antilles, where no bottleneck affected the dynamics of adapted clones, (ii) Vat resistance will be durable in south-west France, where both bottlenecks affected the dynamics of adapted clones and (iii) Vat resistance will be less durable in south-east France, where only one of the two bottlenecks was observed.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02633315/file/Thomas_etal_2016_insight_durability_1.pdf BibTex
titre
Etude des déterminants génétiques et moléculaires de caractères influencés par le changement climatique chez l'abricotier et le cerisier
auteur
José Quero-Garcia, Guillaume Roch, Gérard Charlot, Christian Hilaire, Teresa Barreneche, José Antonio Campoy-Corbalan, Elisabeth Dirlewanger, Loick Le Dantec, Bénédicte Wenden, Jean Marc Audergon
article
Innovations Agronomiques, 2016, 50, pp.51-58. ⟨10.15454/1.472108874009284E12⟩
resume
In the context of temperature increase due to climate change, a study was conducted on adaptation of sweet cherry (Prunus avium) and apricot (Prunus armeniaca) to these modifications, with the help of the Ministry of Agriculture. A QTL search was undertaken by dealing with traits related to flowering phenology: bloom dates were decomposed into chilling and heat requirements and the quality of flowering was assessed by quantifying floral necrosis or abnormalities. For the bloom date and its components, stable and important QTL were detected on linkage groups (LG) 4, 1 and 6 on both species, which confirmed the high level of synteny within the Prunus genus. QTL for flowering quality were less significant and stable; nevertheless, promising QTL were highlighted on LG1 and 5, only for apricot. Candidate-genes (CG) involved in the flowering phenology were identified on sweet cherry and will soon be validated in both species. Classical phenology models, used for the prediction of bloom dates, were optimised on apricot and similar analyses are on-going on sweet cherry. Finally, data on QTL and CG are now being incorporated into the marker-assisted selection programmes.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01578240/file/2016_Quero-Garcia%20Innovations%20Agronomiques%2050.pdf BibTex
titre
Synthesis of new dicinnamoyl 4-deoxy quinic acid and methyl ester derivatives and evaluation of the toxicity against the pea aphid Acyrthosiphon pisum.
auteur
Xiubin Li, Lucie Grand, Thomas Pouleriguen, Yves Queneau, Pedro da Silva, Yvan Rahbé, Jean-Luc Poëssel, Sylvie Moebs-Sanchez
article
Organic & Biomolecular Chemistry, 2016, 14 (8), pp.2487-2497. ⟨10.1039/c5ob02483h⟩
resume
New dicinnamoyl (caffeoyl, feruloyl, ortho and para-coumaroyl) 4-deoxyquinic acid and esters were synthesized by using a new 4-deoxy quinic acid triol intermediate. The optimisation of both coupling and deprotection steps allowed the preparation in good yields of the target products either as the carboxylic acid or the methyl ester form. Eight new compounds were evaluated for their ability to influence the feeding behaviour of the pea aphid Acyrthosiphon pisum. Artificial diet bioassays showed that two compounds are toxic (mortality and growth inhibition) at lower concentrations than the reference 3,5-dicaffeoyl quinic acid.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01263941/file/Li_2016-17282b.pdf BibTex
titre
Rationalization of genes for resistance to[i] Bremia lactucae[/i] in lettuce
auteur
Lorena Parra, Brigitte Maisonneuve, Ales Lebeda, Johan Schut, Marilena Christopoulou, Marieke Jeuken, Leah Mchale, Maria-Jose Truco, Ian Crute, Richard Michelmore
article
Euphytica, 2016, 210 (3), pp.309-326. ⟨10.1007/s10681-016-1687-1⟩
resume
Lettuce downy mildew caused by[i] Bremia lactucae[/i] is the most important disease of lettuce worldwide. Breeding for resistance to this disease is a major priority for most lettuce breeding programs. Many genes and factors for resistance to [i]B. lactucae[/i] have been reported by multiple researchers over the past *50 years. Their nomenclature has not been coordinated, resulting in duplications and gaps in nominations. We have reviewed the available information and rationalized it into 51 resistance genes and factors and 15 quantitative trait loci along with supporting documentation as well as genetic and molecular information. This involved multiple rounds of consultation with many of the original authors. This paper provides the foundation for naming additional genes for resistance to [i]B. lactucae[/i] in the future as well as for deploying genes to provide more durable resistance.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
16S rRNA amplicon sequencing for épidémiologie surveys of bacteria in wildlife
auteur
Maxime Galan, Maria Razzauti, Emilie Bard, Maria Bernard, Carine Brouat, Nathalie Charbonnel, Alexandre Dehne-Garcia, Anne Loiseau, Caroline Tatard, Lucie Tamisier, Muriel Vayssier-Taussat, Hélène Vignes, Jean-François Cosson
article
mSystems, 2016, 1 (4), pp.1-22. ⟨10.1128/mSystems.00032-16⟩
resume
The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other olecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01595274/file/Galan_etal_2016_16S_rRNA_amplicon_%7B52027B95-6F29-4771-8598-12C1B18923E5%7D.pdf BibTex
titre
NBS-LRR-mediated resistance triggered by aphids: viruses do not adapt; aphids adapt via different mechanisms
auteur
Nathalie Boissot, Sophie Thomas, Veronique Chovelon, Hervé Lecoq
article
BMC Plant Biology, 2016, 16, pp.25. ⟨10.1186/s12870-016-0708-5⟩
resume
Background: Aphids are serious pest on crops. By probing with their stylets, they interact with the plant, they vector viruses and when they reach the phloem they start a continuous ingestion. Many plant resistances to aphids have been identified, several have been deployed. However, some resistances breaking down have been observed. In the melon, a gene that confers resistance to aphids has been deployed in some melon-producing areas, and aphid colony development on Vat-carrying plants has been observed in certain agrosystems. The Vat gene is a NBS-LRR gene that confers resistance to the aphid species Aphis gossypii and exhibits the unusual characteristic of also conferring resistance to non-persistently transmitted viruses when they are inoculated by the aphid. Thus, we characterized patterns of resistance to aphid and virus using the aphid diversity and we investigated the mechanisms by which aphids and viruses may adapt to the Vat gene. Results: Using a Vat-transgenic line built in a susceptible background, we described the Vat- spectrum of resistance to aphids, and resistance to viruses triggered by aphids using a set of six A. gossypii biotypes. Discrepancies between both resistance phenotypes revealed that aphid adaptation to Vat-mediated resistance does not occur only via avirulence factor alterations but also via adaptation to elicited defenses. In experiments conducted with three virus species serially inoculated by aphids from and to Vat plants, the viruses did not evolve to circumvent Vat-mediated resistance. We confirmed discrepancies between both resistance phenotypes by testing each aphid biotype with a set of thirteen melon accessions chosen to reflect the natural diversity of the melon. Inheritance studies revealed that patterns of resistance to virus triggered by aphids are controlled by different alleles at the Vat locus and at least another locus located at a short genetic distance. Therefore, resistance to viruses triggered by aphids is controlled by a gene cluster. Conclusions: Under the Flor model, changes in the avirulence gene determine the ability of the pathogen to overcome the resistance conferred by a plant gene. The Vat gene belongs to a resistance gene family that fits this pest/pathogen–plant interaction, and we revealed an additional mechanism of aphid adaptation that potentially exists in other interactions between plants and pests or pathogens.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02641458/file/2016_Boissot_BMC%20Biology_1.pdf BibTex

2015

Journal articles

titre
Allelic variation at the rpv1 locus controls partial resistance to Plum pox virus infection in Arabidopsis thaliana
auteur
Sylvain Poque, Gaëlle Pagny, Laurence Ouibrahim, Aurélie Chague, Jean-Philippe Eyquard, Mélodie Caballero, Thierry Candresse, Carole Caranta, Stéphanie Mariette, Véronique Decroocq
article
BMC Plant Biology, 2015, 15 (159), pp.159. ⟨10.1186/s12870-015-0559-5⟩
resume
Sharka is caused by Plum pox virus (PPV) in stone fruit trees. In orchards, the virus is transmitted by aphids and by grafting. In Arabidopsis, PPV is transferred by mechanical inoculation, by biolistics and by agroinoculation with infectious cDNA clones. Partial resistance to PPV has been observed in the Cvi-1 and Col-0 Arabidopsis accessions and is characterized by a tendency to escape systemic infection. Indeed, only one third of the plants are infected following inoculation, in comparison with the susceptible Ler accession. Genetic analysis showed this partial resistance to be monogenic or digenic depending on the allelic configuration and recessive. It is detected when inoculating mechanically but is overcome when using biolistic or agroinoculation. A genome-wide association analysis was performed using multiparental lines and 147 Arabidopsis accessions. It identified a major genomic region, rpv1. Fine mapping led to the positioning of rpv1 to a 200 kb interval on the long arm of chromosome 1. A candidate gene approach identified the chloroplast phosphoglycerate kinase (cPGK2) as a potential gene underlying the resistance. A virus-induced gene silencing strategy was used to knock-down cPGK2 expression, resulting in drastically reduced PPV accumulation. These results indicate that rpv1 resistance to PPV carried by the Cvi-1 and Col-0 accessions is linked to allelic variations at the Arabidopsis cPGK2 locus, leading to incomplete, compatible interaction with the virus.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://inria.hal.science/hal-01262384/file/Ouibrahim_Caranta%202015%20BMC%20Plant%20Biology%201-14_1.pdf BibTex
titre
Leaf mineral nutrient remobilization during leaf senescence and modulation by nutrient deficiency
auteur
Anne Maillard, Vincent Billard, Maria Garnica, Marion Prudent, Maria Garcia-Mina, Jean-Claude Yvin, Alain A. Ourry
article
Frontiers in Plant Science, 2015, 6, ⟨10.3389/fpls.2015.00317⟩
resume
Higher plants have to cope with fluctuating mineral resource availability. However, strategies such as stimulation of root growth, increased transporter activities, and nutrient storage and remobilization have been mostly studied for only a few macronutrients. Leaves of cultivated crops (Zea mays, Brass/ca napus, Pisum sativum, Triticum aestivum, Hordeum vulgare) and tree species (Quercus robur, Populus nigra, Alnus glutinosa) grown under field conditions were harvested regularly during their life span and analyzed to evaluate the net mobilization of 13 nutrients during leaf senescence. While N was remobilized in all plant species with different efficiencies ranging from 40% (maize) to 90% (wheat), other macronutrients (K-P-S-Mg) were mobilized in most species. Ca and Mn, usually considered as having low phloem mobility were remobilized from leaves in wheat and barley. Leaf content of Cu-Mo-Ni-B-Fe-Zn decreased in some species, as a result of remobilization. Overall, wheat, barley and oak appeared to be the most efficient at remobilization while poplar and maize were the least efficient. Further experiments were performed with rapeseed plants subjected to individual nutrient deficiencies. Compared to field conditions, remobilization from leaves was similar (N-S-Cu) or increased by nutrient deficiency (K-P-Mg) while nutrient deficiency had no effect on Mo-Zn-B-Ca-Mn, which seemed to be non-mobile during leaf senescence under field conditions. However, Ca and Mn were largely mobilized from roots (-97 and -86% of their initial root contents, respectively) to shoots. Differences in remobilization between species and between nutrients are then discussed in relation to a range of putative mechanisms.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://normandie-univ.hal.science/hal-02183523/file/2015_Maillard_Frontiers%20in%20Plant%20Science_1.pdf BibTex
titre
Innovation variétale en Prunus, 1960-2013 : les enseignements d’une analyse socio-historique co-construite avec les acteurs
auteur
Claire Lamine, Jean Pluvinage, Régis Aubenas, Vincent Faugier, Sylvaine Simon, Guy Clauzel, Magali Lamberet, Servane Penvern, Sophie Stévenin, Sophie Buléon, Lucile Garçon, Sibylle Bui, Jean Marc Audergon
article
Le Courrier de l'environnement de l'INRA, 2015, 65 (65), pp.5-18
resume
L’arboriculture fruitière se trouve dans un contexte notoirement difficile : elle est exposée non seulement à une crise que l’on qualifie désormais de structurelle, mais aussi à des attentes et contraintes à la fois contradictoires et interdépendantes, portant notamment sur la qualité environnementale, les performances agronomiques, la qualité gustative et l’aptitude à une mise en marché de plus en plus contraignante – d’autant plus qu’en cultures pérennes, les pas de temps contraignent fortement les possibilités d’évolution, par rapport aux cultures annuelles. Dans ce contexte, explorer les évolutions passées et possibles de l’arboriculture, en particulier dans une perspective de réduction des intrants et d’écologisation des pratiques, suppose de traiter des interdépendances entre les stratégies et contraintes des divers acteurs du secteur. Cet article analyse les évolutions, depuis les années 1960 jusqu’à aujourd’hui, de la sélection génétique et de l’offre variétale en pêche et abricot, dans leur interaction avec les autres éléments du système socio-technique : évolution du marché, organisation des acteurs de la filière, politiques publiques, stratégies et pratiques des exploitations agricoles.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Cooperative insertion of CO2 in diamine-appended metal-organic frameworks
auteur
Thomas M. Mcdonald, Jarad A. Mason, Xueqian Kong, Eric D. Bloch, David Gygi, Alessandro Dani, Valentina Crocellà, Filippo Giordanino, Samuel O. Odoh, Walter S. Drisdell, Bess Vlaisavljevich, Allison L. Dzubak, Roberta Poloni, Sondre K. Schnell, Nora Planas, Kyuho Lee, Tod Pascal, Liwen F. Wan, David Prendergast, Jeffrey B. Neaton, Berend Smit, Jeffrey B. Kortright, Laura Gagliardi, Silvia Bordiga, Jeffrey A. Reimer, Jeffrey R. Long
article
Nature, 2015, 519 (7543), ⟨10.1038/nature14327⟩
resume
The process of carbon capture and sequestration has been proposed as a method of mitigating the build-up of greenhouse gases in the atmosphere. If implemented, the cost of electricity generated by a fossil fuel-burning power plant would rise substantially, owing to the expense of removing CO2 from the effluent stream. There is therefore an urgent need for more efficient gas separation technologies, such as those potentially offered by advanced solid adsorbents. Here we show that diamine-appended metal-organic frameworks can behave as 'phase-change' adsorbents, with unusual step-shaped CO2 adsorption isotherms that shift markedly with temperature. Results from spectroscopic, diffraction and computational studies show that the origin of the sharp adsorption step is an unprecedented cooperative process in which, above a metal-dependent threshold pressure, CO2 molecules insert into metal-amine bonds, inducing a reorganization of the amines into well-ordered chains of ammonium carbamate. As a consequence, large CO2 separation capacities can be achieved with small temperature swings, and regeneration energies appreciably lower than achievable withstate-of-the-art aqueous amine solutions become feasible. The results provide a mechanistic framework for designing highly efficient adsorbents for removing CO2 from various gas mixtures, and yield insights into the conservation of Mg2+ within the ribulose-1,5-bisphosphate carboxylase/oxygenase family of enzymes
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Pollen tube cell walls of wild and domesticated tomatoes contain arabinosylated and fucosylated xyloglucan
auteur
Flavien Dardelle, François Le Mauff, Arnaud Lehner, Corinne Loutelier-Bourhis, Muriel Bardor, Christophe Rihouey, Mathilde Causse, Patrice Lerouge, Azeddine Driouich, Jean-Claude Mollet
article
Annals of Botany, 2015, 115 (1), pp.55-66. ⟨10.1093/aob/mcu218⟩
resume
Background and Aims In flowering plants, fertilization relies on the delivery of the sperm cells carried by the pollen tube to the ovule. During the tip growth of the pollen tube, proper assembly of the cell wall polymers is required to maintain the mechanical properties of the cell wall. Xyloglucan (XyG) is a cell wall polymer known for maintaining the wall integrity and thus allowing cell expansion. In most angiosperms, the XyG of somatic cells is fucosylated, except in the Asterid clade (including the Solanaceae), where the fucosyl residues are replaced by arabinose, presumably due to an adaptive and/or selective diversification. However, it has been shown recently that XyG of Nicotiana alata pollen tubes is mostly fucosylated. The objective of the present work was to determine whether such structural differences between somatic and gametophytic cells are a common feature of Nicotiana and Solanum (more precisely tomato) genera. Methods XyGs of pollen tubes of domesticated (Solanum lycopersicum var. cerasiforme and var. Saint-Pierre) and wild (S. pimpinellifolium and S. peruvianum) tomatoes and tobacco (Nicotiana tabacum) were analysed by immunolabelling, oligosaccharide mass profiling and GC-MS analyses. Key Results. Pollen tubes from all the species were labelled with the mAb CCRC-M1, a monoclonal antibody that recognizes epitopes associated with fucosylated XyG motifs. Analyses of the cell wall did not highlight major structural differences between previously studied N. alata and N. tabacum XyG. In contrast, XyG of tomato pollen tubes contained fucosylated and arabinosylated motifs. The highest levels of fucosylated XyG were found in pollen tubes from the wild species. Conclusions The results clearly indicate that the male gametophyte (pollen tube) and the sporophyte have structurally different XyG. This suggests that fucosylated XyG may have an important role in the tip growth of pollen tubes, and that they must have a specific set of functional XyG fucosyltransferases, which are yet to be characterized.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The origin of the self-compatible almond ‘Guara’
auteur
Federico Dicenta, Raquel Sánchez-Pérez, Manuel Rubio, José Egea, I. Batlle, X. Miarnau, M. Palasciano, E. Lipari, Carole C. Confolent, Pedro Martínez-Gómez, Henri Duval
article
Scientia Horticulturae, 2015, 197, pp.1-4. ⟨10.1016/j.scienta.2015.11.005⟩
resume
‘Guara’ has been the most planted almond cultivar in Spain in recent years. The introducers of this cultivar reported its origin as unknown and suggested that it is related to the Italian almond cultivar ‘Tuono’. Indeed, the experience of farmers and researchers has revealed strong similarities between ‘Guara’ and ‘Tuono’. In order to compare the identity of the two cultivars, their genetic profiles (fingerprints) were determined with a set of 12 SSR markers used to analyse the INRA clones of ‘Guara’ and ‘Tuono’ as well as two clones considered synonymous with ‘Tuono’, namely ‘Supernova’ and ‘Mazzetto’. A supplementary set of 23 SSRs was also analysed in ‘Guara’ and ‘Tuono’ samples from different reference collections of CEBAS-CSIC (Murcia, Spain), INRA (Avignon, France), IRTA (Constantí, Spain), and the University of Bari (Bari, Italy). The results confirmed that ‘Guara’ and ‘Tuono’ present identical DNA fingerprints for the 35 SSRs analysed. This genotypic information together with the similar characteristics of the two cultivars demonstrates that Spanish ‘Guara’ is actually the same cultivar as the Italian ‘Tuono’
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Whole-genome analysis of diversity and SNP-major gene association in peach germplasm
auteur
Diego Micheletti, Maria Teresa Dettori, Sabrina Micali, Valeria Aramini, Igor Pacheco, Cassia da Silva Linge, Stefano Foschi, Elisa Banchi, Teresa Barreneche, Bénédicte Quilot-Turion, Patrick Lambert, Thierry Pascal, Iglesias Ignasi, Joachim Carbo, Li-Rong Wang, Rui-Juan Ma, Xiongwei Li, Zhong-Shan Gao, Nelson Nazzicari, Michela Troggio, Danièle Bassi, Laura Rossini, Ignazio Verde, Francois Laurens, Pere Arús, Maria José Aranzana
article
PLoS ONE, 2015, 10 (9), 19 p. ⟨10.1371/journal.pone.0136803⟩
resume
Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding program
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01210020/file/Quilot-Turion_Lambert%202015%20PlosOne%201-19_1.pdf BibTex
titre
Genome-enabled phylogeographic investigation of the quarantine pathogen Ralstonia solanacearum race 3 biovar 2 and screening for sources of resistance against its core effectors
auteur
Christopher R. Clarke, David J Studholme, Byron Hayes, Brendan Runde, Alexandra Weisberg, Rongman Cai, Tadeusz Wroblewski, Marie-Christine Daunay, Emmanuel Wicker, Jose Castillo, Boris Vinatzer
article
Phytopathology, 2015, 105, pp.1-54. ⟨10.1094/PHYTO-12-14-0373-R⟩
resume
Phylogeographic studies inform about routes of pathogen dissemination and are instrumental for improving import/export controls. Genomes of seventeen isolates of the bacterial wilt and potato brown rot pathogen Ralstonia solanacearum race 3 biovar 2 (R3bv2), a select agent in the USA, were thus analyzed to get insight into the phylogeography of this pathogen. Thirteen of fourteen isolates from Europe, Africa, and Asia were found to belong to a single clonal lineage while isolates from South America were genetically diverse and carried ancestral alleles at the analyzed genomic loci consistent with a South American origin of R3bv2. The R3bv2 isolates share a core repertoire of thirty-one type III-secreted effector genes representing excellent candidates to be targeted with resistance genes in breeding programs to develop durable disease resistance. Towards this goal, 27 R3bv2 effectors were tested in eggplant, tomato, pepper, tobacco, and lettuce for induction of a hypersensitive-like response indicative of recognition by cognate resistance receptors. Fifteen effectors, eight of them core effectors, triggered a response in one or more plant species. These genotypes may harbor resistance genes that could be identified and mapped, cloned and expressed in tomato or potato, for which sources of genetic resistance to R3bv2 are extremely limited.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A multi-Ievel omic approach of tomato fruit quality
auteur
Jiaxin Xu, Laura Pascual-Banuls, Nelly Desplat, Mireille Faurobert, Yves Gibon, Annick Moing, Mickaël Maucourt, P. Ballias, Catherine Deborde, Jean-Paul Bouchet, Dominique Brunel, Marie-Christine Le Paslier, Mathilde Causse
article
Acta Horticulturae, 2015, 1099, pp.793-800. ⟨10.17660/ActaHortic.2015.1099.100⟩
resume
Improvement of fruit quality traits is a major goal for tomato breeding. Deciphering the genetic diversity and inheritance of fruit quality components is thus necessary. For this purpose, we carried out a large multi-level omic experiment. Eight contrasted lines and 4 of their F-1 hybrids were phenotyped for fruit development traits. Fruit pericarp samples were analysed at 2 stages (cell expansion and orange ripe) and different scales: (1) untargeted profiling of major polar metabolites, (2) activities of 28 enzymes involved in primary metabolism, (3) proteome profiles revealed by 2D-PAGE and identification of 470 protein spots showing quantitative variations and (4) gene expression analysis by Digital Gene Expression. In parallel, the 8 lines were resequenced and more than 3 million SNPs identified when aligned on the reference tomato genome. This experiment allowed us to assess and compare the range of variability and inheritance mode of the metabolic traits and expression data. Correlation networks were constructed within and between levels of analysis to identify regulatory networks. Diversity of candidate genes could thus be analysed, relating the polymorphisms at the sequence levels with their expression.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Des légumes qui grimpent
auteur
Michel Pitrat
article
Jardins de France, 2015, 638, pp.24-25
resume
Plusieurs espèces légumières sont des plantes grimpantes, soit par des vrilles comme le pois ou les Cucurbitacées (melon, concombre, courge, pastèque…), soit grâce à une tige volubile comme le haricot ou, parmi les espèces tropicales, l’igname et plusieurs espèces de [i]Vigna[/i]. Les formes sauvages de ces espèces sont à longue tige grimpante mais, à la suite de la domestication, au cours de la diversification, des mutants ont été sélectionnés. Ils sont caractérisés par des entre-nœuds plus courts, la perte de la volubilité de la tige et éventuellement la disparition des vrilles.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01312115/file/2015_Pitrat_Jardins%20de%20France%20638_1.pdf BibTex
titre
L’aubergine, de l’état sauvage ancestral à aujourd’hui
auteur
Marie-Christine Daunay
article
Jardins de France, 2015, 635, pp.39-41
resume
L’aubergine (Solanum melongena L.) est une espèce légumière associée dans notre inconscient collectif à l’été et au régime alimentaire méditerranéen. Pourtant, on la trouve toute l’année sur les étals car sa production s’est désaisonnalisée en Europe depuis une trentaine d’années, avec le développement des cultures sous abris en contre saison, et l’importation en provenance en particulier d’Espagne. Plante de lumière et de chaleur par nature, elle est appréciée des cuisiniers pour ses qualités texturales, de rétention des saveurs dans les plats cuisinés et son goût propre, parfois légèrement amer
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02637174/file/Daunay-2015%20histoire-de-plantes_1.pdf BibTex
titre
Nanoparticles functionalised with an anti-platelet human antibody for in vivo detection of atherosclerotic plaque by magnetic resonance imaging.
auteur
Marie-Josée Jacobin-Valat, Jeanny Laroche-Traineau, Mélusine Larivière, Stéphane Mornet, Stephane Sanchez, Marc Biran, Caroline Lebaron, Julien Boudon, Sabrina Lacomme, Martine Cérutti, Gisèle Clofent-Sanchez
article
Nanomedicine: Nanotechnology, Biology and Medicine, 2015, 11 (4), pp.927-937. ⟨10.1016/j.nano.2014.12.006⟩
resume
Atherosclerosis is an inflammatory disease associated with the formation of atheroma plaques likely to rupture in which platelets are involved both in atherogenesis and atherothrombosis. The rupture is linked to the molecular composition of vulnerable plaques, causing acute cardiovascular events. In this study we propose an original targeted contrast agent for molecular imaging of atherosclerosis. Versatile USPIO (VUSPIO) nanoparticles, enhancing contrast in MR imaging, were functionalised with a recombinant human IgG4 antibody, rIgG4 TEG4, targeting human activated platelets. The maintenance of immunoreactivity of the targeted VUSPIO against platelets was confirmed in vitro by flow cytometry, transmission electronic and optical microscopy. In the atherosclerotic ApoE(-/-) mouse model, high-resolution ex vivo MRI demonstrated the selective binding of TEG4-VUSPIO on atheroma plaques. It is noteworthy that the rationale for targeting platelets within atherosclerotic lesions is highlighted by our targeted contrast agent using a human anti-αIIbβ3 antibody as a targeting moiety. Current clinical assessment of atherosclerotic plagues is suboptimal. The authors in the article designed functionalized superparamagnetic iron oxide nanoparticles with TEG4, a recombinant human antibody, to target activated platelets. By using MRI, these nanoparticles can be utilized to study the process of atheroma pathogenesis.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01228125/file/2015-166.pdf BibTex
titre
The spatial distribution of [i]Mustelidae[/i] in France.
auteur
Clément Calenge, Joel Chadoeuf, Christophe Giraud, Sylvie Huet, Romain Julliard, Pascal Monestiez, Jeremy Piffady, David Pinaud, Sandrine Ruette
article
PLoS ONE, 2015, 10 (3), pp.e0121689. ⟨10.1371/journal.pone.0121689⟩
resume
We estimated the spatial distribution of 6 Mustelidae species in France using the data collected by the French national hunting and wildlife agency under the "small carnivorous species logbooks" program. The 1500 national wildlife protection officers working for this agency spend 80% of their working time traveling in the spatial area in which they have authority. During their travels, they occasionally detect dead or living small and medium size carnivorous animals. Between 2002 and 2005, each car operated by this agency was equipped with a logbook in which officers recorded information about the detected animals (species, location, dead or alive, date). Thus, more than 30000 dead or living animals were detected during the study period. Because a large number of detected animals in a region could have been the result of a high sampling pressure there, we modeled the number of detected animals as a function of the sampling effort to allow for unbiased estimation of the species density. For dead animals -- mostly roadkill -- we supposed that the effort in a given region was proportional to the distance traveled by the officers. For living animals, we had no way to measure the sampling effort. We demonstrated that it was possible to use the whole dataset (dead and living animals) to estimate the following: (i) the relative density -- i.e., the density multiplied by an unknown constant -- of each species of interest across the different French agricultural regions, (ii) the sampling effort for living animals for each region, and (iii) the relative detection probability for various species of interest.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01139313/file/journal.pone.0121689_%7B9E0313FC-B1B2-4270-AED0-C28F1708ECC1%7D.pdf BibTex
titre
Evolution of diversity of fruits and vegetables crops
auteur
Michel Pitrat, Jean Marc Audergon
article
Acta Horticulturae, 2015, 1099, pp.567-576
resume
Due to climatic conditions and cultural traditions, only a part of the world fruit and vegetable diversity is cultivated in Europe. Since the 1950s, major evolutions have affected most of the cultivated species at several levels: (i) an enlargement of the number of cultivated species, with the introduction for instance of kiwi (Actinidia), nashi (Pyrus pyrifolia) or Japanese plums (Prunus salicina); (ii) new cultigroups or botanical varieties have been introduced or created introducing market segmentation for instance red apricot, flat peach, parthenocarpic cucumber, or red Belgian endive; (iii) a tremendous increase of the number of available cultivars with almost 20000 cultivars of vegetables registered in the European catalogue. Nevertheless for most of the species, the number of cultivars has a tendency to increase in the most important cultigroups and to decrease in minor cultigroups (winter radish, running beans, peas, etc.). The diversity at the genotypic level can be estimated by neutral molecular markers like microsatellites or SNPs. Several situations have been described: (i) a good relationship between genotype and phenotype for instance in cherry tomatoes versus large-fruited types or in peach; (ii) a correlation between genotype and geographical origin; (iii) or a mix of both with foundation effects of a small number of parental accessions. New prospects or concerns based onto climatic change potential impacts and production durability have to be addressed. Development of future cultivars requires the mobilization of new adapted germplams. The characterization of the world existing resources on both morphological and genotypic bases is of major importance.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A cucurbit androecy gene reveals how unisexual flowers develop and dioecy emerges
auteur
Adnane Boualem, Christelle Troadec, Céline Camps, Afef Lemhemdi, Halima Morin, Marie-Agnès Sari, Rina Fraenkel-Zagouri, Irina Kovalski, Catherine Dogimont, Rafael Perl-Treves, Abdelhafid Bendahmane
article
Science, 2015, 350 (6261), pp.688-691. ⟨10.1126/science.aac8370⟩
resume
Understanding the evolution of sex determination in plants requires identifying the mechanisms underlying the transition from monoecious plants, where male and female flowers coexist, to unisexual individuals found in dioecious species. We show that in melon and cucumber, the androecy gene controls female flower development and encodes a limiting enzyme of ethylene biosynthesis, ACS11. ACS11 is expressed in phloem cells connected to flowers programmed to become female, and ACS11 loss-of-function mutants lead to male plants (androecy). CmACS11 represses the expression of the male promoting gene CmWIP1 to control the development and the coexistence of male and female flowers in monoecious species. Because monoecy can lead to dioecy, we show how a combination of alleles of CmACS11 and CmWIP1 can create artificial dioecy
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genomic variation in tomato, from wild ancestors to contemporary breeding accessions
auteur
José Blanca, Javier Montero-Pau, Christopher Sauvage, Guillaume Bauchet, Eudald Illa, María José Díez, David Francis, Mathilde M. Causse, Esther van Der Knaap, Joaquin Canizares
article
BMC Genomics, 2015, 16, 19 p. ⟨10.1186/s12864-015-1444-1⟩
resume
Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection. Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencie for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and "cherry tomato" are not synonymous terms. The morphologically-based term "cherry tomato" included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups. This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02638064/file/Blanca_BMCgenomics_2015_1.pdf BibTex
titre
Towards the identification of Type III effectors associated to Ralstonia solanacearum virulence on tomato and eggplant
auteur
Flora Pensec, Aurore Lebeau, Marie-Christine Daunay, Frédéric Chiroleu, Alice Guidot, Emmanuel Wicker
article
Phytopathology, 2015, 105 (12), pp.1529-1544. ⟨10.1094/PHYTO-06-15-0140-R⟩
resume
For the development of pathogen-informed breeding strategies, identifying the microbial genes involved in interactions with the plant is a critical step. To identify Type III effector (T3E) repertoires associated to virulence of the bacterial wilt (BW) pathogen Ralstonia solanacearum on Solanaceous crops, we used an original association genetics approach combining DNA microarray data and pathogenicity data on resistant eggplant, pepper and tomato accessions. From this first screen, twenty-five Type III effectors were further full-length PCR-amplified within a 35-strain field collection, to assess their distribution and allelic diversity. Six T3E repertoire groups were identified, within which 11 representative strains were chosen to challenge the BW-resistant eggplants "Dingras multiple Purple" and "AG91-25", and the tomato Hawaii 7996. The virulence or avirulence phenotypes could not be explained by specific T3E repertoires, but rather by individual T3E genes. We identified seven highly avirulence-associated genes, among which ripP2, primarily referenced as conferring avirulence to Arabidopsis thaliana. Interestingly, no T3E was associated to avirulence to both eggplants. Highly virulence-associated genes were also identified: ripA5_2, ripU, and ripV2. This study should be regarded as a first step towards investigating both avirulence or virulence function of the highlighted genes, but also their evolutionary dynamics in natural R. solanacearum populations
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02637870/file/phyto-06-15-0140-r_1.pdf BibTex
titre
Fusarium oxysporum f. sp. melonis chez le melon, enseignements issus du projet VASCUlég
auteur
François Villeneuve, François Latour, Théophile Théry, Véronique Edel-Hermann, Christian Steinberg, Michel Pitrat
article
Infos CTIFL, 2015, 315, pp.45-47
resume
Fusarium wilt of melon, caused by Fusariumoxysporum f.sp. melonis (F.o.melonis),is still a major problem for growers. Aresearch programme was therefore developpedincluding 23 partners (VASCUlég).Analysing the situation revealed that thebioagressors are adapting, particularlyF.o.melonis race 1.2 whether it be on its ownor associated with other pathogens. Molecularcharacterisation of the F.o.melonisstrains shows strong genetic diversity.However, new sources of resistance to therace 1.2 of F.o.melonis were identified. Thisresult must be used in combination with acertain number of other complementarytechniques tested within the framework ofthe project, such as the cropping system,biofumigation, companion plants, biocontrolagents and plant defence stimulators.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Le greffage des légumes : l’intérêt et la pratique
auteur
Michel Javoy, Michel Pitrat, Jean-Daniel Arnaud
article
Jardins de France, 2015, 637, pp.6-8
resume
Le greffage est une technique horticole très ancienne, le plus souvent utilisée pour des plantes pérennes ligneuses. Le greffage des rosiers est le plus emblématique aux yeux des jardiniers. Le greffage des légumes, qui ne se pratique que pour les légumes fruits, est plus récent. Il a débuté en France avec les premières cultures maraîchères sous serres à grande échelle vers 1960.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Integrative approach of tomato fruit texture using multiblock analysis
auteur
Rémy Aurand, Mireille Faurobert, Mohamed Hanafi, Gerard Mazerolles, Raphael Tisiot, Laurent Rosso, Brigitte Navez, Nadia Bertin
article
Acta Horticulturae, 2015, 1099, pp.827-834. ⟨10.17660/ActaHortic.2015.1099.105⟩
resume
Tomato fruit texture is one of the most critical quality traits for both the consumer and the production chain. Texture is a complex trait for which several QTL and genes were found. However, interactions between the molecular, histological, physical and biochemical components of fruit texture have been rarely investigated. In this work an integrative approach based on multiple co-inertia analysis (MCOA) was applied to point out links among the different levels: from protein to fruit, then to identify main physiological mechanisms involved in fruit texture. Three contrasted parental lines (‘Cervil’, ‘Levovil’, ‘VilB’) and three derived QTL-NILs harbouring texture QTL on chromosome 4 and 9 were analyzed. Measurements were performed at cell expansion stage, at red ripe stage and after 7-days postharvest storage at 20°C. To increase texture variability, water deficit was induced by decreasing water supply by 40% from flowering of the third truss. Three blocks of data (texture, physico-chemical traits and proteome datasets) were analysed. Results showed a common multi-scale structure obtained from the three datasets with a main contribution of texture and biochemical blocks. At all levels, MCOA outlined strong genotype discrimination, indicating that the genetic factor was the main factor of variability, in contrast with water deficit. The first common component separated the genetic background and correlated with firmness and sugar traits. The second component represented QTL effect. The percentage of the variance of the protein block taken into account to build the common structure was low. Proteins which mainly contributed to the common components at the three developmental stages were implicated in carbohydrate metabolism. Multiple co-inertia analysis provides an interesting tool to characterize complex trait such as fleshy fruit texture by integrating several levels of studies.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La parthénocarpie : des fruits sans graines
auteur
Michel Pitrat
article
Jardins de France, 2015, 633, pp.1-2
resume
Il nous paraît normal qu’il y ait des graines dans les fruits charnus : pépins des pommes, des poires ou des agrumes, noyaux des cerises, des pêches ou des abricots, graines des melons ou des pastèques... Mais les clémentines n’en ont pas et qui a vu des graines de banane ? Les fruits parthénocarpiques ou apyrènes sont des fruits sans graines (seedless en anglais).
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02641619/file/2015_Pitrat%20_Jardins%20de%20France_1.pdf BibTex
titre
Petites et grandes histoires de l’aubergine
auteur
Marie-Christine Daunay, Harry S. Paris, Jules Janick
article
Jardins de France, 2015, 637, pp.4-6
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02630000/file/Daunay%202015%20Histoire-de-plantes%204-6_1.pdf BibTex
titre
La protection intégrée : alternative efficace au « tout phytosanitaire »
auteur
Maurice Jullian, Véronique Lefebvre
article
Cahier des Techniques de l'INRA, 2015, 86, 14 p
resume
Dès les années 2000, l’Unité de Recherche en Génétique et amélioration des fruits et légumes (GAFL, INRA) avait constaté la perte d’efficacité des applications de produits phytosanitaires sur la protection des cultures dans ses espaces confinés et extérieurs ; ce constat suggérait clairement l’adaptation des populations de bioagresseurs aux méthodes de lutte chimique. L’Unité décide alors collégialement d’appliquer sur son site la protection biologique intégrée, qui connait ses premiers succès sur les cultures de fruits et légumes dans les centres expérimentaux des alentours et à l’étranger. La mise en oeuvre de cette solution alternative nécessitait une analyse globale et en profondeur de l’écosystème du site et des contraintes expérimentales liées aux programmes de recherche développés par l’Unité. Les mesures prises ont donc ciblé d’abord l’environnement écosystémique du site, les infrastructures expérimentales, les pratiques culturales et le comportement du personnel y travaillant, et enfin bien sûr la conduite de la culture elle-même. Elles se sont appuyées sur l’association de multiples mesures prophylactiques et de moyens de lutte biologique. En 15 ans, les pratiques expérimentales de l’Unité GAFL se sont profondément transformées pour arriver à une situation d’équilibre stable sur le long terme entre l’arrivée régulière de bio-agresseurs et la diminution de leur nombre en dessous d’un seuil de nocivité grâce à la l’installation d’auxiliaires indigènes ou d’élevage. La réussite de cette méthode de lutte exige une surveillance quotidienne du site au sens large (abords, infrastructures, plante à plante) ainsi qu’une réactivité accrue dès l’apparition d’un foyer infectieux. L’équilibre entre ravageurs et auxiliaires est fragile ; son maintien repose sur l’implication de l’ensemble du personnel, celui dédié au suivi des installations expérimentales et celui des équipes de recherche intervenant sur les plantes ; il demande, en outre, des actions de formation et de communication continues au sein de l’Unité. Les efforts consentis par le collectif du GAFL sur les 15 dernières années ont permis ainsi de réduire les applications de produits phytosanitaires de près de 80% et contribuent aujourd’hui à la fois à offrir un lieu de travail sain à son personnel, ainsi qu’à maintenir une certaine harmonie avec l’environnement.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02634924/file/Jullian_Lefebvre%20cahiers%20des%20tech.%202015%201-14_1.pdf BibTex
titre
Efficiency of selection in early generations of potato families with a view toward heat tolerance
auteur
Izabel Cristina Rodrigues de Figueiredo, César Augusto Brasil Pereira Pinto, Guilherme Henrique Martins Rodrigues Ribeiro, Leandro de Oliveira-Lino, Danilo Hottis Lyra, Carolina Mariane Moreira
article
Crop Breeding and Applied Biotechnology, 2015, 15 (4), pp.210-217. ⟨10.1590/1984-70332015v15n4a37⟩
resume
The aim of this study was to evaluate the efficiency of selection of potato families in early generations for heat tolerance. Thirty families were evaluated in the seedling generation (SG), first clonal generation (FCG) in the field and greenhouse under high temperature conditions, and second clonal generation (SCG) under mild temperatures. The mean of the families was obtained in each generation. The 16 most productive families in FCG were selected, and the clones of these families were evaluated in experiments in the winter and rainy crop seasons. The results showed that family selection for tuber shape may be applied as of the SG. It was also observed that family selection in the FCG and SCG for yield and tuber specific gravity contributed to identification of clones tolerant to heat and responsive to environmental improvement
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01273699/file/cbab_2015_%7B7E4FF425-3E44-42F4-8D12-C0DD7C603C4F%7D.pdf BibTex
titre
Host genetic resistance to root-knot nematodes, Meloidogyne spp., in Solanaceae: from genes to the field
auteur
Arnaud Barbary, Caroline Djian-Caporalino, Alain Palloix, Philippe Castagnone-Sereno
article
Pest Management Science, 2015, 71 (12), pp.1591-1598. ⟨10.1002/ps.4091⟩
resume
Root-knot nematodes (RKNs) heavily damage most solanaceous crops worldwide. Fortunately, major resistance genes are available in a number of plant species, and their use provides a safe and economically relevant strategy for RKN control. From a structural point of view, these genes often harbour NBS-LRR motifs and are organized in syntenic clusters in solanaceous genomes. Their introgression from wild to cultivated plants remains a challenge for breeders, although facilitated by marker-assisted selection. As shown with other pathosystems, the genetic background into which the resistance genes are introgressed is of prime importance on both the expression of the resistance and its durability, as exemplified with the recent discovery of QTLs conferring quantitative resistance to RKNs in pepper. The deployment of resistance genes at a large scale may result in the emergence and spread of virulent nematode populations able to overcome them, as already reported in tomato and pepper. Therefore, careful management of the resistance genes available in solanaceous crops is crucial to avoid significant reduction of the duration of the RKN genetic control in the field. From that perspective, only rational management combining breeding and cultivation practices will allow the design and implementation of innovative, sustainable crop production systems that protect the resistance genes and maintain their durability
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The potential for crop to wild hybridization in eggplant (Solanum melongena; Solanaceae) in southern India
auteur
Priya Davidar, Allison A. Snow, Muthu Rajkumar, Rémy Pasquet, Marie-Christine Daunay, Evans Mutegi
article
American Journal of Botany, 2015, 102 (1), pp.129-139. ⟨10.3732/ajb.1400404⟩
resume
Premise of the study: In India and elsewhere, transgenic Bt eggplant (Solanum melongena) has been developed to reduce insect herbivore damage, but published studies of the potential for pollen-mediated, crop-to-wild gene flow are scant. This information is useful for risk assessments as well as in situ conservation strategies for wild germplasm. Methods: In 2010-2014, we surveyed 23 populations of wild/weedy eggplant (Solanum insanum; known as wild brinjal), carried out hand-pollination experiments, and observed pollinators to assess the potential for crop-to-wild gene flow in southern India. Key results: Wild brinjal is a spiny, low-growing perennial commonly found in disturbed sites such as roadsides, wastelands, and sparsely vegetated areas near villages and agricultural fields. Fourteen of the 23 wild populations in our study occurred within 0.5 km of cultivated brinjal and at least nine flowered in synchrony with the crop. Hand crosses between wild and cultivated brinjal resulted in seed set and viable F-1 progeny. Wild brinjal flowers that were bagged to exclude pollinators did not set fruit, and fruit set from manual self-pollination was low. The exserted stigmas of wild brinjal are likely to promote outcrossing. The most effective pollinators appeared to be bees (Amegilla, Xylocopa, Nomia, and Heterotrigona spp.), which also were observed foraging for pollen on crop brinjal. Conclusion: Our findings suggest that hybridization is possible between cultivated and wild brinjal in southern India. Thus, as part of the risk assessment process, we assume that transgenes from the crop could spread to wild brinjal populations that occur nearby.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum, Solanaceae) in southern India: implications for conservation
auteur
Evans Mutegi, Allison A. Snow, Muthu Rajkumar, Rémy Pasquet, Hopeland Ponniah, Marie-Christine Daunay, Priya Davidar
article
American Journal of Botany, 2015, 102 (1), pp.140-148. ⟨10.3732/ajb.1400403⟩
resume
Premise of the study: Crop wild relatives represent important genetic resources for crop improvement and the preservation of native biodiversity. Eggplant (Solanum melongena), known as brinjal in India, ranks high among crops whose wild gene pools are underrepresented in ex situ collections and warrant urgent conservation. Knowledge of outcrossing rates and patterns of genetic variation among wild populations can aid in designing strategies for both in situ and ex situ preservation. Methods: We used 14 microsatellite (simple sequence repeat) markers to examine genetic diversity, population structure, and outcrossing in 10 natural populations of wild/weedy eggplant (S. insanum = S. melongena var. insanum) and three cultivated populations in southern India. Key results: Multilocus F-ST analyses revealed strong differentiation among populations and significant isolation by distance. Bayesian model-based clustering, principal coordinate analysis, and hierarchical cluster analysis grouped the wild/weedy populations into three major clusters, largely according to their geographic origin. The three crop populations were similar to each other and grouped with two wild/weedy populations that occurred nearby. Outcrossing rates among the wild/weedy populations ranged from 5-33%, indicating a variable mixed-mating system. Conclusion: Geographic isolation has played a significant role in shaping the contemporary patterns of genetic differentiation among these populations, many of which represent excellent candidates for in situ conservation. In two cases, close genetic affinity between cultivars and nearby wild/weedy populations suggests that gene flow has occurred between them. To our knowledge, this is the first study investigating population-level patterns of genetic diversity in wild relatives of eggplant.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Potyviruses differ in their requirement for TOR signaling
auteur
Laurence Ouibrahim, Ana Giner Rubio, André Moretti, Marie-Helene Montane, Benoît Menand, Christian Meyer, Christophe Robaglia, Carole Caranta
article
Journal of General Virology, 2015, in press (9), 17 p. ⟨10.1099/vir.0.000186⟩
resume
Potyviruses are important plant pathogens that rely on many plant cellular processes for successful infection. TOR (target of rapamycin) signaling is a key eukaryotic energy signaling pathway controlling many cellular processes such as translation and autophagy. The dependence of potyviruses for an active TOR signaling was examined. Arabidopsis lines downregulated for TOR by RNAi were challenged with potyviruses Watermelon Mosaic (WMV) and Turnip Mosaic (TuMV). WMV accumulation was found to be severely altered while TuMV accumulation was only slightly delayed. In another approach, using AZD-8055, an active site inhibitor of the TOR kinase, WMV infection was found to be strongly affected. Moreover, AZD-8055 application can cure WMV infection. In contrast, TuMV infection was not affected by AZD-8055. This suggests that potyviruses have different cellular requirements for an active plant TOR signaling
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Les plantes potagères dans les livres de Vilmorin-Andrieux et Cie
auteur
Michel Pitrat
article
Jardins de France, 2015, 637
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Resistances to anthracnose (Colletotrichum acutatum) of Capsicum mature green and ripe fruit are controlled by a major dominant cluster of QTLs on chromosome P5
auteur
Chunying Sun, Sheng Li Mao, Zheng Haia Zhang, Alain Palloix, Li Hao Wang, Bao Xi Zhang
article
Scientia Horticulturae, 2015, 181, pp.81-88. ⟨10.1016/j.scienta.2014.10.033⟩
resume
Anthracnose (Colletotrichum spp.) is a serious disease worldwide in pepper (Capsicum) production. Inher-itance of resistance to Colletotrichum acutatum from a Capsicum chinense accession (PBC932) was studiedin a BC1population derived from a hybrid with Capsicum annuum line 77013 (susceptible) using a QTLanalysis method. Resistance test was performed on detached mature green and mature red fruit underlaboratory conditions by evaluated in disease incidence, true lesion diameter and overall lesion diameter.Based on a linkage map with 14 linkage groups, 385 markers (SSR, InDel and CAPS), 1310.2 cM in length,inclusive Composite Interval Mapping (ICIM) revealed main effect QTLs located in a close marker intervalon P5 chromosome for all fruit stages and resistance criteria, and four minor-effect QTLs only at greenmature stage. Identification of recombinant individuals suggested that resistance in green versus red fruitmay be controlled by distinct genes within the QTL interval on P5
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Snapmelon ([i]Cucumis melo[/i] L. [i]Momordica[/i] group), an indigenous cucurbit from India with immense value for melon breeding
auteur
Narinder P.S. Dhillon, H. Singh, Michel Pitrat, Antonio J. Monforte, James D. Mccreight
article
Acta Horticulturae, 2015, 1102, pp.99-108
resume
Snapmelon ([i]Cucumis melo[/i] L. [i]Momordica[/i] Group; 2n=2x=24) is native to India, where it is widely cultivated and is commonly called ‘phut’, which means to split. Immature fruits are cooked or eaten raw. In this paper we review the wealth of genetic resources in Indian snapmelon landraces for resistance to fungal and viral diseases, nematodes, and insects, and tolerance to drought, soil salinity, and high temperature. Global melon breeding programs have transferred many of these qualities into openpollinated and hybrid cultivars of sweet melons cultivated in Africa, Asia, Australia, Europe, and the Americas. Snapmelon is a source of high fruit acidity, a trait that has been utilized to breed uniquely flavored melon cultivars. Resistance genes to combat pathogens and pests, and to strengthen crop resilience against climate change have been identified in snapmelon collections from various parts of India. More effort is needed to collect, characterize, evaluate and preserve snapmelon diversity in genebanks
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01351898/file/Pitrat%202015%20Acta%20Hort%2099-108_1.pdf BibTex
titre
Building high-density peach linkage maps based on the ISPC 9K SNP chip for mapping mendelian traits and QTLS: benefits and drawbacks
auteur
Jehan-Baptiste Mauroux, Bénédicte Quilot-Turion, Thierry Pascal, Patrick Lambert, Michela Troggio, Ignazio Verde, Diego Micheletti, Maria José Aranzana
article
Acta Horticulturae, 2015, 1084, pp.113-118. ⟨10.17660/ActaHortic.2015.1084.13⟩
resume
FruitBreedomics" European project has been designed by an international consortium including scientists, stakeholders and breeding companies. One of its aims is to increase the efficiency of breeding programs in apple Malus xdomestica) and peach Prunus persica) by enabling Marker Assisted Breeding MAB) using novel genomic tools. In the frame of this project, five peach mapping populations from the UGAFL (Unite de Genetique et Amelioration des Fruits et Legumes) peach breeding program two intraspecific F-2, two interspecific F-1 derived from P. davidiana and one self-pollinated derived from 'Bolinha') segregating for mendelian traits and/or Quantitative Trait Loci QTLs) for pest resistance and fruit quality were genotyped using the 9K SNP Illumina Infinium II Bead-chip delivered by the International Peach SNP Consortium IPSC). Based on these data, genetic maps were then constructed; however mapping results were contrasted depending on the population considered. All maps aligned with the 8 pseudo-molecules of the Prunus persica Whole Genome sequence v1.0 IPGI), but the best polymorphisms and coverage were obtained with the F-2 populations, for which twenty to twenty-nine percent of the SNPs were polymorphic covering 500 loci on average. However, these loci were unevenly distributed, although covering most of the peach genome. In contrast, for the F-1 populations, only 5% of the SNPs were polymorphic in P. davidiana and the selfing of 'Bolinha' resulting in low coverage and very heterogeneous distributions. As primary consequence, this demonstrates the poor transferability of such a tool between species, even tightly related, and additionally highlights the relatively low efficiency of SNPs in term of useful polymorphism when parents belong to close peach germplasms. Consequently, regions containing QTLs and major genes could be insufficiently covered and need additional SNP development for MAB. The relevancy of using general medium-range SNP bead-chips for breeding purposes is discussed in this study.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01349159/file/Mauroux_Lambert%202015%20Acta%20Horticulturae%201084_1.pdf https://hal.science/hal-01349159/file/Mauroux_Lambert%202015%20Acta%20Horticulturae%201084_2.docx BibTex
titre
Use of [i]Prunus[/i] genetic diversity for peach rootstocks
auteur
Henri Duval
article
Acta Horticulturae, 2015, 1084, pp.277-282
resume
In the Redher classification, the most widely adopted classification of Prunus L., there are more than 200 species divided into five subgenera with three for the stone fruits: Amygdalus, Prunophora and Cerasus. The major peach rootstocks are included in the subgenera Amygdalus (peach and almond species), mainly because there are no or very few problems of incompatibility grafting. Currently, the peach seedlings that are easy to produce and productive, are often used as peach rootstock, except in the calcareous soils where peachxalmond hybrids are preferred. Prunophora species are chosen for a better adaptability to heavy soils, or for introducing resistance genes to nematodes, to fungus or bacterial soil-diseases. The grafting of Prunophora species induces lower vigor for Amygdalus species and can initiate more problems of grafting-incompatibility. So, a breeding program which integrates Prunophora species will be longer in time than one using only Amygdalus species. The main selected traits in the world peach rootstock breeding programs worldwide are still nematode resistance, waterlogging, vigor control, calcareous soils, and drought. For each trait, several Prunus genotypes may fit the requested characteristics, and it is important to choose the best crossing strategy which allows the breeder to obtain the best performance for all traits in order to replace an existing rootstock.
typdoc
Journal articles
Accès au bibtex
BibTex

2014

Journal articles

titre
Measurement of delta C-13 values of soil amino acids by GC-C-IRMS using trimethylsilylation: a critical assessment
auteur
Mauro Rubino, Sylvie Milin, Antonio d'Onofrio, Patrick Signoret, Christine Hatté, Jérôme Balesdent
article
Isotopes in Environmental and Health Studies, 2014, 50 (4), pp.516-530. ⟨10.1080/10256016.2014.959444⟩
resume
In this study, we evaluated trimethylsilyl (TMS) derivatives as derivatization reagents for the compound-specific stable carbon isotope analysis of soil amino acids by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). We used non-proteinogenic amino acids to show that the extraction-derivatization-analysis procedure provides a reliable method to measure delta C-13 values of amino acids extracted from soil. However, we found a number of drawbacks that significantly increase the final total uncertainty. These include the following: production of multiple peaks for each amino acid, identified as di-, tri- and tetra-TMS derivatives; a number of TMS-carbon (TMS-C) atoms added lower than the stoichiometric one, possibly due to incomplete combustion; different TMS-C delta C-13 for di-, tri- and tetra-TMS derivatives. For soil samples, only four amino acids (leucine, valine, threonine and serine) provide reliable delta C-13 values with a total average uncertainty of 1.3 parts per thousand. We conclude that trimethylsilyl derivatives are only suitable for determining the C-13 incorporation in amino acids within experiments using C-13-labelled tracers but cannot be applied for amino acids with natural carbon isotope abundance until the drawbacks described here are overcome and the measured total uncertainty significantly decreased.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Special Issue for the Plant Resistance Sustainability International Conference, La Colle sur Loup, France, 16-19 October 2012
auteur
Carole Caranta, François Coléno, Charles-Eric Durel, Marie-Helene Jeuffroy, Christian Lannou, Benoît Moury, Alain Palloix
article
Infection, Genetics and Evolution, 2014, 27, pp.445. ⟨10.1016/j.meegid.2014.09.011⟩
resume
absent
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Variability of morphological charters among Tunisian apricot germplasm
auteur
Lamia Krichen, Jean Marc Audergon, Neïla Trifi-Farah
article
Scientia Horticulturae, 2014, 179, pp.328-339. ⟨10.1016/j.scienta.2014.09.054⟩
resume
Morphological characters were assessed for 112 Tunisian apricot accessions using 42 qualitative and quantitative traits according to the UPOV descriptor. The results showed a distinction among all the accessions, and each morphological variable tested was polymorphic except mucron and rootstock. This characterization revealed that Tunisian apricot germplasm complied with many of the listed UPOV descriptor modalities, with the exception of a rectangular-plate fruit shape, which is characteristic of six Tunisian cultivars and not included in the UPOV apricot testing guidelines. The morphological characters with the best discriminatory ability included fruit size, fruit shape, over color of the fruit skin and flesh, and leaf size. The variability structure highlighted two different apricot categories: (i) Bargougs characterized by very small fruit size with high FW/FLW and absence of over color, (ii) grafted cultivars characterized by medium to relatively large fruit and the presence of over color. Morphological variability was structured according to the geographical origin of the plant material. Four regions were clearly distinguished: north, center, south and oasis. The assessed Tunisian apricot germplasm presented great variability, similar to that of Turkish, Spanish and Italian apricots.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The plant genetic background affects the efficiency of the pepper major nematode resistance genes Me1 and Me3
auteur
Arnaud Barbary, Alain Palloix, Ariane Fazari, Nathalie Marteu, Philippe Castagnone-Sereno, Caroline Djian-Caporalino
article
TAG Theoretical and Applied Genetics, 2014, 127 (2), pp.499-507. ⟨10.1007/s00122-013-2235-1⟩
resume
Key message The plant genetic background influences the efficiency of major resistance genes to root-knot nematodes in pepper and has to be considered in breeding strategies. Root-knot nematodes (RKNs), Meloidogyne spp., are extremely polyphagous plant parasites worldwide. Since the use of most chemical nematicides is being prohibited, genetic resistance is an efficient alternative way to protect crops against these pests. However, nematode populations proved able to breakdown plant resistance, and genetic resources in terms of resistance genes (R-genes) are limited. Sustainable management of these valuable resources is thus a key point of R-gene durability. In pepper, Me1 and Me3 are two dominant major R-genes, currently used in breeding programs to control M. arenaria, M. incognita and M. javanica, the three main RKN species. These two genes differ in the hypersensitive response induced by nematode infection. In this study, they were introgressed in either a susceptible or a partially resistant genetic background, in either homozygous or heterozygous allelic status. Challenging these genotypes with an avirulent M. incognita isolate demonstrated that (1) the efficiency of the R-genes in reducing the reproductive potential of RKNs is strongly affected by the plant genetic background, (2) the allelic status of the R-genes has no effect on nematode reproduction. These results highlight the primary importance of the choice of both the R-gene and the genetic background into which it is introgressed during the selection of new elite cultivars by plant breeders.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Resource competition modulates the seed number-fruit size relationship in a genotype-dependent manner: a modeling approach in grape and tomato
auteur
Marion Prudent, Zhanwu Dai, Michel Génard, Nadia Bertin, Mathilde Causse, Philippe Vivin
article
Ecological Modelling, 2014, 290, pp.54-64. ⟨10.1016/j.ecolmodel.2013.10.023⟩
resume
Fruit size is a key criterion of the external quality of the fruit and may affect consumer acceptance. We used a model to analyze the effects of seed number on fruit size in two fleshy fruits, grape and tomato, of different genotypes, grown in different carbohydrate availability conditions. The two-parameter model described within-fruit resource competition and accurately represented the commonly observed decrease in fresh weight per seed with increasing seed number, regardless of the species, genotype or carbohydrate level considered. However, carbohydrate levels strongly modified the correlation between seed number and fresh weight per fruit, resulting in an increase, no change, or a decrease in individual fruit weight with increasing seed number per fruit. In grape, lowering carbohydrate levels decreased the parameter reflecting the potential fresh weight of one-seeded fruit under a given resource availability, whereas the response to carbohydrate level was genotype-dependent in tomato and more strongly reflected the level of competition for resources. The values obtained for this parameter suggested that there was an undercompensating competition for resources in domesticated grape and tomato genotypes. Finally, colocalizations of quantitative trait loci for fruit fresh weight and model parameters indicated that plant susceptibility to competition might determine fruit fresh weight
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Variétés et systèmes de culture de tomate : les apports conjoints de la génétique et de l'agronomie
auteur
François Lecompte, Mathilde M. Causse
article
Agronomie, Environnement & Sociétés, 2014, 4 (2), pp.23-34
resume
Tomatoes are produced in various conditions, ranging from the open field (mainly for processing tomatoes) to soilless greenhouses. This adaptation of cropping systems and the technological innovations that have accompanied it largely drove the evolution of varieties in recent decades. Varieties were acclimated to protected cultivation throughout the year. Varietal resistances to specific pests, adapted to the different conditions, were introduced from wild related species. In addition, varietal diversification for different markets, focusing on fruit size and shape, has emerged as a new breeding objective. However progress has been more limited for complex traits related to fruit quality or adaptation to abiotic stress. Yields and input efficiencies have also benefited from advances in agronomic sciences: nutrient recycling in soilless cultivation, fine tuning of the greenhouse climate or introduction of efficient biological control methods have characterized the recent evolution of cropping systems. A more thorough understanding of genotype x environment interactions, which is of importance for plant resilience against stresses, and a better control of fruit flavour and nutritional quality, are major challenges for the scientific community. Rapid changes in plant breeding methods, the description of the tomato genome and enhanced capacities for crop modelling foreshadow major developments in tomato varieties and cropping systems in the near future
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Disease and frost damage of woody plants caused by Pseudomonas syringae: Seeing the forest for the trees
auteur
Jay Ram Lamichhane, Leonardo Varvaro, Luciana Parisi, Jean Marc Audergon, Cindy E. Morris
article
Advances in Agronomy, 2014, 126, pp.235-295. ⟨10.1016/B978-0-12-800132-5.00004-3⟩
resume
Pseudomonas syringae is a phytopathogenic bacterium that causes diseases of monocots, herbaceous dicots, and woody dicots, worldwide. On woody plants, reports of disease due to P. syringae have markedly increased in the last years and the diseases have been recognized as a major threat to the primary products of agroforestry practices. Detection in Italy of a new highly aggressive population of P. syringae in 2008 on kiwifruit, which caused severe epidemics in the following years throughout the kiwifruit-growing areas of Asia, Europe, Oceania, and South America, rendered the entire kiwifruit industry vulnerable to the disease. Similarly, occurrence of an aggressive population of P. syringae on horse chestnut in 2002 in the Netherlands has rapidly established itself as a major threat to horse chestnut throughout Northwest Europe. To better understand the origin of such disease epidemics, a thorough knowledge of the pathogen is needed in sensu lato. Here, we report the most important features of the pathogen and its hosts in an attempt to clarify some key aspects. In particular, the diseases and the economic losses they cause, disease epidemiology, pathogen diversity, and the possible means of disease control have been discussed throughout the manuscript. In addition to the ability to cause the disease, the damage caused to woody plants through the ice nucleation activity of this bacterium is discussed
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02638003/file/Audergon%202014%20Advances%20in%20agronomy%20237-295_1.pdf BibTex
titre
High rates of gene flow by pollen and seed in oak populations across Europe
auteur
Sophie Gerber, Joel J. Chadoeuf, Felix Gugerli, Martin Lascoux, Joukje Buiteveld, Joan Cottrell, Aikaterini Dounavi, Silvia Fineschi, Laura L. Forrest, Johan Fogelqvist, Pablo G. Goicoechea, Jan Svejgaard Jensen, Daniela Salvini, Giovanni G. Vendramin, Antoine Kremer
article
PLoS ONE, 2014, 9 (1), 16 p. ⟨10.1371/journal.pone.0085130⟩
resume
Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe. Adult trees within a given area in each stand were exhaustively sampled (range [239, 754], mean 423), mapped, and acorns were collected ([17,147], 51) from several mother trees ([3], [47], 23). Seedlings ([65,387], 178) were harvested and geo-referenced in six of the eight stands. Genetic information was obtained from screening distinct molecular markers spread across the genome, genotyping each tree, acorn or seedling. All samples were thus genotyped at 5–8 nuclear microsatellite loci. Fathers/parents were assigned to acorns and seedlings using likelihood methods. Mating success of male and female parents, pollen and seed dispersal curves, and also hybridisation rates were estimated in each stand and compared on a continental scale. On average, the percentage of the wind-borne pollen from outside the stand was 60%, with large variation among stands (21–88%). Mean seed immigration into the stand was 40%, a high value for oaks that are generally considered to have limited seed dispersal. However, this estimate varied greatly among stands (20–66%). Gene flow was mostly intraspecific, with large variation, as some trees and stands showed particularly high rates of hybridisation. Our results show that mating success was unevenly distributed among trees. The high levels of gene flow suggest that geographically remote oak stands are unlikely to be genetically isolated, questioning the static definition of gene reserves and seed stands.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02640758/file/journal.pone.0085130_1.pdf BibTex
titre
The relationship between metaheuristics stopping criteria and performances: Cases of NSGA-II and MOPSO-CD for sustainable peach fruit design
auteur
Mohamed Ould Sidi, Bénédicte Quilot-Turion, Abdeslam Kadrani, Michel M. Génard
article
International Journal of Applied Metaheuristic Computing, 2014, 5 (3), pp.47-74. ⟨10.4018/ijamc.2014070104⟩
resume
A major difficulty in the use of metaheuristics (i.e. evolutionary and particle swarm algorithms) to deal with multi-objective optimization problems is the choice of a convenient point at which to stop computation. Indeed, it is difficult to find the best compromise between the stopping criterion and the algorithm performance. This paper addresses this issue using the Non-dominated Sorting Genetic Algorithm (NSGA-II) and the Multi- Objective Particle Swarm Optimization with Crowding Distance (MOPSO-CD) for the model-based design of sustainable peach fruits. The optimization problem of interest contains three objectives: maximize fruit fresh mass, maximize fruit sugar content, and minimize the crack density on the fruit skin. This last objective targets a reduction in the use of fungicides and can thus enhance preservation of the environment and human health. Two versions of the NSGA-II and two of the MOPSO-CD were applied to tackle this difficult optimization problem: the original versions with a maximum number of generations used as stopping criterion and modified versions using the stopping criterion proposed by the authors of (Roudenko & Schoenauer, 2004). This second stopping criterion is based on the stabilization of the maximal crowding distance and aims to stop computation when many generations are performed without further improvement in the quality of the solutions. A benchmark consisting of four plant management scenarios has been used to compare the performances of the original versions (OV) and the modified versions (MV) of the NSGA-II and the MOPSO-CD. Twelve independent simulations were performed for each version and for each scenario, and a high number
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Variation in Tomato Fruit Ascorbate Levels and Consequences of Manipulation of Ascorbate Metabolism on Drought Stress Tolerance
auteur
V Truffault, N Gest, C Garchery, M Causse, R Duboscq, G Riqueau, C Sauvage, H Gautier, Pierre Baldet, Rebecca Stevens
article
Acta Horticulturae, 2014, pp.75-84. ⟨10.17660/ActaHortic.2014.1048.8⟩
resume
Tomato is an important crop worldwide and one of the major sources of vitamin C (ascorbate) in the human diet. Ascorbate contributes both to tomato nutritional quality and has roles in stress tolerance and adaptation to the environment. In this study we show the variability that exists in tomato germplasm in terms of ascorbate content (10 to 90 mg/100 g fwt) which could be starting point for evaluating correlations with physiological traits potentially linked to ascorbate. We have then manipulated genes involved in ascorbate metabolism, using RNA interference, to investigate their influence on fruit ascorbate levels, fruit physiology and yield under both normal and drought stress conditions. There is some evidence that one of the genes chosen affects fruit size and yield under different conditions, but clear effects on the fruit ascorbate pool are not seen. We conclude that ascorbate metabolism is complex and can also have wider effects on fruit physiology and growth.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03371257/file/actahort2014-truffault.pdf BibTex
titre
Quantitative trait loci from the host genetic background modulate the durability of a resistance gene: a rational basis for sustainable resistance breeding in plants
auteur
Julie Quenouille, Estelle Paulhiac, Benoît Moury, Alain Palloix
article
Heredity, 2014, 112 (6), pp.579-587. ⟨10.1038/hdy.2013.138⟩
resume
The combination of major resistance genes with quantitative resistance factors is hypothesized as a promising breeding strategy to preserve the durability of resistant cultivar, as recently observed in different pathosystems. Using the pepper (Capsicum annuum)/Potato virus Y (PVY, genus Potyvirus) pathosystem, we aimed at identifying plant genetic factors directly affecting the frequency of virus adaptation to the major resistance gene pvr2(3) and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h(2)=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr2(3) breakdown frequency. Three of the four QTLs controlling pvr2(3) breakdown frequency were also involved in quantitative resistance, strongly suggesting that QTLs controlling quantitative resistance have a pleiotropic effect on the durability of the major resistance gene. With the first mapping of QTLs directly affecting resistance durability, this study provides a rationale for sustainable resistance breeding. Surprisingly, a genetic trade-off was observed between the durability of PVY resistance controlled by pvr2(3) and the spectrum of the resistance against different potyviruses. This trade-off seemed to have been resolved by the combination of minor-effect durability QTLs under long-term farmer selection.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02630950/file/2014_Quenouille_Heredity_postprint_1.pdf BibTex
titre
High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae
auteur
Sami Doganlar, Amy Frary, Marie-Christine Daunay, Koen Huvenaars, Rolf Mank, Anne Frary
article
Euphytica, 2014, 198 (2), pp.231 - 241. ⟨10.1007/s10681-014-1096-2⟩
resume
A linkage map of eggplant was constructed for an interspecific F-2 population derived from a cross between Solanum linnaeanum MM195 and S. melongena MM738. The map contains 400 AFLP(A (R)) (amplified fragment length polymorphism), 348 RFLP (restriction fragment length polymorphism) and 116 COSII (conserved ortholog set) markers. The 864 mapped markers encompass 12 linkage groups, span 1,518 cM and are spaced at an average interval of 1.8 cM. Use of orthologous markers allowed confirmation of the established syntenic relationships between eggplant and tomato chromosomes and helped delineate the nature of the 33 chromosomal rearrangements and 11 transpositions distinguishing the two species. This genetic map provides a 2- to 3-fold improvement in marker density compared to previously published interspecific maps. Because the interspecific mapping population is rich in morphological variation, this greater genome saturation will be useful for QTL (quantitative trait locus) analyses. The recent release of the tomato genome sequence will provide additional opportunities for exploiting this map for comparative genomics and crop improvement.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Comment rationaliser le stockage d’échantillons dans les congélateurs - 80°C ?
auteur
Veronique Signoret, Esther Pelpoir, Elsa Desnoues
article
Cahier des Techniques de l'INRA, 2014, 82, 5 p
resume
Avant 2011, à l’UGAFL (Unité de Génétique et Amélioration des fruits et légumes, INRA), l’utilisation démesurée de la place dans les congélateurs - 80°C pénalisait les futures expérimentations. La réflexion menée dans l’Unité pour gérer le stockage d’échantillons dans les congélateurs -80°C, a permis de sensibiliser les utilisateurs à anticiper le volume d’échantillons à stocker lors de leurs expérimentations. Cette réflexion avait plusieurs objectifs : gérer au mieux l’espace dans ces appareils, faciliter la traçabilité des échantillons, diminuer l’utilisation de consommables et économiser le temps passé à la préparation des échantillons. La validation de cette procédure de stockage s’est faite sur deux années consécutives, dans le contexte d’une thèse au laboratoire pour doser des métabolites et des activités enzymatiques sur la plateforme métabolomique et fluxomique de Bordeaux. Concrètement, nous avons gagné 50% de place dans les congélateurs, tout en conservant un pot d’échantillon de réserve. La traçabilité des échantillons a été facilitée. L’économie de temps passé à la préparation des échantillons a permis d’aborder les campagnes fruitières avec plus de sérénité. Aujourd’hui, cette procédure est utilisée par d’autres équipes de l’Unité de recherche pour l’ensemble des congélateurs
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02636531/file/OK%20Signoret%202014%20les%20cahiers%20des%20techniques%20de%20l%27Inra%201-5_1.pdf BibTex
titre
Le génome de la tomate séquencé, une manne pour les sélectionneurs
auteur
Mondher Bouzayen, Mathilde M. Causse
article
Jardins de France, 2014, 1, pp.71
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02632122/file/Causse%202014%20Jardins%20de%20France%2071_1.pdf BibTex
titre
Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era
auteur
Laura Pascual-Banuls, Nelly Desplat, Bevan E. Huang, Aurore Desgroux, Laure Bruguier, Jean-Paul Bouchet, Quang H. Le, Betty Chauchard, Philippe Verschave, Mathilde Causse
article
Plant Biotechnology Journal, 2014, 13 (4), pp.565-77. ⟨10.1111/pbi.12282⟩
resume
Identification of the polymorphisms controlling quantitative traits remains a challenge for plant geneticists. Multiparent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage or association mapping populations by increasing the precision of quantitative trait loci (QTL) mapping. Here, we present the first tomato MAGIC population and highlight its potential for the valorization of intraspecific variation, QTL mapping and causal polymorphism identification. The population was developed by crossing eight founder lines, selected to include a wide range of genetic diversity, whose genomes have been previously resequenced. We selected 1536 SNPs among the 4 million available to enhance haplotype prediction and recombination detection in the population. The linkage map obtained showed an 87% increase in recombination frequencies compared to biparental populations. The prediction of the haplotype origin was possible for 89% of the MAGIC line genomes, allowing QTL detection at the haplotype level. We grew the population in two greenhouse trials and detected QTLs for fruit weight. We mapped three stable QTLs and six specific of a location. Finally, we showed the potential of the MAGIC population when coupled with whole genome sequencing of founder lines to detect candidate SNPs underlying the QTLs. For a previously cloned QTL on chromosome 3, we used the predicted allelic effect of each founder and their genome sequences to select putative causal polymorphisms in the supporting interval. The number of candidate polymorphisms was reduced from 12 284 (in 800 genes) to 96 (in 54 genes), including the actual causal polymorphism. This population represents a new permanent resource for the tomato genetics community
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01208731/file/OK%20Pascual_Causse%202014%20Plant%20Biotechnology%20Journal%201-13_1.pdf BibTex
titre
The Vat locus encodes for a CC-NBS-LRR protein that confers resistance to Aphis gossypii infestation and A. gossypii-mediated virus resistance
auteur
Catherine Dogimont, Veronique Chovelon, Jérôme Pauquet, Adnane Boualem, Abdelhafid A. Bendahmane
article
The Plant Journal, 2014, 80 (6), pp.993-1004. ⟨10.1111/tpj.12690⟩
resume
Aphis gossypii is a polyphagous sucking aphid and a vector for many viruses. In Cucumis melo, a dominant locus, Vat, confers a high level of resistance to Aphis gossypii infestation and to viruses transmitted by this vector. To investigate the mechanism underlying this double resistance, we first genetically dissected the Vat locus. We delimited the double resistance to a single gene that encodes for a coiled-coil-nucleotide-binding-site-leucine-rich repeat (CC-NBS-LRR) protein type. To validate the genetic data, transgenic lines expressing the Vat gene were generated and assessed for the double resistance. In this analysis, Vat-transgenic plants were resistant to A.gossypii infestation as well as A.gossypii-mediated virus transmission. When the plants were infected mechanically, virus infection occurred on both transgenic and non-transgenic control plants. These results confirmed that the cloned CC-NBS-LRR gene mediates both resistance to aphid infestation and virus infection using A.gossypii as a vector. This resistance also invokes a separate recognition and response phases in which the recognition phase involves the interaction of an elicitor molecule from the aphid and Vat from the plant. The response phase is not specific and blocks both aphid infestation and virus infection. Sequence analysis of Vat alleles suggests a major role of an unusual conserved LRR repeat in the recognition of A.gossypii.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Pyramiding, alternating or mixing: comparative performances of deployment strategies of nematode resistance genes to promote plant resistance efficiency and durability
auteur
Caroline Djian-Caporalino, Alain Palloix, Ariane Fazari, Nathalie Marteu, Arnaud Barbary, Pierre Abad, Anne-Marie Sage-Palloix, Thierry Mateille, Sabine Risso, Roger Lanza, Catherine Taussig, Philippe Castagnone-Sereno
article
BMC Plant Biology, 2014, 14, ⟨10.1186/1471-2229-14-53⟩
resume
Background: Resistant cultivars are key elements for pathogen control and pesticide reduction, but their repeated use may lead to the emergence of virulent pathogen populations, able to overcome the resistance. Increased research efforts, mainly based on theoretical studies, explore spatio-temporal deployment strategies of resistance genes in order to maximize their durability. We evaluated experimentally three of these strategies to control root-knot nematodes: cultivar mixtures, alternating and pyramiding resistance genes, under controlled and field conditions over a 3-years period, assessing the efficiency and the durability of resistance in a protected crop rotation system with pepper as summer crop and lettuce as winter crop. Results: The choice of the resistance gene and the genetic background in which it is introgressed, affected the frequency of resistance breakdown. The pyramiding of two different resistance genes in one genotype suppressed the emergence of virulent isolates. Alternating different resistance genes in rotation was also efficient to decrease virulent populations in fields due to the specificity of the virulence and the trapping effect of resistant plants. Mixing resistant cultivars together appeared as a less efficient strategy to control nematodes. Conclusions: This work provides experimental evidence that, in a cropping system with seasonal sequences of vegetable species, pyramiding or alternating resistance genes benefit yields in the long-term by increasing the durability of resistant cultivars and improving the long-term control of a soil-borne pest. To our knowledge, this result is the first one obtained for a plant-nematode interaction, which helps demonstrate the general applicability of such strategies for breeding and sustainable management of resistant cultivars against pathogens.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02633649/file/2014_Dijan-Caporalino_BMC-Plant-Biology_1.pdf BibTex
titre
Comparison of evolutionary and swarm intelligence-based approaches in the improvement of peach fruit quality
auteur
A. Kadrani, Bénédicte Quilot-Turion, Michel M. Génard, Francoise F. Lescourret, Mohamed Ould Sidi
article
Annals of Management Science, 2014, 3 (1), pp.129-142
resume
The design of peach ideotypes that satisfy the requirement of high fruit quality and low sensitivity to fungal diseases in a given environment is a very challenging problem. In this paper, we propose a model-based design approach to deal with this challenge. First, we formulate it as a multi-objective optimization problem. Two well-known multi-objective optimization algorithms i.e. the Non-dominated Sorting Genetic Algorithm II (NSGA-II) and the Multi-Objective Particle Swarm Optimization with the Crowding Distance (MOPSO-CD) were then used to find the best combinations of genetic resources and cultural practices adapted to, and respectful of specific environments. Statistically significant performance measures are employed to compare the two algorithms. The results obtained demonstrate that NSGA-II is able to yield a wide spread of solutions with good coverage and convergence to Pareto fronts.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The coolbox: a greenhouse cooling system that uses recycled water
auteur
Patricia Le Crenn, Max Escoffier, Alain Goujon, Jean-Marc Bastien
article
Lettre aux Entreprises - INRA, 2014, N° 65, Juillet 2014
resume
320m² of greenhouses on the 4700m² estate of Domaine de Saint Maurice in Avignon (PACA), are cooled by spraying water onto thick pads of wood shavings through which air is pumped. This system, called the coolbox, has been developed by the GAFL in the context of efforts to optimise existing resources.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02634291/file/2014_Escoffier_lettre%20aux%20entreprises_1.pdf BibTex
titre
Selecting with markers linked to the PPVres major QTL is not sufficient to predict resistance to Plum Pox Virus (PPV) in apricot
auteur
Stephane Decroocq, Aurélie Chague, Patrick Lambert, Guillaume Roch, Jean Marc Audergon, F. Geuna, R. Chiozzotto, D. Bassi, L. Dondini, S. Tartarini, J. Salava, B. Krska, F. Palmisano, I. Karayiannis, Véronique Decroocq
article
Tree Genetics and Genomes, 2014, 10 (5), pp.1161-1170. ⟨10.1007/s11295-014-0750-0⟩
resume
Sharka is one of the most serious viral diseases affecting stone fruit species and, in apricot, resistance to its viral agent, the Plum Pox Virus (PPV), is conferred by one major quantitative trait locus (QTL), named PPVres for PPV resistance. Previous studies indicated that PPV-resistant cultivars and breeding progenies can be selected by using a set of SSR markers (named PGS) targeting the PPVres locus. However, before these markers can be employed for marker-assisted selection, they were validated in a wide range of genetic backgrounds and environments. We used a total of 11 mapping populations issued from three distinct environments to confirm that this marker set located within the QTL adequately predicted PPV resistance. In this study, we show that selection of PPV-resistant material based only on markers co-localizing with the PPVres major locus is not fully reliable. Indeed, genotype-phenotype discrepancies were observed depending on the progeny and the PPV-resistant/susceptible parents. While most of the PPV-resistant individuals displayed the resistant alleles, a significant number of PPV-susceptible individuals showed the same resistant haplotype. An effect of the PPV strain used for phenotyping was also demonstrated. We thus hypothesize that the presence of other factors or genes involved in the mechanism of resistance to sharka in apricot could explain these unexpected results. Our work indicates that the current PGS marker set is not broadly applicable for MAS and that marker-assisted breeding based on the sole PPVres locus is not sufficient to unambiguously select PPV-resistant apricot cultivars.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Cloning of the Arabidopsis rwm1 gene for resistance to Watermelon mosaic virus points to a new function for natural virus resistance genes
auteur
Laurence Ouibrahim, Marianne Mazier, Joan Estevan, Gaelle G. Pagny, Véronique Decroocq, Cecile Desbiez, André Moretti, Jean-Luc J.-L. Gallois, Carole Caranta
article
The Plant Journal, 2014, 79 (5), pp.705-716. ⟨10.1111/tpj.12586⟩
resume
Arabidopsis thaliana represents a valuable and efficient model to understand mechanisms underlying plant susceptibility to viral diseases. Here, we describe the identification and molecular cloning of a new gene responsible for recessive resistance to several isolates of Watermelon mosaic virus (WMV, genus Potyvirus) in the Arabidopsis Cvi-0 accession. rwm1 acts at an early stage of infection by impairing viral accumulation in initially infected leaf tissues. Map-based cloning delimited rwm1 on chromosome 1 in a 114-kb region containing 30 annotated genes. Positional and functional candidate gene analysis suggested that rwm1 encodes cPGK2 (At1g56190), an evolutionary conserved nucleus-encoded chloroplast phosphoglycerate kinase with a key role in cell metabolism. Comparative sequence analysis indicates that a single amino acid substitution (S78G) in the N-terminal domain of cPGK2 is involved in rwm1-mediated resistance. This mutation may have functional consequences because it targets a highly conserved residue, affects a putative phosphorylation site and occurs within a predicted nuclear localization signal. Transgenic complementation in Arabidopsis together with virus-induced gene silencing in Nicotiana benthamiana confirmed that cPGK2 corresponds to rwm1 and that the protein is required for efficient WMV infection. This work uncovers new insight into natural plant resistance mechanisms that may provide interesting opportunities for the genetic control of plant virus diseases. This article is protected by copyright. All rights reserved.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Nouvelles sources de résistance au puceron Aphis gossypii chez le melon
auteur
Nathalie Boissot, Sophie Thomas, Pascale Mistral, Virginie Chareyron
article
Innovations Agronomiques, 2014, 35, pp.89-95. ⟨10.17180/q3gf-7g30⟩
resume
Aphis gossypii, unique puceron ravageur du melon est cosmopolite. Il s’est adapté à la plupart des insecticides utilisés pour le contrôler, aussi la lutte génétique, encore peu utilisée au niveau mondial dans les variétés, est-elle plus que jamais d’actualité. Une source de résistance a été fortement utilisée dans les variétés inscrites au catalogue français, la résistance est jugée lors de l’inscription en utilisant un seul clone alors qu’une vingtaine sont connus pour coloniser le melon. En utilisant neuf de ces clones, nous avons révélé différents profils de résistance aux pucerons chez 13 accessions de melon, qui correspondent soit à de nouveaux allèles au locus Vat, soit à des fonds génétiques plus performants. Pour lutter contre les clones présents dans le Sud-Est de la France sur les melons résistants, ce sont surtout des facteurs présents dans ces nouveaux fonds génétiques qui seraient intéressants
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02638897/file/OK%20Boissot_2014-Innov%20Agronomiques_1.pdf BibTex
titre
Specific requirement for translation initiation factor 4E or its isoform drives plant host susceptibility to tobacco etch virus.
auteur
Joan Estevan, Aramata Marena, Caroline Callot, Séverine Lacombe, André Moretti, Carole Caranta, Jean-Luc J.-L. Gallois
article
BMC Plant Biology, 2014, 14 (67), 10 p. ⟨10.1186/1471-2229-14-67⟩
resume
Background: In plants, eIF4E translation initiation factors and their eIFiso4E isoforms are essential susceptibility factors for many RNA viruses, including potyviruses. Mutations altering these factors are a major source of resistance to the viruses. The eIF4E allelic series is associated with specific resistance spectra in crops such as Capsicum annum. Genetic evidence shows that potyviruses have a specific requirement for a given 4E isoform that depends on the host plant. For example, Tobacco etch virus (TEV) uses eIF4E1 to infect Capsicum annuum but uses eIFiso4E to infect Arabidopsis thaliana. Here, we investigated how TEV exploits different translation initiation factor isoforms to infect these two plant species. Results: A complementation system was set up in Arabidopsis to test the restoration of systemic infection by TEV. Using this system, Arabidopsis susceptibility to TEV was complemented with a susceptible pepper eIF4E1 allele but not with a resistant allele. Therefore, in Arabidopsis, TEV can use the pepper eIF4E1 instead of the endogenous eIFiso4E isoform so is able to switch between translation initiation factor 4E isoform to infect the same host. Moreover, we show that overexpressing the pepper eIF4E1 alleles is sufficient to make Arabidopsis susceptible to an otherwise incompatible TEV strain. Lastly, we show that the resistant eIF4E1 allele is similarly overcome by a resistance-breaking TEV strain as in pepper, confirming that this Arabidopsis TEV-susceptibility complementation system is allele-specific. Conclusion: We report here a complementation system in Arabidopsis that makes it possible to assess the role of pepper pvr2-eIF4E alleles in susceptibility to TEV. Heterologous complementation experiments showed that the idiosyncratic properties of the 4E and iso4E proteins create a major checkpoint for viral infection of different hosts. This system could be used to screen natural or induced eIF4E alleles to find and study alleles of interest for plant breeding
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02630878/file/main.pdf BibTex
titre
Genome-wide association in tomato Reveals 44 candidate loci for fruit metabolic traits
auteur
Christopher Sauvage, Vincent Segura, Guillaume Bauchet, Rebecca Stevens, Phuc Thi Do, Zoran Nikoloski, Alisdair R Fernie, Mathilde Causse
article
Plant Physiology, 2014, 165 (3), pp.1120-1132. ⟨10.1104/pp.114.241521⟩
resume
Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato ([i]Solanum lycopersicum[/i]) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed of [i]S. lycopersicum,[/i] [i]S. lycopersicum var cerasiforme[/i], and [i]Solanum pimpinellifolium[/i] to map loci controlling variation in fruit metabolites. Fruits were phenotyped for a broad range of metabolites, including amino acids, sugars, and ascorbate. In parallel, the accessions were genotyped with 5,995 single-nucleotide polymorphism markers spread over the whole genome. Genome-wide association analysis was conducted on a large set of metabolic traits that were stable over 2 years using a multilocus mixed model as a general method for mapping complex traits in structured populations and applied to tomato. We detected a total of 44 loci that were significantly associated with a total of 19 traits, including sucrose, ascorbate, malate, and citrate levels. These results not only provide a list of candidate loci to be functionally validated but also a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genomic analyses provide insights into the history of tomato breeding
auteur
Tao Lin, Guangtao Zhu, Junhong Zhang, Xiangyang Xu, Qinghui Yu, Zheng Zheng, Zhonghua Zhang, Yaoyao Lun, Shuai Li, Xiaoxuan Wang, Zejun Huang, Junming Li, Chunzhi Zhang, Taotao Wang, Yuyang Zhang, Aoxue Wang, Yancong Zhang, Kui Lin, Chuanyou Li, Guosheng Xiong, Yongbiao Xue, Andrea Mazzucato, Mathilde M. Causse, Zhangjun Fei, James J. Giovannoni, Roger T. Chetelat, Dani Zamir, Thomas Staedler, Jingfu Li, Zhibiao Ye, Yongchen Du, Sanwen Huang
article
Nature Genetics, 2014, 46 (11), pp.1220 - 1226. ⟨10.1038/ng.3117⟩
resume
The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit similar to 100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Varietal and technical innovations for the sustainable and integrated management of root-knot nematodes
auteur
Caroline Djian-Caporalino, Mireille Navarrete, Alain Palloix, Thierry Mateille, Amélie Lefevre, Arnaud Barbary, Ariane Fazari, Nathalie Marteu, Mathilde Chapuis, Marc Tchamitchian, Arnaud Dufils, Anne-Marie Sage-Palloix, Johannes Tavoillot, Laure Pares, Hélène Védie, Claire Goillon, Catherine Taussig, Sabine Risso, R. Lanza, Philippe Castagnone-Sereno
article
Journal of Nematology, 2014, 46 (2), pp.154
resume
The current restrictions on the use of chemical nematicides have contributed to increased root-knot nematodes (Meloidogyne spp.) problems in horticultural crops. In this context, plant resistance (R) appears as the most effective method of control, but the restricted number of cultivated vegetable species with root-knot nematode R-genes available (tomato, pepper), and the possible occurrence of virulent nematodes able to reproduce on R-plants may constitute a severe threat to this control strategy. To increase the sustainability of the protection, a scientific challenge exists in building cropping strategies based on the combination of genetic resistance with cultivation practices. Our projects aimed at assessing such innovative strategies in a multi-site device in research stations and commercial farms. First, we looked at three components of crop protection, i.e., R-efficiency, R-durability, and sustainability of rotating cultivation. Overall, a constant hierarchy of management strategies was observed, with Pyramyding > Alternating > Mixture of R-genes > Sequential use of a single R-gene introgressed in a susceptible background. We are currently analysing (1) the impact of agronomic practices on the parasite pressure in the soil and on ecological diversity including other nematode species, (2) the linkage between reduction of Meloidogyne populations in the soil and increase of R-genes durability, and (3) the sustainability assessment of such varietal and technical innovations. Multidisciplinary approaches were combined to foster synergistic and long-term goals. The diversity of partners and associated forces brought all the complementary expertise needed for answering specific short-term questions as well as generic mid- to long-term expectations.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Histological and cell wall polysaccharide chemical variability among apricot varieties
auteur
Marc Lahaye, Xavier Falourd, Bernard Quemener, Marie Francoise M. F. Devaux, Jean Marc Audergon
article
LWT - Food Science and Technology, 2014, 58, pp.486-496. ⟨10.1016/j.lwt.2014.04.009⟩
resume
The variability of histological and cell wall chemical characteristics of apricot were assessed in nine apricot varieties: Harogem, Goldrich, Hargrand, Iranien, Moniqui, Orangered ! Bhart, Stark Early Orange, Ravicille and Rouge du Roussillon. For chemical analyses, Iranien and Moniqui were harvested twice at two weeks interval and Goldrich parenchyma was subdivided into inner and outer tissue. Image texture analysis of parenchyma tissue sections allowed distinguishing varieties on the basis of cell and vascular bundle size distributions and tissue organization. Whole parenchyma cell wall sugar composition failed to distinguish varieties. Goldrich outer tissue was richer in arabinose and mannose compared to inner parenchyma. Methyl and acetyl esteri ! cation of polysaccharides were better dis- criminants. The distribution of methyl and acetyl esters on pectin varied among varieties. The tissue regions studied in Goldrich and the different harvests studied in Moniqui and Iranien affected pectin esteri ! cation. Hemicellulose ! ne structure pro ! les discriminated varieties on the basis of xyloglucan and galactoglucomannan structures proportion. The results point to variations in chemical and histological characteristics that can be of importance in studies on the understanding the genetics of apricots texture variations
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection
auteur
Guillaume Bauchet, Stephane Munos, Christopher Sauvage, Julien Bonnet, Laurent Grivet, Mathilde M. Causse
article
BMC Plant Biology, 2014, 14, n.p. ⟨10.1186/s12870-014-0279-2⟩
resume
Background: Domestication and selection of crops have notably reshaped fruit morphology. With its large phenotypic diversity, tomato (Solanum lycopersicum) illustrates this evolutive trend. Genes involved in flower meristem development are known to regulate also fruit morphology. To decipher the genetic variation underlying tomato fruit morphology, we assessed the nucleotide diversity and selection footprints of candidate genes involved in flower and fruit development and performed genome-wide association studies. Results: Thirty candidate genes were selected according to their similarity with genes involved in meristem development or their known causal function in Arabidopsis thaliana. In tomato, these genes and flanking regions were sequenced in a core collection of 96 accessions (including cultivated, cherry-type and wild relative accessions) maximizing the molecular diversity, using the Roche 454 technology. A total amount of 17 Mb was sequenced allowing the discovery of 6,106 single nucleotide polymorphisms (SNPs). The annotation of the 30 gene regions identified 231 exons carrying 517 SNPs. Subsequently, the nucleotide diversity (p) and the neutral evolution of each region were compared against genome-wide values within the collection, using a SNP array carrying 7,667 SNPs mainly distributed in coding sequences. About half of the genes revealed footprints of selection and polymorphisms putatively involved in fruit size variation by showing negative Tajima's D and nucleotide diversity reduction in cultivated tomato compared to its wild relative. Among the candidates, FW2.2 and BAM1 sequences revealed selection footprints within their promoter regions suggesting their potential involvement in their regulation. Two associations co-localized with previously identified loci: LC (locule number) and Ovate (fruit shape). Conclusion: Compared to whole genome genotypic data, a drastic reduction of nucleotide diversity was shown for several candidate genes. Strong selection patterns were identified in 15 candidates highlighting the critical role of meristem maintenance genes as well as the impact of domestication on candidates. The study highlighted a set of polymorphisms putatively important in the evolution of these genes.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02641364/file/2014_Bauchet_BMC%20Plant_Biol_1.pdf BibTex
titre
Multicriteria sorting methods to select virtual peach ideotypes
auteur
Mohamed-Mahmoud Memmah, Bénédicte Quilot-Turion, Antoine Rolland
article
International Journal of Multicriteria Decision Making, 2014, Operational Management and Marketing, 4 (4), pp.348 - 366. ⟨10.1504/IJMCDM.2014.066874⟩
resume
The model-based design of virtual fruit ideotypes using multi-objective optimisation algorithms could produce a high number of contrasted fruits. The breeder (decision-maker) will need an automatic tool allowing him/her to sort these contrasted ideotypes into predefined categories corresponding to several targeted traits. This paper aims to develop such a decision-making module to sort a set of fruit ideotypes into one of five preference-ordered categories in the context of brown rot-peach fruit pathosystem. First, a set of ideotypes with contrasted trade-off between three criteria was produced using multi-objective optimisation algorithms. Then, two multi-criteria decision-making methods (ELECTRE-Tri and DRSA: dominance-based rough set approach) were tested in order to reproduce the classification made by the decision-maker. Such a non-typical classification seemed difficult to be reproduced by the ELECTRE-TRI method while the decision rule-based method gave very good results (only 10% wrong assignments). The proposed decision-making tool is very useful to speed-up the model-based design of fruit ideotypes, i.e., breeding.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01201746/file/2014_Memmah_IJMDM_1.pdf BibTex
titre
QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis
auteur
Amy Frary, Anne Frary, Marie-Christine Daunay, Koen Huvenaars, Rolf Mank, Sami Doganlar
article
Euphytica, 2014, 197 (2), pp.211-228. ⟨10.1007/s10681-013-1060-6⟩
resume
Fifty-eight F-2 individuals derived from an interspecific cross between cultivated eggplant, Solanum melongena, and its wild relative, S. linnaeanum, were phenotyped for 42 plant, leaf, flower, and fruit traits. Composite interval mapping analysis using genotypic data from 736 molecular markers revealed the positions of 71 statistically significant (P a parts per thousand currency sign 0.05) quantitative trait loci (QTL) influencing 32 of the morphological traits. Although most QTL were location-specific, QTL governing three traits (leaf lobing, leaf prickles and prickle anthocyanin) were detected in both experimental locations. Analysis of three additional traits (stem prickles, fruit calyx prickles and fruit length) in both locations yielded QTL in similar but non-overlapping map positions. The majority (69 %) of the QTL corresponded closely with those detected in previous analyses of this data set. However the increased resolution of the linkage map combined with advances in QTL mapping permitted more precise localization, such that the average interval length of these QTL was reduced by 93 %. Thirty-one percent of the QTL were novel, suggesting that simple linear regression with a low density linkage map (the method used in previous studies of this population) missed a substantial portion of significant QTL. Hotspots of QTL affecting plant hairiness, prickliness, and pigmentation were identified on chromosomes 3, 6, and 10, respectively, and may reflect the pleiotropic activity of single structural or regulatory genes at these positions. Based on synteny between the eggplant, tomato, potato and pepper genomes, putative orthologs were identified for 35 % of the QTL suggesting strong conservation of gene function within the Solanaceae. These results should make it easier to target particular loci for map-based cloning and marker-assisted selection studies
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Pyramiding resistances based on translation initiation factors in Arabidopsis is impaired by male gametophyte lethality
auteur
Caroline Callot, Jean-Luc J.-L. Gallois
article
Plant Signaling and Behavior, 2014, 9, pp.e27940;
resume
In eukaryotes, ei F4E translation initiation factors are essential proteins encoded by a small multigene family. In plants, they are a major source of host plant resistance to potyviruses that require specific 4E factors to infect cells. Combining mutations in different eiF4E genes could be a way of broadening the spectrum of plant resistance to viruses. We attempted to combine null mutations affecting the two main Arabidopsis thaliana 4E factors eiF4E1 and eiFiso4E but discovered that this combination is lethal. Transmission through the male gametophyte is completely abolished in the eif4e1 and eifiso4e double mutant. This shows that eIF4E1 and eIFiso4E are essential for male gametophyte development and act redundantly. These results may have implications for ei F4E-based pyramiding strategies to improve crop resistance
typdoc
Journal articles
Accès au bibtex
BibTex
titre
How to estimate variability in affinity relationships in partially observed groups of domestic herbivores?
auteur
Lia Della-Rossa, Bertrand Dumont, Joel J. Chadoeuf
article
Animal, 2014, 8 (5), pp.817-826. ⟨10.1017/S175173111400024X⟩
resume
Animal sociability measurements based on inter-individual distances or nearest-neighbour distributions can be obtained automatically with telemetry collars. So far, all the indices that have been used require the whole group to be observed. Here, we propose an index of the variability in affinity relationships in groups of domestic herbivores, whose definition does not depend on group size and that can be used even if some data are missing. This index and its estimators are based on a function that measures how frequently an animal is closer than another one from a third animal. When no data are missing, we show that our estimator and the variance of the sociability matrix sensu Sibbald (considered as the reference method) are strongly correlated. We then consider two cases of missing data. In the first case, some animals are randomly missing, that is, to account for random breakdown of telemetry collars. Our estimator is unbiased by such missing data and its variance decreases as the number of observation dates increases. In the second case, the same animals are missing at all observation dates, that is, in large herds where there are more individuals to be observed than available telemetry collars. Our estimator of affinity variance within a group is biased by such missing data. Thus, it requires changing animals equipped with telemetry collars regularly during the experiment. Conversely, the estimator remains unbiased at the population level, that is, if several independent groups are being analysed. We finally illustrate how this estimator can be used by investigating changes in the variability of affinities according to group size in grazing heifers.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Evolution of plant eukaryotic initiation factor 4E (eIF4E) and potyvirus genome-linked protein (VPg): A game of mirrors impacting resistance spectrum and durability
auteur
Benoît Moury, Carine Charron, Bérenger Janzac, Vincent Simon, Jean-Luc Gallois, Alain Palloix, Carole Caranta
article
Infection, Genetics and Evolution, 2014, 27, pp.472-480. ⟨10.1016/j.meegid.2013.11.024⟩
resume
Polymorphism in the plant eukaryotic translation initiation factor 4E (eIF4E) and potyvirus genomelinked protein (VPg) determine, in many cases, the outcome of the confrontation between these two organisms: compatibility (i.e. infection of the plant by the virus) or incompatibility (i.e. resistance of the plant to the virus). The two interacting proteins eIF4E and VPg show strikingly similar evolution patterns. Most codon positions in their coding sequences are highly constrained for nonsynonymous substitutions but a small number shows evidence for positive selection. Several of these latter positions were shown to be functionally important, conferring resistance to the host or pathogenicity to the virus. Determining the mutational pathways involved in pepper eIF4E diversification revealed a link between an increase of the pepper resistance spectrum towards a panel of potyvirus species and an increase of durability of the resistance towards Potato virus Y. This relationship questions the interest of using more generally the spectrum of action of a plant resistance gene as a predictor of its durability potential
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Bottleneck and gene flow effects impact the genetic structure of seed-propagated apricot populations in Moroccan oasis agroecosystems
auteur
Ali Mamouni, Ahmed El Bakkali, Patrick Lambert, Lamia Krichen, Ahmed Oukabli, Jean Marc Audergon, Philippe Chatelet, Cherkaoui El Modafar, Bouchaib Khadari
article
Plant Genetic Resources, 2014, pp.1-11. ⟨10.1017/S1479262113000543⟩
resume
In order to highlight the genetic status and origin of Moroccan apricot populations, trees were collected from ten oasis agroecosystems and analysed with AFLP markers. A total of 87 accessions and 12 cultivars grown in Moroccan orchards, including ‘Canino’ and ‘Del Patriarca’ cultivars, were surveyed and compared with in situ Tunisian and ex situ Montfavet (France) collections. Our results highlighted a narrow genetic diversity in the Maghreb region (Tunisia and Morocco) associated with a strong differentiation from the other groups, which supports a bottleneck effect. A similar model was illustrated at a finer geographical scale, i.e. the Draa Valley in Morocco. Genetic structure appeared as two major clusters subdivided into six sub-clusters in which Moroccan germplasm constituted specific groups in comparison with other Mediterranean apricots. Moroccan germplasm was classified into three sub-clusters, two of which were formed by genotypes related to ‘Del Patriarca’ and ‘Canino’, respectively. The present study highlights the wide Moroccan apricot’s diversity in traditional agroecosystems, and also suggests a substantial gene flow occurring from recently introduced cultivars (‘Canino’ and ‘Del Patriarca’) to local apricot populations, thus leading to local germplasm diversification through seedling propagation. If we consider its geographical position, the historical diffusion of the species and farming practices, Morocco could be viewed as an additional centre of secondary diversification for apricot. Understanding the origin and specificity of local apricot populations is crucial for managing local collections in regard to adaptive traits for arid and Saharan conditions as well as for introducing local genetic resources into current breeding programmes
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Interaction pattern between Potato virus Y and eIF4E-mediated recessive resistance in the Solanaceae
auteur
Benoît Moury, Bérenger Janzac, Youna Ruellan, Vincent Simon, Mekki Ben Khalifa, Hatem Fakhfakh, Frédéric Fabre, Alain Palloix
article
Journal of Virology, 2014, 88 (17), pp.9799-9807. ⟨10.1128/JVI.00930-14⟩
resume
The structural pattern of infectivity matrices, where a set of parasites is confronted to a set of hosts, is a key parameter for our understanding of biological interactions and their evolution. This pattern determines evolution of parasite pathogenicity and host resistance, the spatio-temporal distribution of host and parasite genotypes and the efficiency of disease control strategies. Two major patterns have been proposed for plant-virus genotypes infectivity matrices. In the gene-for-gene model, infectivity matrices show a nested pattern, where the host range of specialist virus genotypes is a subset of the host range of less-specialized viruses. In contrast, in the matching-allele (MA) model, each virus genotype is specialized to infect one (or a small set of) host genotype(s). The corresponding infectivity matrix shows a modular pattern, where infection is frequent for plants and viruses belonging to the same module but rare for those belonging to different modules. We analyzed the structure of infectivity matrices between Potato virus Y (PVY) and plant genotypes in the family Solanaceae carrying different eukaryotic initiation factor 4E (eIF4E)-coding alleles conferring recessive resistance. Whereas this system corresponds mechanistically to a MA model, the expected modular pattern was rejected for our experimental data. This was mostly because PVY mutations involved in adaptation to a particular plant genotype displayed frequent pleiotropic effects, conferring simultaneously an adaptation to additional plant genotypes carrying different eIF4E alleles. Such effects should be taken into account for the design of strategies of sustainable control of PVY through plant varietal mixtures or rotations.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02631938/file/2014_Moury_J%20Virol_1.pdf BibTex
titre
Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to [i]Leptosphaeria maculans[/i] in oilseed rape
auteur
Régine Delourme, Lydia Bousset, Magali Ermel, Philippe Duffe, Anne-Laure Besnard, Bruno Marquer, Isabelle Fudal-Grolier, Juliette Linglin, Joel Chadoeuf, Hortense Brun
article
Infection, Genetics and Evolution, 2014, 27, pp.490-499. ⟨10.1016/j.meegid.2013.12.019⟩
resume
Quantitative resistance mediated by multiple genetic factors has been shown to increase the potential for 29 durability of major resistance genes. This was demonstrated in the [i]Leptosphaeria maculans / Brassica napus[/i] 30 pathosystem in a 5 year recurrent selection field experiment on lines harboring the qualitative resistance 31 gene Rlm6 combined or not with quantitative resistance. The quantitative resistance limited the size of 32 the virulent isolate population. In this study we continued this recurrent selection experiment in the 33 same way to examine whether the pathogen population could adapt and render the major gene ineffec- 34 tive in the longer term. The cultivars Eurol, with a susceptible background, and Darmor, with quantitative 35 resistance, were used. We confirmed that the combination of qualitative and quantitative resistance is an 36 effective approach for controlling the pathogen epidemics over time. This combination did not prevent 37 isolates virulent against the major gene from amplifying in the long term but the quantitative resistance 38 significantly delayed for 5 years the loss of effectiveness of the qualitative resistance and disease severity 39 was maintained at a low level on the genotype with both types of resistance after the fungus population 40 had adapted to the major gene. We also showed that diversity at the AvrLm6 virulence allele was com- 41 parable in isolates recovered after the recurrent selection on lines carrying either the major gene alone 42 or in combination with quantitative resistance: a single repeat-induced point mutation and deletion 43 events were observed in both situations. Breeding varieties which combine qualitative and quantitative 44 resistance can effectively contribute to disease control by increasing the potential for durability of major 45 resistance genes
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Profiling sugar metabolism during fruit development in a peach progeny with different fructose-to-glucose ratios.
auteur
Elsa Desnoues, Yves Y. Gibon, Valentina Baldazzi, Veronique Signoret, Michel M. Génard, Bénédicte Quilot-Turion
article
BMC Plant Biology, 2014, 14 (1), pp.336 : 1-12. ⟨10.1186/s12870-014-0336-x⟩
resume
BackgroundFruit taste is largely affected by the concentration of soluble sugars and organic acids and non-negligibly by fructose concentration, which is the sweetest-tasting sugar. To date, many studies investigating the sugars in fruit have focused on a specific sugar or enzyme and often on a single variety, but only a few detailed studies addressing sugar metabolism both as a whole and dynamic system are available. In commercial peach fruit, sucrose is the main sugar, followed by fructose and glucose, which have similar levels. Interestingly, low fructose-to-glucose ratios have been observed in wild peach accessions. A cross between wild peach and commercial varieties offers an outstanding possibility to study fruit sugar metabolism.ResultsThis work provides a large dataset of sugar composition and the capacities of enzymes that are involved in sugar metabolism during peach fruit development and its genetic diversity. A large fraction of the metabolites and enzymes involved in peach sugar metabolism were assayed within a peach progeny of 106 genotypes, of which one quarter displayed a low fructose-to-glucose ratio. This profiling was performed at six stages of growth using high throughput methods. Our results permit drawing a quasi-exhaustive scheme of sugar metabolism in peach. The use of a large number of genotypes revealed a remarkable robustness of enzymatic capacities across genotypes and years, despite strong variations in sugar composition, in particular the fructose-to-glucose ratio, within the progeny. A poor correlation was also found between the enzymatic capacities and the accumulation rates of metabolites.ConclusionsThese results invalidate the hypothesis of the straightforward enzymatic control of sugar concentration in peach fruit. Alternative hypotheses concerning the regulation of fructose concentration are discussed based on experimental data. This work lays the foundation for a comprehensive study of the mechanisms involved in sugar metabolism in developing fruit.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02631892/file/Desnoues-BMCPlantBiology-2014_1.pdf BibTex
titre
Lettuce cropping with less pesticides. A review
auteur
Virginie Barrière, François Lecompte, Philippe C. Nicot, Brigitte Maisonneuve, Marc Tchamitchian, Françoise Lescourret
article
Agronomy for Sustainable Development, 2014, 34 (1), pp.175-198. ⟨10.1007/s13593-013-0158-5⟩
resume
Agricultural intensification has increased crop productivity but decreased agroecosystem services. Agricultural intensification is occurring notably for horticultural crops such as lettuce. In conventional agriculture, lettuce protection is achieved mostly by preventive applications of pesticides with about eight treatments for a 60–90-day-long cycle in the Mediterranean region. However, new sustainable control strategies are needed due to pesticide impact on environment and human health, emerging pesticide resistance, and stricter policies on levels of pesticide residues in food. Here, we review knowledge and methods allowing to grow lettuce with less pesticides. Advances shown are based on pest ecology and pathogen control by the agroecosystem. The major points are as follows: (1) pest and pathogen community composition depends partly on climatic conditions. The identification of pests and pathogens that can threaten the crop is the first step to design innovative lettuce cropping systems less dependent on pesticides. (2) The numerous alternative techniques currently available should be combined to control lettuce pests and pathogens. The effects of alternative techniques on non-target organisms including non-target pests are poorly known so far. (3) Designing sustainable systems requires taking into account ecological interactions and suitability of different management techniques of low impact.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01234783/file/13593_2013_Article_158.pdf BibTex
titre
Assessing the genetic diversity and population structure of Tunisian apricot germplasm
auteur
L. Krichen, Jean Marc Audergon, N. Trifi-Farah
article
Scientia Horticulturae, 2014, 172, pp.86-100. ⟨10.1016/j.scienta.2014.03.038⟩
resume
Tunisian apricot germplasm consists of two kinds of material: grafted cultivars and seed-propagated Bargougs. A total of 144 accessions were selected for this study, including 109 cultivars accessions and 35 Bargoug accessions. A comparative analysis of the genetic structure was carried out utilizing morphological characters and AFLP molecular markers separately and in combination, with the aim of estimating the genetic diversity and identifying relationships with the geographical origins of the accessions. The hierarchical clustering structure obtained with each dataset revealed that the accessions could be divided into two different genetic groups, indicating two distinct gene pools. This result highlighted the existence of two distinct genetic origins of apricot genotypes in Tunisia. Moreover, Tunisian apricot diversity was classified according to the geographical origins of the accessions, with four regions being distinguished: North, Center, South-East and South-West (Oasis). The perfect accession distribution was based on the four predefined regions, as confirmed by the discriminant analysis. Furthermore, a correspondence analysis revealed a structure in two distinct groups and the existence of accessions from the four predefined regions in each group, which is evidence that Bargougs and grafted cultivars share the same genetic origin. Both markers (morphological and AFLPs markers) were complementary and contributed substantially to the diversity analysis with the best structure obtained from the combined dataset
typdoc
Journal articles
Accès au bibtex
BibTex
titre
High-resolution mapping of the RMia gene for resistance to root-knot nematodes in peach
auteur
Henri Duval, Mathilde Hoerter, Joel Polidori, Carole C. Confolent, Martin Masse, André Moretti, Cyril van Ghelder, Daniel Esmenjaud
article
Tree Genetics and Genomes, 2014, on-line, 10 p. ⟨10.1007/s11295-013-0683-z⟩
resume
The RMia gene, which confers resistance (R) to the root-knot nematodes (RKN) Meloidogyne incognita and Meloidogyne arenaria, has been shown to segregate in the peach rootstocks Nemared, Shalil, and Juseitou on LG2 of the Prunus map. Here, we report the high-resolution mapping of RMia in Nemared, using the peach genome sequence and 790 individuals from two segregating peach populations, the F2 crossMontclar x Nemared and the four-way cross [(Pamirskij × Rubira) × (Montclar × Nemared)], in which Montclar, Pamirskij, and Rubira are susceptible (S) to RKN. Among the simple sequence repeat (SSR) markers designed for an initial flanking region of more than 1 Mb, five SSR markers specific for Nemared were characterized. The genotyping and phenotyping of recombinant individuals in this interval narrowed the gene’s location to a 300 kb physical distance between the SSR markers AMPP117 and AMPP116. In this interval, SNP polymorphisms were recovered from 1-kb-sequenced DNA fragments that were selected at 20 kb intervals. Two SNP markers (A20SNP and SNP_APP91) were shown to flank the gene in a final 92-kb region, containing four candidate genes from the TIR–NBS– LRR family. Finally, we studied the polymorphism of three closely linked markers, SNP_APP92, SNP_APP91, and AMPP117, on 28 R or S accessions fromdiverse Prunus species or hybrids. These markers discriminated between most R and S accessions, suggesting that at least the R sources of Nemared, Nemaguard, and Shalil share a common resistant ancestor
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Conception d'associations en maraîchage de plein champ : exemple de production de melons associés à des bandes fleuries pour lutter contre les pucerons et les virus
auteur
Alexandra Schoeny, Nathalie Boissot, Jérôme Lambion, Catherine Wipf-Scheibel, Pascale Mistral, Patrick Gognalons, Karine Nozeran, Hervé Lecoq
article
Innovations Agronomiques, 2014, 40, pp.113-124. ⟨10.17180/rtc4-gs06⟩
resume
Une expérimentation pluriannuelle et multidisciplinaire a permis une évaluation du rôle potentiel des bandes fleuries pour diminuer le risque de colonisation aphidienne et le risque d’épidémie virale en cultures de melon. L’implantation de bandes fleuries a favorisé le développement d’une importante entomofaune auxiliaire à proximité des cultures. Les auxiliaires spécifiques des pucerons, notamment les Coccinellidés, ont été plus fréquents sur les melons côté bandes fleuries que sur les melons côté sol nu. Les niveaux moyens de colonisation par Aphis gossypii ont toutefois été équivalents quel que soit le type d’aménagement. L’efficacité du gène Vat sur la colonisation par Aphis gossypii mais également sur le développement de certains virus (CABYV et CMV) a été confirmée. De plus, le développement du WMV, non contrôlé par Vat, a été réduit certaines années en présence de bandes fleuries.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02638166/file/2014_Schoeny_Innovations%20agronomiques_1.pdf BibTex
titre
Spanish onion landraces (Allium cepa L.) as sources of germplasm for breeding cal double dagger ots: a morphological and molecular survey
auteur
J. Simo, Laura Pascual-Banuls, J. Canizares, F. Casanas
article
Euphytica, 2014, 195 (2), pp.287 - 300. ⟨10.1007/s10681-013-0995-y⟩
resume
Cal double dagger ots are the immature floral stems of second-year resprouts of the 'Blanca Tardana de Lleida' (BTL) onion landrace, and to date, breeding has used only a few populations. So, we aimed to increase our knowledge of the variability of BTL and to explore its characteristics and genetic dissimilarity with other varieties that might be used in cal double dagger ot breeding programs. We analyzed the agronomic and morphological traits of four populations of BTL, two synthetic varieties of BTL, 20 prestigious Spanish landraces, and 4 exotic onion landraces. Furthermore, we used three combinations of AFLP primers and seven microsatellites to analyze their genetic background. The Spanish landraces (including BTL) shared a large part of their genetic background, which showed considerable variability (heterozygosity around 0.5). Morphological traits also had high variability, so multiple breeding strategies can be used, ranging from intravarietal selection to crossings between populations to take advantage of the heterosis, both for the bulb and for the cal double dagger ot improvement.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Inter individual variations of the fish skin microbiota: Host genetics basis of mutualism?
auteur
Sébastien Boutin, Christopher Sauvage, Louis Bernatchez, Céline Audet, Nicolas Derôme
article
PLoS ONE, 2014, 9 (7), 17 p. ⟨10.1371/journal.pone.0102649⟩
resume
The commensal microbiota of fish skin is suspected to provide a protection against opportunist infections. The skin of fish harbors a complex and diverse microbiota that closely interacts with the surrounding water microbial communities. Up to now there is no clear evidence as to whether the host regulates the recruitment of environmental bacteria to build a specific skin microbiota. To address this question, we detected Quantitative Trait Loci (QTL) associated with the abundance of specific skin microbiota bacterial strains in brook charr (Salvelinus fontinalis), combining 16S RNA tagged-amplicon 454 pyrosequencing with genetic linkage analysis. Skin microbiota analysis revealed high inter-individual variation among 86 F2 fish progeny based upon the relative abundance of bacterial operational taxonomic units (OTUs). Out of those OTUs, the pathogenic strain Flavobacterium psychrophilum and the non-pathogenic strain Methylobacterium rhodesianum explained the majority of inter-individual distances. Furthermore, a strong negative correlation was found between Flavobacterium and Methylobacterium, suggesting a mutually competitive relationship. Finally, after considering a total of 266 markers, genetic linkage analysis highlighted three major QTL associated with the abundance of Lysobacter, Rheinheimera and Methylobacterium. All these three genera are known for their beneficial antibacterial activity. Overall, our results provide evidence that host genotype may regulate the abundance of specific genera among their surface microbiota. They also indicate that Lysobacter, Rheinheimera and Methylobacterium are potentially important genera in providing protection against pathogens
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02634270/file/Sauvage%202014%20Plos%20one_1.pdf BibTex
titre
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization
auteur
Cheng Qin, Changshui Yu, Yaou Shen, Xiaodong Fang, Lang Chen, Jiumeng Min, Jiaowen Cheng, Shancen Zhao, Meng Xu, Yong Luo, Yulan Yang, Zhiming Wu, Likai Mao, Haiyang Wu, Changying Ling-Hu, Huangkai Zhou, Haijian Lin, Sandra Gonzalez-Morales, Diana L. Trejo-Saavedra, Hao Tian, Xin Tang, Maojun Zhao, Zhiyong Huang, Anwei Zhou, Xiaoming Yao, Junjie Cui, Wenqi Li, Zhe Chen, Yongqiang Feng, Yongchao Niu, Shimin Bi, Xiuwei Yang, Weipeng Li, Huimin Cai, Xirong Luo, Salvador Montes-Hernandez, Marco A. Leyva-Gonzalez, Zhiqiang Xiong, Xiujing He, Lijun Bai, Shu Tan, Xiangqun Tang, Dan Liu, Jinwen Liu, Shangxing Zhang, Maoshan Chen, Lu Zhang, Li Zhang, Yinchao Zhang, Weiqin Liao, Yan Zhang, Min Wang, Xiaodan Lv, Bo Wen, Hongjun Liu, Hemi Luan, Yonggang Zhang, Shuang Yang, Xiaodian Wang, Jiaohui Xu, Xueqin Li, Shuaicheng Li, Junyi Wang, Alain Palloix, Paul W. Bosland, Yingrui Li, Anders Krogh, Rafael F. Rivera-Bustamante, Luis Herrera-Estrella, Ye Yin, Jiping Yu, Kailin Hu, Zhiming Zhang
article
Proceedings of the National Academy of Sciences of the United States of America, 2014, 111 (14), pp.5135-5140. ⟨10.1073/pnas.1400975111⟩
resume
As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded similar to 0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of similar to 81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Understanding dormancy release in apricot flower buds ([i]Prunus armeniaca[/i] L.) using several process-based phenological models
auteur
Lucia Andreini, Inaki Garcia de Cortazar Atauri, Isabelle Chuine, Raffaella Viti, Susanna Bartolini, David Ruiz, José Antonio Campoy-Corbalan, Jean-Michel Legave, Jean Marc Audergon, Patrick Bertuzzi
article
Agricultural and Forest Meteorology, 2014, 184, pp.210- 219. ⟨10.1016/j.agrformet.2013.10.005⟩
resume
The present study was an initial attempt to calibrate a phenological process-based model of dormancy release with experimental data for apricot flower buds. A large experimental database (88 data points) on dormancy release, concerning several cultivars grown at different geographical sites, was used for the model parameterization. We compared five phenological models. None of them provided accurate prediction of the date of dormancy release at the species level. This inaccuracy appeared to be due to the high variance in dormancy release dates among cultivars. Models fitted for different dormancy release precocity groups provided much more accurate predictions. Parameter estimate analysis of the best model for each cultivar group showed very marked differences in apricot flower bud response to temperature within the species. While in early cultivars dormancy release seemed to be driven by the daily minimum temperature, the daily mean temperature appeared to be the controlling factor in intermediate and late cultivars. Our results show that the apricot dormancy release date cannot be predicted accurately at the species level and that different models should be used for different precocity groups.
typdoc
Journal articles
Accès au bibtex
BibTex

2013

Journal articles

titre
Dual resistance of melon to Fusarium oxysporum races 0 and 2 and to papaya ring-spot virus is controlled by a pair of head-to-head-oriented NB-LRR genes of unusual architecture
auteur
Yariv Brotman, Michael Normantovich, Zachi Goldenberg, Zvi Zvirin, Irina Kovalski, Nastacia Stovbun, Tirza Doniger, Anthony M. Bolger, Christelle Troadec, Abdelhafid A. Bendahmane, Roni Cohen, Nurit Katzir, Michel Pitrat, Catherine Dogimont, Rafael Perl-Treves
article
Molecular Plant, 2013, 6 (1), pp.235-238. ⟨10.1093/mp/sss121⟩
resume
Potyviruses such as Papaya ring-spot virus (PRSV) cause important yield losses in cucurbits. Two distinct resistant alleles were identified in the Cucumis melo germplasm. Accession PI 414723 ( Supplemental Table 1) possesses mono-genic resistance, controlled by the Prv2 allele, and reacts to PRSV by systemic necrotic lesions; plants with the Prv1 allele, described in cultivar WMR-29, remain symptomless (Pitratand Lecoq, 1983). Fusarium oxysporum f. sp. melonis (FUS) exclusively attacks melon, causing severe wilt. Monogenic dominant resistance was described against races 0, 1, and 2. The Fom-2 gene, controlling resistance to races 0 and 1, was cloned by Joobeur et al. (2004), and encodes a nucleotide binding domain (NB)–leucine rich repeat (LRR) protein. Our study focused on the Fom-1 gene, which confers resistance to races 0 and 2 (Risser et al., 1976), and on the Prv gene; the two are tightly linked on melon linkage group IX. Molecular markers were developed for the Fom-1/Prv locus, but no study has provided the resolution required for positional cloning.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Closely related poleroviruses depend on distinct translation Initiation factors to infect Arabidopsis thaliana
auteur
Catherine Reinbold, Séverine Lacombe, Véronique Ziegler-Graff, D Scheidecker, Louis Wiss, Monique M. Beuve, Carole Caranta, Véronique Brault
article
Molecular Plant-Microbe Interactions, 2013, 26 (2), pp.257-265. ⟨10.1094/MPMI-07-12-0174-R⟩
resume
En plus d'être essentiel pour la traduction de l'ARNm eucaryote, facteurs d'initiation de traduction sont également des éléments clés des interactions plante-virus. Afin de répondre à l'implication de ces facteurs dans le cycle infectieux de poleroviruses (transmis par les pucerons, les virus limité au phloème), l'accumulation de trois poleroviruses a été suivie en lignées mutantes d'Arabidopsis thaliana ayant une déficience dans la synthèse des facteurs d'initiation de traduction dans le eIF4E et eIF4G familles. Nous avons constaté que l'accumulation efficace de virus de la jaunisse du navet (TuYV) chez A. thaliana repose sur la présence de eIF (iso) 4G1, alors betterave doux virus jaunissement (BMYV) et betteraves jaunes de l'Ouest virus USA (BWYV-USA) comptent, au lieu , sur eIF4E1. Un rôle de ces facteurs dans les processus infectieux de TuYV et BMYV a été confirmée par une interaction directe dans la levure entre ces facteurs spécifiques et l'extrémité 5 'du génome viral lié à une protéine du virus apparenté. Bien que le mécanisme moléculaire sous-jacente est encore inconnue, cette étude révèle une situation totalement imprévue dans lequel des virus appartenant au même genre d'utilisation différents facteurs d'initiation de traduction pour une infection efficace de A. thaliana étroitement liés.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02644720/file/Closely%20Related%20Poleroviruses%20Depend_1.pdf BibTex
titre
Decreased monodehydroascorbate reductase activity reduces tolerance to cold storage in tomato and affects fruit antioxidant levels.
auteur
Hicham El Airaj, Noé Gest, Vincent Truffault, Cécile Garchery, Gisèle Riqueau, Barbara Gouble, David Page, Rebecca Stevens
article
Postharvest Biology and Technology, 2013, 86, pp.502-510. ⟨10.1016/j.postharvbio.2013.07.035⟩
resume
Fruit antioxidants are necessary for human health and also have physiological roles in protecting fruit against oxidative stress. Our previous work has shown that monodehydroascorbate reductase (MDHAR) activity was positively correlated with fruit resistance to cold storage in introgression lines of tomato, Solanum lycopersicum. We have produced transgenic lines with reduced MDHAR activity to directly study the impact of this gene on fruit resistance to chilling and the antioxidant pool in two different genetic backgrounds: M82, a processing tomato with low to medium ascorbate levels, and IL925, an introgression line of M82 containing a fragment of the wild tomato Solanum pennellii genome, including the S. pennelli MDHAR allele. Large decreases in fruit MDHAR activity were obtained and correlated with slight losses in fruit firmness and fruit ascorbate, an effect that was independent of the genetic background. Fruit colour after chilling was also positively correlated with the redox state of the ascorbate pool and fruit firmness, although at harvest these correlations were less significant. Furthermore, other modifications in fruit of transgenic lines were observed as red fruit showed increased glutathione levels. Therefore manipulation of MDHAR activity confirms the link between antioxidant protection, fruit tolerance to chilling and fruit ripening at low temperatures, although the strength of the phenotypes indicates that other factors are involved.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Deciphering genetic diversity and inheritance of tomato fruit weight and composition through a systems biology approach
auteur
Laura Pascual-Banuls, Jiaxin Xu, Benoit Biais, Mickael Maucourt, Patricia Ballias, Stéphane Bernillon, Catherine Deborde, Daniel Jacob, Aurore Desgroux, Mireille Faurobert, Jean-Paul Bouchet, Yves Gibon, Annick Moing, Mathilde Causse
article
Journal of Experimental Botany, 2013, 64 (18), pp.1-16. ⟨10.1093/jxb/ert349⟩
resume
Integrative systems biology proposes new approaches to decipher the variation of phenotypic traits. In an effort to link the genetic variation and the physiological and molecular bases of fruit composition, the proteome (424 protein spots), metabolome (26 compounds), enzymatic profile (26 enzymes), and phenotypes of eight tomato accessions, covering the genetic diversity of the species, and four of their F1 hybrids, were characterized at two fruit developmental stages (cell expansion and orange-red). The contents of metabolites varied among the genetic backgrounds, while enzyme profiles were less variable, particularly at the cell expansion stage. Frequent genotype by stage interactions suggested that the trends observed for one accession at a physiological level may change in another accession. In agreement with this, the inheritance modes varied between crosses and stages. Although additivity was predominant, 40% of the traits were non-additively inherited. Relationships among traits revealed associations between different levels of expression and provided information on several key proteins. Notably, the role of frucktokinase, invertase, and cysteine synthase in the variation of metabolites was highlighted. Several stress-related proteins also appeared related to fruit weight differences. These key proteins might be targets for improving metabolite contents of the fruit. This systems biology approach provides better understanding of networks controlling the genetic variation of tomato fruit composition. In addition, the wide data sets generated provide an ideal framework to develop innovative integrated hypothesis and will be highly valuable for the research community.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01208665/file/Pascual_Xu_Integration%20MS_modif%20R2-2_1.pdf https://hal.science/hal-01208665/file/2013_Pascual_Journal%20of%20Experimental%20Botany_2.pdf BibTex
titre
Des plantes alimentaires aquatiques
auteur
Michel Pitrat
article
Jardins de France, 2013, 624
resume
L’homme ne consomme que très peu de plantes poussant en permanence dans l’eau. Celles que l’on considère comme plantes aquatiques sont la plupart du temps des végétaux poussant en milieux humides, voire très humides, comme le riz ou le cresson. Si leur multiplication est aisée, il faut veiller à leur état sanitaire face au risque de transmission de maladies à l’homme.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02642493/file/2013_Pitrat_Jardins%20de%20France%20624_1.pdf BibTex
titre
Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles
auteur
Jean Colcombet, Mauricio Lopez-Obando, Laure Heurtevin, Clément Bernard, Karine Martin, Richard R. Berthomé, Claire Lurin
article
RNA Biology, 2013, 10 (9), pp.1557-1575. ⟨10.4161/rna.26128⟩
resume
Four hundred and fifty-eight genes coding for PentatricoPeptide Repeat (PP R) proteins are annotated in the Arabidopsis thaliana genome. Over the past 10 years, numerous reports have shown that many of these proteins function in organelles to target specific transcripts and are involved in post-transcriptional regulation. Therefore, they are thought to be important players in the coordination between nuclear and organelle genome expression. Only four of these proteins have been described to be addressed outside organelles, indicating that some PP Rs could function in posttranscriptional regulations of nuclear genes. In this work, we updated and improved our current knowledge on the localization of PP R proteins of Arabidopsis within the plant cell. We particularly investigated the subcellular localization of 166 PP R proteins whose targeting predictions were ambiguous, using a combination of high-throughput cloning and microscopy. Through systematic localization experiments and data integration, we confirmed that PP R proteins are largely targeted to organelles and showed that dual targeting to both the mitochondria and plastid occurs more frequently than expected. These results allow us to speculate that dual-targeted PP R proteins could be important for the fine coordination of gene expressions in both organelles.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Determination of the Composition in Sugars and Organic Acids in Peach Using Mid Infrared Spectroscopy: Comparison of Prediction Results According to Data Sets and Different Reference Methods.
auteur
Sylvie Bureau, Bénédicte Quilot-Turion, Véonique Signoret, Christel Renaud, Mickael Maucourt, Doriane Bancel, Catherine C. Renard
article
Analytical Chemistry, 2013, 85 (23), pp.11312-11318. ⟨10.1021/ac402428s⟩
resume
The prediction of internal quality properties, such as sweetness and acidity, in peach fruit by mid infrared spectroscopy is of interest for rapid determination. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was tested here on two populations of peach fruits issued from contrasting genitors providing a large phenotypic variability. Over two successive years, 284 samples in 2006 and 483 samples in 2007 were characterized for soluble solids content (SSC), titratable acidity (TA), glucose, fructose, sucrose, malic acid, and citric acid contents. Sugar and organic acid composition were determined by three methods: colorimetric enzymatic measurements (ENZ), high-performance liquid chromatography (HPLC), or proton NMR spectroscopy (1H NMR), depending on the samples. For all samples, fruit homogenates were analyzed in ATR-FTIR using the same methodology and the same spectrometer. The objective here was to evaluate the effect of reference methods on the prediction performance. The best results were generally observed for SSC and TA, the percentage of the root-mean-square error of cross validation (RMSECV%) ranging respectively between 5.8% and 8.7% and between 5.9% and 8.0%, depending on the samples. For individual sugars and organic acids, the best correlations were obtained between ATR-FTIR data and ENZ reference data followed by HPLC and 1H NMR ones.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic relationships between local North African apricot (Prunus armeniaca L.) germplasm and recently introduced varieties
auteur
Hedia Bourguiba, Bouchaib Khadari, Oumeima Selma Krichen, Neila Trifi-Farah, Ali Mamouni, Samia Trabelsi, Jean Marc Audergon
article
Scientia Horticulturae, 2013, 152, pp.61-69. ⟨10.1016/j.scienta.2013.01.012⟩
resume
Graft and seed propagated apricots in North Africa (Algeria, Morocco and Tunisia) are identified as being from the southwestern Mediterranean gene pool. However, recently introduced varieties from northern Mediterranean areas are also encountered in this region. Do gene exchanges occur between local apricot and introduced varieties? We addressed this question by analyzing the genetic structure of 183 accessions using 24 nuclear microsatellite markers and a model-based Bayesian clustering method. We classified these accessions into 4 genetic clusters: cluster 1 from Morocco, cluster 2 from northern, central and southern Tunisia which were all propagated by grafting, cluster 3 from the oasis region in Tunisia and the Messaad region in Algeria, and finally, cluster 4 (green) included accessions belonging to the northern Mediterranean gene pool. These accessions were more diversified and genetically differentiated with respect to local North African apricot. The results revealed the presence of admixed accessions between the local gene pool and introduced varieties, mainly in seed propagated populations, thus highlighting the presence of gene exchanges between northern and southern Mediterranean countries. Our findings should be useful for improving the management and conservation of Maghrebian apricot genetic resources.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A cytochrome P450 regulates a domestication trait in cultivated tomato
auteur
Manohar Chakrabarti, Na Zhang, Christopher Sauvage, Stephane Munos, José Blanca, Joaquin Canizares, María José Díez, Rhiannon Schneider, Michael Mazourek, Jammi Mcclead, Mathilde M. Causse, Esther van Der Knaap
article
Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (42), pp.17125-17130. ⟨10.1073/pnas.1307313110⟩
resume
Domestication of crop plants had effects on human lifestyle and agriculture. However, little is known about the underlying molecular mechanisms accompanying the changes in fruit appearance as a consequence of selection by early farmers. We report the fine mapping and cloning of a tomato (Solanum lycopersicum) fruit mass gene encoding the ortholog of KLUH, SlKLUH, a P450 enzyme of the CYP78A subfamily. The increase in fruit mass is predominantly the result of enlarged pericarp and septum tissues caused by increased cell number in the large fruited lines. SlKLUH also modulates plant architecture by regulating number and length of the side shoots, and ripening time, and these effects are particularly strong in plants that transgenically down-regulate SlKLUH expression carrying fruits of a dramatically reduced mass. Association mapping followed by segregation analyses revealed that a single nucleotide polymorphism in the promoter of the gene is highly associated with fruit mass. This single polymorphism may potentially underlie a regulatory mutation resulting in increased SlKLUH expression concomitant with increased fruit mass. Our findings suggest that the allele giving rise to large fruit arose in the early domesticates of tomato and becoming progressively more abundant upon further selections. We also detected association of fruit weight with CaKLUH in chile pepper (Capsicum annuum) suggesting that selection of the orthologous gene may have occurred independently in a separate domestication event. Altogether, our findings shed light on the molecular basis of fruit mass, a key domestication trait in tomato and other fruit and vegetable crops.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02646387/file/PNAS_revised%20submission9EvdK_1.pdf BibTex
titre
Potato virus Y: a major crop pathogen that has provided major insights into the evolution of viral pathogenicity
auteur
Julie Quenouille, Nikon Vassilakos, Benoît Moury
article
Molecular Plant Pathology, 2013, 14 (5), pp.439 - 452. ⟨10.1111/mpp.12024⟩
resume
Taxonomy Potato virus Y (PVY) is the type member of the genus Potyvirus in the family Potyviridae. Virion and genome properties PVY virions have a filamentous, flexuous form, with a length of 730nm and a diameter of 12nm. The genomic RNA is single stranded, messenger sense, with a length of 9.7kb, covalently linked to a viral-encoded protein (VPg) at the 5' end and to a 3' polyadenylated tail. The genome is expressed as a polyprotein of approximately 3062 amino acid residues, processed by three virus-specific proteases into 11 mature proteins. Hosts PVY is distributed worldwide and has a broad host range, consisting of cultivated solanaceous species and many solanaceous and nonsolanaceous weeds. It is one of the most economically important plant pathogens and causes severe diseases in cultivated hosts, such as potato, tobacco, tomato and pepper, as well as in ornamental plants. Transmission PVY is transmitted from plant to plant by more than 40 aphid species in a nonpersistent manner and, in potato, by planting contaminated seed tubers. Diversity Five major clades, named C1, C2, Chile, N and O, have been described within the PVY species. In recent decades, a strong increase in prevalence of N x O recombinant isolates has been observed worldwide. A correlation has been observed between PVY phylogeny and certain pathogenicity traits. Genetic control of PVY Resistance genes against PVY have been used widely in breeding programmes and deployed in the field. These resistance genes show a large diversity of spectrum of action, durability and genetic determinism. Notably, recessive and dominant major resistance genes show highly contrasting patterns of interaction with PVY populations, displaying rapid co-evolution or stable relationships, respectively.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Multi-trait and multi-environment QTL analyses of yield and a set of physiological traits in pepper
auteur
Nurudeen Adeniyi Alimi, M. C. A. M. Bink, J. A. Dieleman, J. J. Magan, A. M. Wubs, Alain Palloix, F. A. van Eeuwijk
article
TAG Theoretical and Applied Genetics, 2013, 126 (10), pp.2597-2625. ⟨10.1007/s00122-013-2160-3⟩
resume
A mixed model framework was defined for QTL analysis of multiple traits across multiple environments for a RIL population in pepper. Detection power for QTLs increased considerably and detailed study of QTL by environment interactions and pleiotropy was facilitated. For many agronomic crops, yield is measured simultaneously with other traits across multiple environments. The study of yield can benefit from joint analysis with other traits and relations between yield and other traits can be exploited to develop indirect selection strategies. We compare the performance of three multi-response QTL approaches based on mixed models: a multi-trait approach (MT), a multi-environment approach (ME), and a multitrait multi-environment approach (MTME). The data come from a multi-environment experiment in pepper, for which 15 traits were measured in four environments. The approaches were compared in terms of number of QTLs detected for each trait, the explained variance, and the accuracy of prediction for the final QTL model. For the four environments together, the superior MTME approach delivered a total of 47 regions containing putative QTLs. Many of these QTLs were pleiotropic and showed quantitative QTL by environment interaction. MTME was superior to ME and MT in the number of QTLs, the explained variance and accuracy of predictions. The large number of model parameters in the MTME approach was challenging and we propose several guidelines to help obtain a stable final QTL model. The results confirmed the feasibility and strengths of novel mixed model QTL methodology to study the architecture of complex traits.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Susceptibility of Prunus rootstocks against Marcus and Dideron isolates of Plum pox virus by graft-inoculation
auteur
M. Rubio, F. Dicenta, Martin Masse, Henri Duval
article
Annals of Applied Biology, 2013, 162 (2), pp.214 - 220. ⟨10.1111/aab.12015⟩
resume
Sharka (Plum pox virus, PPV) is one of the most important diseases affecting stone fruits. While there is much information on the reaction of cultivars to PPV infection, details about rootstocks are scarce. In this study, we evaluated 28 stone fruit rootstocks belonging to different Prunus species against the Marcus and Dideron strains of PPV. Rootstocks were evaluated under controlled conditions during two growing seasons using two inoculation methods: direct inoculation of own-rooted rootstocks and grafting onto PPV-infected GF305 peach seedlings. Our results showed a generalised susceptibility of the rootstocks evaluated. Evaluating own-rooted rootstocks was more efficient than the traditional method of grafting onto infected GF305 seedlings. As expected, PPV-M was found to be more aggressive than PPV-D, producing symptoms and occurring in a higher number of plants, as shown by ELISA. The most susceptible rootstocks were Myran, Viking, Myro pg Pecher, Julior, Myrobolan 29C, Rubira, Myrobolan B, MrS 2/5, Jaspi and MP8. The least susceptible were GF677, Myrotop, Citation and ZH6. These results highlight the necessity to breed PPV-resistant rootstocks for the different stone fruit species.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Home conservation strategies for tomato (Solanum lycopersicum): Storage temperature vs. duration – Is there a compromise for better aroma preservation?
auteur
Catherine C. Renard, Christian Ginies, Barbara Gouble, Sylvie Bureau, Mathilde Causse
article
Food Chemistry, 2013, 139 (1-4), pp.825-836. ⟨10.1016/j.foodchem.2013.01.038⟩
resume
Expression of dissatisfaction with tomato aroma prompted us to lead this study on the impact of domestic storage conditions on volatile compounds. Two storage modalities (20 and 4 °C) and two cultivars (Levovil and LCx) were used. Volatile compounds were analysed by gas chromatography–mass spectrometry detection after accelerated solvent extraction. Physical characteristics, lipoxygenase activity, hydroperoxide lyase activity; linoleic acid and linolenic acid were monitored. Storing tomatoes at 4 °C induced a drastic loss in volatiles, whatever their biosynthetic origin. After 30 days at 4 °C, the concentration of volatiles had decreased by 66%. Reconditioning for 24 h at 20 °C was able to recover some aroma production after up to 6 days storage at 4 °C. Volatile degradation products arising from carotenoids and amino acids increased when tomatoes were kept at 20 °C, while lipid degradation products did not vary. Storing tomatoes at fridge temperature, even for short durations, was detrimental for their aroma. This should be taken into account to formulate practical advice for consumers.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01328646/file/2013%20-%20Renard-Ginies-Gouble-Bureau_1.pdf BibTex
titre
Quelques exemples d’intérêts et de limites de la sélection assistée par marqueurs chez la pomme de terre
auteur
Marie-Claire Kerlan, Sylvie Marhadour, Bernard Caromel, E. Bonnel, Sarah Danan, Véronique Lefebvre, Jean-Eric Chauvin
article
Innovations Agronomiques, 2013, 27, pp.111-122. ⟨10.17180/8a3r-m431⟩
resume
Marker-assisted selection (MAS) is only possible if molecular markers are easy to handle and informative. In potato, a tetraploid and highly heterozygous species, SAM is poorly developed. In our study we developed two approaches: 1) search for molecular markers linked to traits of interest in diploid segregating populations and test of their transferability at the tetraploid level and 2) test of molecular markers that have already been published in different tetraploid genetic backgrounds. The targeted traits were resistance to pathogens (late blight caused by Phytophthora infestans, cyst nematodes Globodera rostochiensis and G. pallida, virus Y) and glycoalkaloid content in tubers. In the case of a monogenic control (like resistance to late blight conferred by the R1 gene originating from Solanum demissum or the resistance to the Y virus conferred by the Ry gene originating from S. stoloniferum), the published markers have been validated in different genetic backgrounds. For the H1 gene conferring resistance to G. rostochiensis, markers available at the time of the project were not found to be associated with resistance in our material but other markers have since been validated. In the case of oligogenic resistance, illustrated by the resistance to G. pallida, which is controlled by two QTL, markers flanking the large effect QTL GpaVspl were tested successfully in different diploid and tetraploid backgrounds. Two markers linked to the low effect QTL GpaXIspl were also validated. These markers were transferred to the French breeders who are now using them in their breeding programs. For polygenic quantitative traits (partial resistance to late blight and glycoalkaloid content), it seems not realistic to consider SAM for the moment.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01208610/file/Vol27-10-Kerlan_1.pdf BibTex
titre
Pericarp tissue microstructure and cell wall polysaccharide chemistry are differently affected in lines of tomato with contrasted firmness
auteur
Marc Lahaye, Marie Francoise M. F. Devaux, Mervin Poole, Graham B. Seymour, Mathilde M. Causse
article
Postharvest Biology and Technology, 2013, 76, pp.83-90. ⟨10.1016/j.postharvbio.2012.09.009⟩
resume
The contribution of tissue histology and cell wall polysaccharides chemistry to describing ripe tomato fruit texture was addressed in near isogenic lines of fruits harboring firmness QTL. These lines were constructed in Levovil (L), VilB (B), M82 (P) and Moneyberg (Mbg) genetic backgrounds and carried introgressed fragments from three origins on chromosomes 2, 3, 4, 5 or 9 (and two sub-regions a and b). The firmness of their pericarp tissue was measured by compression testing and related to cell size distribution and to published data on their cell wall polysaccharide chemistry. The pericarp tissue from all L9 lines, B9 and P3.4 was firmer than the respective parental line while that from Mbg9 and P9.2.5 was softer. The pericarp tissue from L4, L4a and Mbg5 fruit was made of larger cells while that from Mbg2 and Mbg9 had smaller cells than their parents. Correlations were found between firmness and cell size distribution for QTLs only in the Levovil group. Correlations between firmness, histological characteristics and cell wall polysaccharide chemistry indicate positive relations between glucose-containing polysaccharide (cellulose and hemicelluloses) contents and pericarp tissue thickness. Other positive relations were found between galactosylated pectins and hemicelluloses and firmness in QTL lines of the Levovil background. The results show that chromosomes 9, 5, 4 and 2 are associated with pericarp histology in these lines and that pericarp tissue firmness depends on histology and cell wall chemistry according to genetics. These tomato lines represent good models to study the complex contributions of turgor pressure, cell wall chemistry, tissue architecture and their mechanisms of modulation underpinning texture in ripening tomatoes.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Effect of plant genotype on the efficacy of stimulators of plant defences in two horticultural pathosystems
auteur
Brigitte B. Maisonneuve, Caroline Allen-Aubouard, Michel Pitrat
article
IOBC WPRS Bulletin, 2013, 89, pp.327-331
resume
Four stimulators of plant defences (SPD) were tested on two pathosystems: powdery mildew (PM) due to Podosphaera xanthii on melon and downy mildew (DM) due to Bremia lactucae on lettuce. More than 450 accessions of melon were screened for the stimulation of their defence reactions by a formulation with laminarin, BION® 50WG and CalFlux and more than 400 accessions of lettuce with BION, Calflux and a formulation with yeast extract (ABE IT 56). In the PM/melon pathosystem, only BION was able to induce resistance; in the majority of the accessions resistance was not activated but some accessions fully susceptible to PM in the control sprayed with water were very well protected by BION. In the DM/lettuce pathosystem, the three tested SPD could induce resistance, but again BION was the most effective. Close to half accessions of the 300 susceptible to Bl: 25 and a quarter of the 110 accessions tested with Bl: 26 were well protected against the tested strain by BION and some of these were also protected by CalFlux (13% and 14%, respectively) and few by ABE IT 56 (10% and 4%, respectively). In both pathosystems, the induced resistance seems to be strain-specific as some accessions were protected against one strain and not protected against another strain; nevertheless some promising accessions were protected against both strains
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Functional characterization of the plant ubiquitin regulatory X (UBX) domain-containing protein AtPUX7 in Arabidopsis thaliana
auteur
Jean-Luc J.-L. Gallois, Jan J. Drouaud, Alain A. Lecureuil, Anouchka A. Debast Guyon, Sandrine S. Bonhomme, Philippe Guerche
article
Gene, 2013, 526 (2), pp.299-308. ⟨10.1016/j.gene.2013.05.056⟩
resume
p97/CDC48 is a major AAA-ATPase that acts in many cellular events such as ubiquitin-dependent degradation andmembrane fusion. Its specificity depends on a set of adaptor proteins,most of themcontaining the ubiquitin regulatory X (UBX) domain. Using a differential hybridization system, we isolated a UBX-containing protein that is expressed during the early phase of male gametophyte development in the crop Brassica napus and isolated and characterized its closest Arabidopsis thaliana homolog, AtPUX7. The AtPUX7 gene is expressed broadly in both the sporophyte and gametophyte due to regulation inferred by its first intron. The subcellular localization of AtPUX7 was assigned mainly to the nucleus in both the sporophyte and in pollen, mirroring the AAA-ATPase AtCDC48A localization. Furthermore, AtPUX7 interacts specificallywith AtCDC48A in yeast as well as in planta in the nucleus. This interaction was mediated through the AtPUX7 UBX domain, which is located at the protein C-terminus, while an N-terminal UBA domain mediated its interaction with ubiquitin. Consistent with those results, a yeast-three hybrid analysis showed that AtPUX7 can act as a bridge between AtCDC48A and ubiquitin, suggesting a role in targeted protein degradation. It is likely that AtPUX7 acts redundantlywith othermembers of the Arabidopsis PUX family because a null Atpux7-1 mutant does not display obvious developmental defects.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A key QTL cluster is conserved among accessions and exhibits broad-spectrum resistance to Phytophthora capsici: a valuable locus for pepper breeding
auteur
Stephanie Mallard, Melissa Cantet, Anne Massire, Alexandre Bachellez, Sophie Ewert, Véronique Lefebvre
article
Molecular Breeding, 2013, 32 (2), pp.349-364. ⟨10.1007/s11032-013-9875-3⟩
resume
Developing cultivars carrying effective resistance against destructive pathogens has become a priority for breeders. While little is currently known about the genetic basis of durable resistance, it is generally associated with polygenic and broad-spectrum resistance. In this study, we assessed the spectrum of resistance to Phytophthora capsici conferred by a major effect quantitative trait locus (QTL) that has been detected in all of the resistant pepper accessions studied to date. After adding new markers derived from tomato sequences and those from pepper reported in the literature to three maps of pepper chromosome P5, we detected a QTL cluster involved in P. capsici resistance. By means of meta-analyses, we determined the occurrence of these QTLs in different genetic backgrounds and with different P. capsici isolates. Comparative mapping with tomato and potato highlighted a complex mosaic of Phytophthora resistance loci on colinear chromosome segments. We tested different lines with and without one of these QTLs, Pc5.1, with four isolates that we determined to be genetically distinct. Our data demonstrate that Pc5.1 is active against 12 isolates from different geographical origins and that it is conserved in all of the resistant accessions tested. We propose that this QTL is a key element responsible for the broad-spectrum resistance to P. capsici and, therefore, is a valuable locus for improving the effective resistance of pepper to P. capsici.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Identification of reference genes for normalizing RNA expression in potato roots infected with cyst nematodes
auteur
Patricio Castro Quezada, Jawad Aarrouf, Michel Claverie, Bruno Favery, Didier Mugniery, Véronique Lefebvre, Bernard Caromel
article
Plant Molecular Biology Reporter, 2013, 31 (4), pp.936-945. ⟨10.1007/s11105-013-0566-3⟩
resume
Potato cyst nematodes induce changes in plant host gene expression following root invasion. For an accurate comparison of gene expression by reverse transcription quantitative real-time PCR (RT-qPCR), internal reference genes are necessary for transcript normalization. Very few experimental data on suitable reference genes are available for interactions between plant and root pathogens. In this study, we tested eight potential candidate reference genes for normalizing levels of potato gene transcripts by RT-qPCR after inoculation by nematodes. The ranking of candidate reference genes was performed using RefFinder WEB-based software. Four reference genes, RPN7 (26S proteasome regulatory subunit), UBP22 (ubiquitin-specific protease 22), OXA1 (OXA1 protein), and MST2 (mercaptopyruvate sulfurtransferase), were stably expressed in roots of susceptible or resistant potato plants, infected or uninfected by Globodera pallida. A normalization factor based on data from these four genes, highly homologous between potato and tomato, was used to normalize the expression of a chitinase gene, which was induced by nematodes in roots of potatoes carrying the resistance allele at a low-effect QTL, GpaXIspl. .
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01208611/file/2013_Castro-Quezada_Plant%20Molecular%20Biology%20Reporter%20%28Postprint%29_1 BibTex
titre
Whole genome resequencing in tomato reveals variation associated with introgression and breeding events
auteur
Mathilde M. Causse, Nelly Desplat, Laura Pascual-Banuls, Marie-Christine Le Paslier, Christopher Sauvage, Guillaume Bauchet, Aurélie A. Berard, Rémi Bounon, Maria Tchoumakov, Dominique D. Brunel, Jean-Paul Bouchet
article
BMC Genomics, 2013, 14 (791), 14 p. ⟨10.1186/1471-2164-14-791⟩
resume
Background: One of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits. The completion of the tomato genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of genetic variation present in the tomato genome. Like many self-pollinated crops, cultivated tomato accessions show a low molecular but high phenotypic diversity. Here we describe the whole-genome resequencing of eight accessions (four cherry-type and four large fruited lines) chosen to represent a large range of intra-specific variability and the identification and annotation of novel polymorphisms. Results: The eight genomes were sequenced using the GAII Illumina platform. Comparison of the sequences with the reference genome yielded more than 4 million single nucleotide polymorphisms (SNPs). This number varied from 80,000 to 1.5 million according to the accessions. Almost 128,000 InDels were detected. The distribution of SNPs and InDels across and within chromosomes was highly heterogeneous revealing introgressions from wild species and the mosaic structure of the genomes of the cherry tomato accessions. In-depth annotation of the polymorphisms identified more than 16,000 unique non-synonymous SNPs. In addition 1,686 putative copy-number variations (CNVs) were identified. Conclusions: This study represents the first whole genome resequencing experiment in cultivated tomato. Substantial genetic differences exist between the sequenced tomato accessions and the reference sequence. The heterogeneous distribution of the polymorphisms may be related to introgressions that occurred during domestication or breeding. The annotated SNPs, InDels and CNVs identified in this resequencing study will serve as useful genetic tools, and as candidate polymorphisms in the search for phenotype-altering DNA variations
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02652747/file/Causse%202013%20BMC%20genomics_1.pdf BibTex
titre
An extensive proteome map of tomato (Solanum lycopersicum) fruit pericarp
auteur
Jiaxin Xu, Laura Pascual-Banuls, Rémy Aurand, Jean-Paul Bouchet, Benoit B. Valot, Michel M. Zivy, Mathilde M. Causse, Mireille Faurobert
article
Proteomics, 2013, 13 (20), pp.3059 - 3063. ⟨10.1002/pmic.201200438⟩
resume
Tomato (Solanum lycopersicum) is the model species for studying fleshy fruit development. An extensive proteome map of the fruit pericarp is described in light of the high-quality genome sequence. The proteomes of fruit pericarp from 12 tomato genotypes at two developmental stages (cell expansion and orange-red) were analyzed. The 2DE reference map included 506 spots identified by nano-LC/MS and the International Tomato Annotation Group Database searching. A total of 425 spots corresponded to unique proteins. Thirty-four spots resulted from the transcription of genes belonging to multigene families involving two to six genes. A total of 47 spots corresponded to a mixture of different proteins. The whole protein set was classified according to Gene Ontology annotation. The quantitative protein variation was analyzed in relation to genotype and developmental stage. This tomato fruit proteome dataset is currently the largest available and constitutes a valuable tool for comparative genetic studies of tomato genome expression at the protein level. All MS data have been deposited in the ProteomeXchange with identifier PXD000105.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
High temperature inhibits ascorbate recycling and light stimulation of the ascorbate pool in tomato despite increased expression of biosynthesis genes
auteur
Capucine Massot, Doriane Bancel, Félicie Lopez Lauri, Vincent Truffault, Pierre Baldet, Rebecca Stevens, Hélène Gautier
article
PLoS ONE, 2013, 8 (12), 13 p. ⟨10.1371/journal.pone.0084474⟩
resume
Understanding how the fruit microclimate affects ascorbate (AsA) biosynthesis, oxidation and recycling is a great challenge in improving fruit nutritional quality. For this purpose, tomatoes at breaker stage were harvested and placed in controlled environment conditions at different temperatures (12, 17, 23, 27 and 31 °C) and irradiance regimes (darkness or 150 µmol m(-2) s(-1)). Fruit pericarp tissue was used to assay ascorbate, glutathione, enzymes related to oxidative stress and the AsA/glutathione cycle and follow the expression of genes coding for 5 enzymes of the AsA biosynthesis pathway (GME, VTC2, GPP, L-GalDH, GLDH). The AsA pool size in pericarp tissue was significantly higher under light at temperatures below 27 °C. In addition, light promoted glutathione accumulation at low and high temperatures. At 12 °C, increased AsA content was correlated with the enhanced expression of all genes of the biosynthesis pathway studied, combined with higher DHAR and MDHAR activities and increased enzymatic activities related to oxidative stress (CAT and APX). In contrast, at 31 °C, MDHAR and GR activities were significantly reduced under light indicating that enzymes of the AsA/glutathione cycle may limit AsA recycling and pool size in fruit pericarp, despite enhanced expression of genes coding for AsA biosynthesis enzymes. In conclusion, this study confirms the important role of fruit microclimate in the regulation of fruit pericarp AsA content, as under oxidative conditions (12 °C, light) total fruit pericarp AsA content increased up to 71%. Moreover, it reveals that light and temperature interact to regulate both AsA biosynthesis gene expression in tomato fruits and AsA oxidation and recycling.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02645038/file/massot_2013_1.pdf BibTex
titre
Effect of salinity and calcium on tomato fruit proteome
auteur
Arafet Manaa, Mireille Faurobert, Benoit B. Valot, Jean-Paul Bouchet, Dominique Grasselly, Mathilde M. Causse, Hela Ben Ahmed
article
OMICS, 2013, 17 (6), 15 p. ⟨10.1089/omi.2012.0108⟩
resume
Salinity is a major abiotic stress that adversely affects plant growth and productivity. The physiology of the tomato in salty and nonsalty conditions has been extensively studied, providing an invaluable base to understand the responses of the plants to cultural practices. However few data are yet available at the proteomic level looking for the physiological basis of fruit development, under salt stress. Here, we report the effects of salinity and calcium on fruit proteome variations of two tomato genotypes (Cervil and Levovil). Tomato plants were irrigated with a control solution (3 dSm- 1) or with saline solutions (Na or Ca+Na at 7.6 dSm- 1). Tomato fruits were harvested at two ripening stages: green (14 days post-anthesis) and red ripe. Total proteins were extracted from pericarp tissue and separated by two-dimensional gel electrophoresis. Among the 600 protein spots reproducibly detected, 53 spots exhibited significant abundance variations between samples and were submitted to mass spectrometry for identification. Most of the identified proteins were involved in carbon and energy metabolism, salt stress, oxidative stress, and proteins associated with ripening process. Overall, there was a large variation on proteins abundance between the two genotypes that can be correlated to salt treatment or/and fruit ripening stage. The results showed a protective effect of calcium that limited the impact of salinization on metabolism, ripening process, and induced plant salt tolerance. Collectively, this work has improved our knowledge about salt and calcium effect on tomato fruit proteome.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02648418/file/Effect%20of%20Salinity%20and%20Calcium%20on%20Tomato%20Fruit%20Proteome%20%281%29_1.pdf BibTex
titre
Phenotypic diversity in wild and cultivated melons (Cucumis melo)
auteur
Michel Pitrat
article
Plant Biotechnology, 2013, 30 (3), pp.273 - 278. ⟨10.5511/plantbiotechnology.13.0813a⟩
resume
Like many crops, cultivated melons present a very large phenotypic polymorphism compared with the low phenotypic polymorphism of wild melons. Domestication has not been intensively studied and the genetic control of domestication traits is still poorly understood. The results of the subsequent diversification and selection processes are the present day types of melons. Genetic control of a majority of the diversification traits is under recessive genetic control: sex expression, fruit shape, sutures, number of placentas, gelatinous sheath around the seeds, white flesh colour and so on. Other phenotypic traits are dominant (orange flesh colour, netting, yellow colour of mature fruit in the Amarillo type and so on) as are most of the disease resistances. Presence of the same traits in very different botanical groups can be the result of parallel evolution but also of intercrossing between groups and selection of preferred alleles. New results (genome sequencing) and methods will allow a better understanding of the genetic control of domestication and diversification.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02648270/file/Plant%20Biotechnol_1.pdf BibTex
titre
Genetic and QTL analyses of yield and a set of physiological traits in pepper
auteur
Nurudeen Adeniyi Alimi, M. C. A. M. Bink, J. A. Dieleman, Maryse Nicolaï, M. Wubs, E. Heuvelink, J. Magan, R. E. Voorrips, J. Jansen, P. C. Rodrigues, G. W. A. M. van Der Heijden, A. Vercauteren, M. Vuylsteke, Y. Song, C. Glasbey, A. Barocsi, Véronique Lefebvre, Alain Palloix, F. A. van Eeuwijk
article
Euphytica, 2013, 190 (2), pp.181 - 201. ⟨10.1007/s10681-012-0767-0⟩
resume
An interesting strategy for improvement of a complex trait dissects the complex trait in a number of physiological component traits, with the latter having hopefully a simple genetic basis. The complex trait is then improved via improvement of its component traits. As first part of such a strategy to improve yield in pepper, we present genetic and QTL analyses for four pepper experiments. Sixteen traits were analysed for a population of 149 recombinant inbred lines, obtained from a cross between the large-fruited pepper cultivar 'Yolo Wonder' (YW) and the small fruited pepper 'Criollo de Morelos 334' (CM334). The marker data consisted of 493 markers assembled into 17 linkage groups covering 1,775 cM. The trait distributions were unimodal, although sometimes skewed. Many traits displayed heterosis and transgression. Heritabilities were high (mean 0.86, with a range between 0.43 and 0.96). A multiple QTL mapping approach per trait and environment yielded 24 QTLs. The average numbers of QTLs per trait was two, ranging between zero and six. The total explained trait variance by QTLs varied between 9 and 61 %. QTL effects differed quantitatively between environments, but not qualitatively. For stem-related traits, the trait-increasing QTL alleles came from parent CM334, while for leaf and fruit related traits the increasing QTL alleles came from parent YW. The QTLs on linkage groups 1b, 2, 3a, 4, 6 and 12 showed pleiotropic effects with patterns that were consistent with the genetic correlations. These results contribute to a better understanding of the genetics of yield-related physiological traits in pepper and represent a first step in the improvement of the target trait yield.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Role of vernalization and of duplicated FLOWERING LOCUS C in the perennial Arabidopsis lyrata
auteur
Ulla Kemi, Anne Niittyvuopio, Tuomas Toivainen, Anu Pasanen, Bénédicte Quilot-Turion, Karl Holm, Ulf Lagercrantz, Outi Savolainen, Helmi Kuittinen
article
New Phytologist, 2013, 197 (1), pp.323-335. ⟨10.1111/j.1469-8137.2012.04378.x⟩
resume
FLOWERING LOCUS C (FLC) is one of the main genes influencing the vernalization requirement and natural flowering time variation in the annual Arabidopsis thaliana. Here we studied the effects of vernalization on flowering and its genetic basis in the perennial Arabidopsis lyrata. Two tandemly duplicated FLC genes (FLC1 and FLC2) were compared with respect to expression and DNA sequence. The effect of vernalization on flowering and on the expression of FLC1 was studied in three European populations. The genetic basis of the FLC1 expression difference between two of the populations was further studied by expression quantitative trait locus (eQTL) mapping and sequence analysis. FLC1 was shown to have a likely role in the vernalization requirement for flowering in A. lyrata. Vernalization decreased its expression and the northern study populations showed higher FLC1 expression than the southern one. eQTL mapping between two of the populations revealed one eQTL affecting FLC1 expression in the genomic region containing the FLC genes. Most FLC1 sequence differences between the study populations were found in the promoter region and in the first intron. Variation in the FLC1 sequence may cause differences in FLC1 expression between late- and early-flowering A. lyrata populations.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02645614/file/Kemietal_preprint_1.pdf BibTex
titre
Identification and tagging of genetic resistance factors to Sharka disease in apricot trees and Prunus davidiana
auteur
David Tricon, Patrick Lambert, Jean Marc Audergon, Thierry Pascal, Guillaume Roch, Véronique Decroocq
article
Innovations Agronomiques, 2013, 27, pp.31-35. ⟨10.17180/ascb-zj06⟩
resume
The Plum pox virus (PPV), the causal agent of the sharka disease, is the most detrimental virus on stone-fruit trees, worldwide. Infected fruits are not marketable. To date, no stone fruit cultivar (peach, apricot, plum) is resistant. However, sources of resistance have been identified and mapped in apricot and Prunus davidiana, a wild peach-related species. Several of the mapped QTL co-localize with candidate genes previously identified. In the present study, resistance in P. davidiana was confirmed in an F2 population and two new QTL were identified. Quantitative analysis of the apricot cultivars ‘Goldrich’ and ‘SEO’ resistance was also performed. Molecular markers targeting these genes were developed as a tool for marker-assisted selection. This study made it also possible to refine boundaries of the genomic region controlling PPV resistance as well as confirming the robustness and stability of the resistance trait in both species: P. davidiana and P. armeniaca.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02650514/file/Vol27-4-Tricon_1.pdf BibTex
titre
Light-dependent regulation of ascorbate in tomato by a monodehydroascorbate reductase localized in peroxisomes and the cytosol
auteur
Noé Gest, Cecile Garchery, Hélène Gautier, Ana Jimenez, Rebecca Stevens
article
Plant Biotechnology Journal, 2013, 11 (3), pp.344 - 354. ⟨10.1111/pbi.12020⟩
resume
Ascorbate is a powerful antioxidant in plants, and its levels are an important quality criteria in commercial species. Factors influencing these levels include environmental variations, particularly light, and the genetic control of its biosynthesis, recycling and degradation. One of the genes involved in the recycling pathway encodes a monodehydroascorbate reductase (MDHAR), an enzyme catalysing reduction of the oxidized radical of ascorbate, monodehydroascorbate, to ascorbate. In plants, MDHAR belongs to a multigene family. Here, we report the presence of an MDHAR isoform in both the cytosol and peroxisomes and show that this enzyme negatively regulates ascorbate levels in Solanum lycopersicum (tomato). Transgenic lines overexpressing MDHAR show a decrease in ascorbate levels in leaves, whereas lines where MDHAR is silenced show an increase in these levels in both fruits and leaves. Furthermore, the intensity of these differences is light dependent. The unexpected effect of this MDHAR on ascorbate levels cannot be explained by changes in the expression of SmirnoffWheeler pathway genes, or the activity of enzymes involved in degradation (ascorbate peroxidase) or recycling of ascorbate (dehydroascorbate reductase and glutathione reductase), suggesting a previously unidentified mechanism regulating ascorbate levels.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Protein and mineral nutrient contents in kernels from 72 sweet almond cultivars and accessions grown in France, Greece and Italy
auteur
Pavlina D. Drogoudi, Georgios Pantelidis, Loretta Bacchetta, Donato de Giorgio, Henri Duval, Ioannis Metzidakis, Daniella Spera
article
International Journal of Food Sciences and Nutrition, 2013, 64 (2), pp.202-209. ⟨10.3109/09637486.2012.728202⟩
resume
Almond protein and potassium (K), phosphorus (P), calcium (Ca) and magnesium (Mg) contents were determined in 72 cultivars and accessions grown in France, Greece and Italy, as part of the networking of European SAFENUTAGRI GEN RES project, which aimed to explore and valorize the almond genetic resources in Europe. Great variation was found in the nutrient content and the amount of nutrient supplied when consuming the recommended daily amount of one serving of almond, among the different genotypes assayed. The variation among the different genotypes was greatest for Ca, followed by the protein content; the latter also exhibited the lowest variation considering the harvest year. Results from a principal component analysis showed that P and Mg were the most discriminant elements for categorizing samples. Cluster analysis showed groups of samples with interesting characteristics for breeding. There was no clear distinction among the different origins of samples. Correlation analyses between weather conditions and the nutrients assayed showed that the mean temperature recorded in the period between March and September was positively correlated with Ca and P only in France, a place where the greatest climatic difference between years was observed.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02651820/file/Drogoudi%20et%20al%2C%202012%20POSTPRINT_1.pdf BibTex
titre
Genotyping a large collection of pepper (Capsicum spp.) with SSR loci brings new evidence for the wild origin of cultivated C. annuum and the structuring of genetic diversity by human selection of cultivar types
auteur
Maryse Nicolaï, Melissa Cantet, Véronique Lefebvre, Anne-Marie Sage-Palloix, Alain Palloix
article
Genetic Resources and Crop Evolution, 2013, 60 (8), pp.2375-2390. ⟨10.1007/s10722-013-0006-0⟩
resume
Germplasm collections of cultivated plants constitute the source for further genetic progress. These collections gained further interest with approaches for tracking allelic variants associated to phenotypic variations within core collections. In order to explore the structure of genetic variation in pepper (Capsicum spp.) and to select core-collections maximizing the genetic and the phenotypic diversity, a pepper collection including 1352 non redundant accessions from 11 Capsicum species from 89 different countries was genotyped using 28 microsatellite (SSR) markers spanning the whole genome. Model-based analysis structured the collection into 6 clusters, with 3 clusters separating the main species complexes, including cultivated species and wild relatives, according to taxonomic classification (C. frutescens/C. chinense, C. baccatum, C. pubescens), and 3 additional clusters for C. annuum. The relationships between the cultivated C. annuum species and the wild relative (C. annnuum var glabriusculum) was precised. The 3 C. annuum clusters were significantly distinct for plant and fruit descriptors corresponding to cultivar types, showing that the genetic structure of this cultivated species was strongly impacted by the long term human selection of landraces in primary as well as secondary diversification centres. We settled nested core-collections of 8, 16, 32, 64 and 128 C. annuum accessions capturing from 37% to 90% of the genetic diversity for further sequencing efforts and establishment of high throughput genotyping assays. By compiling phenotypic and genotypic data, a larger core-collection of 332 accessions was established, capturing 97% of the C. annuum genetic and phenotypic diversity for further genetic association studies.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Experimental evaluation of resistance genes deployment strategies for the sustainable management of root-knot nematodes
auteur
Caroline Djian-Caporalino, Alain Palloix, Ariane Fazari, Nathalie Marteu, Anne-Marie Sage-Palloix, Thierry Mateille, Johannes Tavoillot, Bruno Martiny, Sabine Risso, Roger Lanza, Catherine Taussig, Philippe Castagnone-Sereno
article
Innovations Agronomiques, 2013, 28, pp.187-199. ⟨10.17180/qytb-9n40⟩
resume
Within the framework of ANR Systerra and GIS PICLeg (projects "Sysbiotel" & "Neoleg"), in collaboration between INRA PACA, IRD, APREL, the Chambre of Agriculture 06 and private seed companies, several resistance genes deployment strategies were evaluated for 3 years in field agronomic conditions to develop a rational management of resistant cultivars for the sustainable control of root-knot nematodes. The alternation of resistance genes in the rotation and the «pyramiding» of such genes in a single cultivar proved to be extremely efficient in suppressing the emergence of virulent populations and decreasing the amount of pathogens in the soil by more than 80% in 3 years. A new project (named "Gedunem") launched in the framework of the INRA Metaprogram SMaCH (Sustainable Management of Crop Health) is now in progress, associating these new varieties to other available control methods (i.e., intercultural management, non-host plants, prophylaxis), to maintain a low parasite pressure, while assessing these new cropping systems for agronomic and socio-economic aspects.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-04534512/file/2013_Dijan_Innovations%20Agronomiques.pdf BibTex
titre
Characterization and genetic mapping of a new blood-flesh trait controlled by the single dominant locus DBF in peach
auteur
Zhijun Shen, Carole C. Confolent, Patrick Lambert, Jean-Luc Poessel, Bénédicte Quilot-Turion, Mingliang Yu, Ruijan Ma, Thierry Pascal
article
Tree Genetics and Genomes, 2013, 9 (6), pp.1435-1446. ⟨10.1007/s11295-013-0649-1⟩
resume
Anthocyanin-rich peaches, because of their antioxydant properties and their strong attractiveness to consumers, are increasingly considered in French peach varietal innovation programs that integrate plant genomics and classical breeding. In this study, we describe a new blood-flesh trait identified in the ‘Wu Yue Xian’ peach accession from China. ‘Wu Yue Xian’ exhibits a fully red mesocarp during the later stages of fruit development, both with green midrib leaf and normal growth of the tree. This blood-flesh phenotype clearly differs from that determined by a single recessive locus (bf) in ‘Harrow Blood’, a clone showing blood-flesh in both immature and mature fruit associated with red midrib leaf and reduced tree height. We have then provided genetic evidence that blood-flesh phenotype of ‘Wu Yue Xian’ was controlled by a single dominant locus, designated DBF, in four successive families derived from this accession. A genetic linkage map of the blood- flesh parent (‘D6090’) of the fourth population was constructed, including 102 SSRs spanning a total distance of 562.3 cM in 8 linkage groups. Whereas the bf locus is located to linkage group 4, we mapped DBF to the top of linkage group 5, thus proving that DBF and bf loci are not alleles. Among 64 predicted genes in the DBF region (505 kbp), three genes of the dihydroflavonol-4-red uctase family were identified as good candidates for the control of the DBF trait. Furthermore, SSR markers flanking DBF, such as AMPP157 and AMPPG178, supply a good basis to implement marker-assisted selection for this trait.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02648172/file/new_proof_Zhijun_ThPascal_PREPRINT_1.pdf BibTex
titre
Proteomic analysis of tomato (Solanum lycopersicum) secretome
auteur
Emadeldin Konozy, Hélène Rogniaux, Mathilde M. Causse, Mireille Faurobert
article
Journal of Plant Research, 2013, 126, pp.251-266. ⟨10.1007/s10265-012-0516-4⟩
resume
In fleshy fruits, fruit texture features are mainly related to chemical and mechanical properties of the cell wall. The description of tomato fruit cell wall proteome is a first step in the process of linking tomato genetic variability to fruit texture phenotypes. In this study, the proteome of 3 ripe tomato fruit lines with contrasted texture traits were studied. Weakly bound and soluble proteins were extracted from cell wall of the three cultivars using both destructive and non-destructive methods, respectively. Wall proteins were separated on 1D-PAGE, bands were excised and identified by LC–MS/MS. The software SignalP which searches for the leader peptide was used to discriminate between protein with or without signal peptide. In combine, seventy-five different cell wall proteins were recorded for both weakly bound and soluble cell wall fractions. The major identified functions included several proteins acting on polysaccharides, proteins involved in ‘‘lipid metabolism’’, proteins having interacting domain, ‘‘oxido-reductases’’ and ‘‘proteases’’ whose putative roles in ripe fruit cell wall is discussed. Several proteins with no obvious signal peptide, however, with accumulating supportive evidences to be bona fide wall proteins, were also identified. Some variations in protein repertories were observed among the lines, demonstrating the possibility to characterize cell wall protein genetic variability by such in muro proteome analyses.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic changes in flowering and morphology in response to adaptation to a high-latitude environment in Arabidopsis lyrata
auteur
Bénédicte Quilot-Turion, Johanna Leppälä, Paivi H. Leinonen, Patrik Waldmann, Outi Savolainen, Helmi Kuittinen
article
Annals of Botany, 2013, 111 (5), pp.957-968. ⟨10.1093/aob/mct055⟩
resume
Background and Aims: The adaptive plastic reactions of plant populations to changing climatic factors, such as winter temperatures and photoperiod, have changed during range shifts after the last glaciation. Timing of flowering is an adaptive trait regulated by environmental cues. Its genetics has been intensively studied in annual plants, but in perennials it is currently not well characterized. This study examined the genetic basis of differentiation in flowering time, morphology, and their plastic responses to vernalization in two locally adapted populations of the perennial Arabidopsis lyrata: (1) to determine whether the two populations differ in their vernalization responses for flowering phenology and morphology; and (2) to determine the genomic areas governing differentiation and vernalization responses. Methods: Two A. lyrata populations, from central Europe and Scandinavia, were grown in growth-chamber conditions with and without cold treatment. A QTL analysis was performed to find genomic regions that interact with vernalization. Key Results: The population from central Europe flowered more rapidly and invested more in inflorescence growth than the population from alpine Scandinavia, especially after vernalization. The alpine population had consistently a low number of inflorescences and few flowers, suggesting strong constraints due to a short growing season, but instead had longer leaves and higher leaf rosettes. QTL mapping in the F2 population revealed genomic regions governing differentiation in flowering time and morphology and, in some cases, the allelic effects from the two populations on a trait were influenced by vernalization (QTL × vernalization interactions). Conclusions: The results indicate that many potentially adaptive genetic changes have occurred during colonization; the two populations have diverged in their plastic responses to vernalization in traits closely connected to fitness through changes in many genomic areas.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species
auteur
Jiaxin Xu, Nicolas N. Ranc, Stephane Munos, Sophie Rolland, Jean-Paul Bouchet, Nelly Desplat, Marie-Christine Le Paslier, Yan Liang, Dominique D. Brunel, Mathilde M. Causse
article
TAG Theoretical and Applied Genetics, 2013, 126 (3), pp.567 - 581. ⟨10.1007/s00122-012-2002-8⟩
resume
Association mapping has been proposed as an efficient approach to assist in the identification of the molecular basis of agronomical traits in plants. For this purpose, we analyzed the phenotypic and genetic diversity of a large collection of tomato accessions including 44 heirloom and vintage cultivars (Solanum lycopersicum), 127 S. lycopersicum var. cerasiforme (cherry tomato) and 17 Solanum pimpinellifolium accessions. The accessions were genotyped using a SNPlex (TM) assay of 192 SNPs, among which 121 were informative for subsequent analysis. Linkage disequilibrium (LD) of pairwise loci and population structure were analyzed, and the association analysis between SNP genotypes and ten fruit quality traits was performed using a mixed linear model. High level of LD was found in the collection at the whole genome level. It was lower when considering only the 127 S. lycopersicum var. cerasiforme accessions. Genetic structure analysis showed that the population was structured into two main groups, corresponding to cultivated and wild types and many intermediates. The number of associations detected per trait varied, according to the way the structure was taken into account, with 0-41 associations detected per trait in the whole collection and a maximum of four associations in the S. lycopersicum var. cerasiforme accessions. A total of 40 associations (30 %) were co-localized with previously identified quantitative trait loci. This study thus showed the potential and limits of using association mapping in tomato populations.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic mapping of a major dominant gene for resistance to ralstonia solanacearum in eggplant
auteur
Aurore Lebeau, Matthieu Gouy, Marie-Christine Daunay, Emmanuel Wicker, Frédéric Chiroleu, Philippe Prior, Anne Frary, Jacques Dintinger
article
TAG Theoretical and Applied Genetics, 2013, 126 (1), pp.143 - 158. ⟨10.1007/s00122-012-1969-5⟩
resume
Resistance of eggplant against ralstonia solanacearum phylotype I strains was assessed in a F-6 population of recombinant inbred lines (RILs) derived from a intra-specific cross between S. melongena MM738 (susceptible) and AG91-25 (resistant). Resistance traits were determined as disease score, percentage of wilted plants, and stem-based bacterial colonization index, as assessed in greenhouse experiments conducted in R,union Island, France. The AG91-25 resistance was highly efficient toward strains CMR134, PSS366 and GMI1000, but only partial toward the highly virulent strain PSS4. The partial resistance found against PSS4 was overcome under high inoculation pressure, with heritability estimates from 0.28 to 0.53, depending on the traits and season. A genetic map was built with 119 AFLP, SSR and SRAP markers positioned on 18 linkage groups (LG), for a total length of 884 cM, and used for quantitative trait loci (QTL) analysis. A major dominant gene, named ERs1, controlled the resistance to strains CMR134, PSS366, and GMI1000. Against strain PSS4, this gene was not detected, but a significant QTL involved in delay of disease progress was detected on another LG. The possible use of the major resistance gene ERs1 in marker-assisted selection and the prospects offered for academic studies of a possible gene for gene system controlling resistance to bacterial wilt in solanaceous plants are discussed.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Exploitation of natural genetic diversity to study plant-virus interactions: what can we learn from Arabidopsis thaliana?
auteur
Laurence Ouibrahim, Carole Caranta
article
Molecular Plant Pathology, 2013, 14 (8), pp.844-854. ⟨10.1111/mpp.12052⟩
resume
The development and use of cultivars that are genetically resistant to viruses is an efficient strategy to tackle the problems of virus diseases. Over the past two decades, the model plant Arabidopsis thaliana has been documented as a host for a broad range of viral species, providing access to a large panel of resources and tools for the study of viral infection processes and resistance mechanisms. Exploration of its natural genetic diversity has revealed a wide range of genes conferring virus resistance. The molecular characterization of some of these genes has unveiled resistance mechanisms distinct from those described in crops. In these respects, Arabidopsis represents a rich and largely untapped source of new genes and mechanisms involved in virus resistance. Here, we review the current status of our knowledge concerning natural virus resistance in Arabidopsis. We also address the impact of environmental conditions on Arabidopsis-virus interactions and resistance mechanisms, and discuss the potential of applying the knowledge gained from the study of Arabidopsis natural diversity for crop improvement.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Medieval iconography of watermelons in Mediterranean Europe
auteur
Harry S. Paris, M-Christin Daunay, Jules Janick
article
Annals of Botany, 2013, 112 (5), pp.867-879. ⟨10.1093/aob/mct151⟩
resume
The watermelon, Citrullus lanatus (Cucurbitaceae), is an important fruit vegetable in the warmer regions of the world. Watermelons were illustrated in Mediterranean Antiquity, but not as frequently as some other cucurbits. Little is known concerning the watermelons of Mediterranean Europe during medieval times. With the objective of obtaining an improved understanding of watermelon history and diversity in this region, medieval drawings purportedly of watermelons were collected, examined and compared for originality, detail and accuracy. The oldest manuscript found that contains an accurate, informative image of watermelon is the Tractatus de herbis, British Library ms. Egerton 747, which was produced in southern Italy, around the year 1300. A dozen more original illustrations were found, most of them from Italy, produced during the ensuing two centuries that can be positively identified as watermelon. In most herbal-type manuscripts, the foliage is depicted realistically, the plants shown as having long internodes, alternate leaves with pinnatifid leaf laminae, and the fruits are small, round and striped. The manuscript that contains the most detailed and accurate image of watermelon is the Carrara Herbal, British Library ms. Egerton 2020. In the agriculture-based manuscripts, the foliage, if depicted, is not accurate, but variation in the size, shape and coloration of the fruits is evident. Both red-flesh and white-flesh watermelons are illustrated, corresponding to the typical sweet dessert watermelons so common today and the insipid citron watermelons, respectively. The variation in watermelon fruit size, shape and coloration depicted in the illustrations indicates that at least six cultivars of watermelon are represented, three of which probably had red, sweet flesh and three of which appear to have been citrons. Evidently, citron watermelons were more common in Mediterranean Europe in the past than they are today.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A diminution in ascorbate oxidase activity affects carbon allocation and improves yield in tomato under water deficit
auteur
Cécile Garchery, Noé Gest, Phuc Thi Do, Moftah Alhagdow, Pierre Baldet, Guillaume Menard, Christophe Rothan, Capucine Massot, Hélène Gautier, Jawad Aarrouf, Alisdair R. A. R. Fernie, Rebecca Stevens
article
Plant, Cell and Environment, 2013, 36 (1), pp.159-175. ⟨10.1111/j.1365-3040.2012.02564.x⟩
resume
The regulation of carbon allocation between photosyn-thetic source leaves and sink tissues in response to stress is an important factor controlling plant yield. Ascorbate oxidase is an apoplastic enzyme, which controls the redox state of the apoplastic ascorbate pool. RNA interference was used to decrease ascorbate oxidase activity in tomato (Solanum lycopersicum L.). Fruit yield was increased in these lines under three conditions where assimilate became limiting for wild-type plants: when fruit trusses were left unpruned, when leaves were removed or when water supply was limited. Several alterations in the transgenic lines could contribute to the improved yield and favour transport of assimilate from leaves to fruits in the ascorbate oxidase lines. Ascorbate oxidase plants showed increases in sto-matal conductance and leaf and fruit sugar content, as well as an altered apoplastic hexose : sucrose ratio. Modifications in gene expression, enzyme activity and the fruit metabolome were coherent with the notion of the ascorbate oxidase RNAi lines showing altered sink strength. Ascor-bate oxidase may therefore be a target for strategies aimed at improving water productivity in crop species.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Methods for controlling Phytophthora in vegetable crops: inputs from microbial core collection in the plant breeding process
auteur
Marie-Line Kuhn, Anne Massire, Melissa Cantet, Rene Damidaux, Elvina Gibowski, Youna Ruellan, Véronique Lefebvre, Franck Panabières
article
Innovations Agronomiques, 2013, 27, pp.47-58. ⟨10.17180/ban1-9868⟩
resume
Among Solanaceous crops, pepper and tomato are damaged by numerous pathogens, including Phytophthora capsici and Phytophthora infestans. Major genes have been identified in tomato to confer resistance against P. infestans, which were rapidly overcome by virulent populations. Pepper resistance towards P. capsici is provided by several quantitative trait loci (QTLs). Efficient exploitation of these polygenic resistance sources in plant breeding requires a good evaluation of their spectrum and durability. This implies a precise knowledge of the genetic and pathogenic diversity of pathogen populations and their adaptive potential. In this context, the establishment of core-collections that would reflect the overall intraspecific diversity of Phytophthora spp. would be useful to assess the a priori durability of resistance sources. The results of the research conducted at INRA reveal the limitations of such a strategy: it may be efficiently developed only locally, requires more knowledge on the structure and epidemiological characteristics of natural pathogen populations, and mainly relies on robust strain storage protocols.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02642876/file/Vol27-6-Panabieres_1.pdf BibTex
titre
Farther, slower, stronger: how the plant genetic background protects a major resistance gene from breakdown
auteur
Julie Quenouille, Josselin Montarry, Alain Palloix, Benoît Moury
article
Molecular Plant Pathology, 2013, 14 (2), pp.109-118. ⟨10.1111/J.1364-3703.2012.00834.X⟩
resume
Genetic resistance provides efficient control of crop diseases, but is limited by pathogen evolution capacities which often result in resistance breakdown. It has been demonstrated recently, in three different pathosystems, that polygenic resistances combining a major-effect gene and quantitative resistance controlled by the genetic background are more durable than monogenic resistances (with the same major gene in a susceptible genetic background), but the underlying mechanisms are unknown. Using the pepper–Potato virus Y system, we examined three mechanisms that could account for the greater durability of the polygenic resistances: (i) the additional quantitative resistance conferred by the genetic background; (ii) the increase in the number of mutations required for resistance breakdown; and (iii) the slower selection of adapted resistance-breaking mutants within the viral population. The three mechanisms were experimentally validated. The first explained a large part of the variation in resistance breakdown frequency and is therefore expected to be a major determinant of resistance durability. Quantitative resistance factors also had an influence on the second mechanism by modifying the virus mutational pathways towards resistance breakdown and could also have an influence on the third mechanism by increasing genetic drift effects on the viral population. The relevance of these results for other plant–pathogen systems and their importance in plant breeding are discussed.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Ascorbate as seen through plant evolution: the rise of a successful molecule?
auteur
Noé Gest, Hélène Gautier, Rebecca Stevens
article
Journal of Experimental Botany, 2013, 64 (1), pp.33 - 53. ⟨10.1093/jxb/ers297⟩
resume
Ascorbate is a widespread and efficient antioxidant that has multiple functions in plants, traditionally associated with the reactions of photosynthesis. This review aims to look at ascorbate from an evolutionary perspective. Cyanobacteria, algae, and bryophytes contain lower concentrations of ascorbate than higher plants, where the molecule accumulates in high concentrations in both photosynthetic and non-photosynthetic organs and tissues. This increase in ascorbate concentration is paralleled by an increase in the number of isoforms of ascorbate peroxidase and the ascorbate regenerating enzymes mono- and dehydroascorbate reductase. One way of understanding the rise in ascorbate concentrations is to consider ascorbate as a molecule among others that has been subject to selection pressures during evolution, due to its cost or benefit for the cell and the organism. Ascorbate has a low cost in terms of synthesis and toxicity, and its benefits include protection of the glutathione pool and proper functioning of a range of enzymes. The hypothesis presented here is that these features would have favoured increasing roles for the molecule in the development and growth of multicellular organisms. This review then focuses on this diversity of roles for ascorbate in both photosynthetic and non-photosynthetic tissues of higher plants, including fruits and seeds, as well as further functions the molecule may possess by looking at other species. The review also highlights one of the trade-offs of domestication, which has often reduced or diluted ascorbate content in the quest for increased fruit growth and yield, with unknown consequences for the corresponding functional diversity, particularly in terms of stress resistance and adaptive responses to the environment.
typdoc
Journal articles
Accès au bibtex
BibTex

2012

Journal articles

titre
Coding Gene Single Nucleotide Polymorphism Mapping and Quantitative Trait Loci Detection for Physiological Reproductive Traits in Brook Charr, Salvelinus fontinalis
auteur
Christopher Sauvage, Marie Vagner, Nicolas N. Derome, Céline Audet, Louis Bernatchez
article
G3, 2012, 2 (3), pp.379-392. ⟨10.1534/g3.111.001867⟩
resume
A linkage map of 40 linkage groups (LGs) was developed for brook charr, Salvelinus fontinalis, using an F2 interstrain hybrid progeny (n = 171) and 256 coding gene SNP developed specifically for brook charr and validated from a large (>1000) subset of putative SNP, as well as 81 microsatellite markers. To identify quantitative trait loci (QTL) related to reproduction functions, these fish were also phenotyped at six physiological traits, including spermatozoid head diameter, sperm concentration, plasma testosterone, plasma 11-keto-testosterone, egg diameter, and plasma 17β-estradiol. Five significant QTL were detected over four LGs for egg diameter and plasma 17β-estradiol concentration in females, and sperm concentration as well as spermatozoid head diameter in males. In females, two different QTLs located on LG 11 and LG 34 were associated with the egg number, whereas one QTL was associated with plasma 17β-estradiol concentration (LG 8). Their total percent variance explained (PVE) was 26.7% and 27.6%, respectively. In males, two QTL were also detected for the sperm concentration, and their PVE were estimated at 18.58% and 14.95%, respectively. The low QTL number, associated with the high PVE, suggests that the variance in these reproductive physiological traits was either under the control of one major gene or a small number of genes. The QTL associated with sperm concentration, plasma 17β-estradiol, and egg diameter appeared to be under a dominance effect, whereas the two others were under a negative additive effect. These results show that genes underlying the phenotypic variance of these traits are under different modes of action (additive vs. dominance) and may be used to predict an increase or a decrease in their phenotypic values in subsequent generations of selective breeding. Moreover, this newly developed panel of mapped SNP located in coding gene regions will be useful for screening wild populations, especially in the context of investigating the genetic impact of massive stocking of domestic brook charr to support the angling industry throughout eastern North America.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-02107010/file/49868_20120323015132794_1.pdf BibTex
titre
Agrobacterium rhizogenes-dependent production of transformed roots from foliar explants of pepper (Capsicum annuum): a new and efficient tool for functional analysis of genes
auteur
Jawad Aarrouf, Patricio Castro Quezada, Simon Mallard, Bernard Caromel, Y Lizzi, Véronique Lefebvre
article
Plant Cell Reports, 2012, 2 (31), pp.391-401. ⟨10.1007/s00299-011-1174-z⟩
resume
Pepper is known to be a recalcitrant species to genetic transformation via Agrobacterium tumefaciens. A. rhizogenes-mediated transformation offers an alternative and rapid possibility to study gene functions in roots. In our study, we developed a new and efficient system for A. rhizogenes transformation of the cultivated species Capsicum annuum. Hypocotyls and foliar organs (true leaves and cotyledons) of Yolo Wonder (YW) and Criollo de Morelos 334 (CM334) pepper cultivars were inoculated with the two constructs pBIN-gus and pHKN29-gfp of A. rhizogenes strain A4RS. Foliar explants of both pepper genotypes infected by A4RS-pBIN-gus or A4RS-pHKN29-gfp produced transformed roots. Optimal results were obtained using the combination of the foliar explants with A4RS-pHKN29-gfp. 20.5% of YW foliar explants and 14.6% of CM334 foliar explants inoculated with A4RS-pHKN29-gfp produced at least one root expressing uniform green fluorescent protein. We confirmed by polymerase chain reaction the presence of the rolB and gfp genes in the co-transformed roots ensuring that they integrated both the T-DNA from the Ri plasmid and the reporter gene. We also demonstrated that co-transformed roots of YW and CM334 displayed the same resistance response to Phytophthora capsici than the corresponding untransformed roots. Our novel procedure to produce C. annuum hairy roots will thus support the functional analysis of potential resistance genes involved in pepper P. capsici interaction. Keywords Capsicum annuum Á Agrobacterium rhizogenes Á Transformation efficiency Á Green fluorescent protein (GFP) Á b-Glucuronidase (GUS) Á Phytophthora capsici
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01332298/file/2012_Aarrouf_Plant%20Cell%20Reports%20%28Postprint%29_2 BibTex
titre
The cucurbits and nightshades of renaissance England: John Gerard and William Shakespeare
auteur
Jules Janick, Harry S. Paris, M-Christin Daunay
article
Horticultural Reviews, 2012, 40, pp.215-257. ⟨10.1002/9781118351871.ch6⟩
resume
John Gerard (1545–1612) author of the most famous English Herball of 1597 and the playwright William Shakespeare (1564–1616) were contemporaries in London. Their references to cucurbits (Cucurbitaceae) and nightshades (Solanaceae) encapsulate knowledge of these plants from both a scientific and a literary perspective in the English Renaissance. The Old World genera of the Cucurbitaceae (Byronia, Citrullus, Cucumis, Ecballium, Lagenaria, Momordica, and Solanaceae ( Hyoscyamus, Mandragora, Physalis, Solanum) had a rich history in both medicine and food production in Antiquity and Medieval times in the Old World. The introduction of new crop species (Capsicum, Datura, Nicotiana, and Solanum) into Europe and Asia after the European encounter with the New World had a profound impact on world agriculture. References to cucurbits and nightshades in the 1597 Herball of John Gerard and the plays of Shakespeare a reflect scientific and public awareness of these species in the English Renassance.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Effet de différentes doses d’UV-C sur l’aspect visuel et les paramètres de fluorescence chlorophyllienne de la laitue Romaine.
auteur
Chayma Ouhibi, H Attia, Laurent Urban, Mokhtar Lachaâl, Jawad Aarrouf
article
Tunisian Journal of Medicinal Plants and Natural Products , 2012
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Review of fruit genetics and breeding programmes and a new European initiative to increase fruit breeding efficiency
auteur
Francois Laurens, M.J. Aranzana, D. Bassi, J. Bonany, L. Corelli, Charles Eric Durel, J. Mes, Thierry Pascal, A. Peil, Bénédicte Quilot-Turion, S. Salvi, S. Tartarini, M. Troggio, A. Vecchietti, R. Velasco, E. van de Weg
article
Acta Horticulturae, 2012, 929, pp.95-102
resume
absent
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01209943/file/Pascal_Quilot-Turion%202012Acta%20Horticulturae%2095-102_1.pdf BibTex
titre
Light affects ascorbate content and ascorbate-related gene expression in tomato leaves more than in fruits
auteur
Capucine Massot, Rebecca Stevens, Michel M. Génard, Jean Jacques Longuenesse, Hélène Gautier
article
Planta, 2012, 235 (1), pp.153-163. ⟨10.1007/s00425-011-1493-x⟩
resume
Little is known about the light regulation of vitamin C synthesis in fruits. In contrast, previous studies in leaves revealed that VTC2 (coding for GDP-l-galactose phosphorylase) was one of the key genes up-regulated by light in leaves. Our objective was to determine how the expression of ascorbate (AsA) synthesis genes in tomato (Solanum lycopersicum) was modified according to light irradiance in both leaves and fruits. Seven days of shading strongly decreased total ascorbate (reduced and oxidized form) content in leaves (50%) and to a lesser extent in fruits (10%). Among the last six steps of AsA biosynthesis, only two genes, VTC2 and GPP1 (one of the two unigenes coding for l-galactose-1-P phosphatase in tomato), were down-regulated by long-term shading in red ripe fruits, compared to seven genes regulated in leaves. This underlines that light affects AsA-related gene expression more in leaves than in ripening fruits. Moreover, this study reveals strong daily changes in transcript levels of enzymes of the AsA biosynthetic pathway in leaves (11 of the 12 studied genes showed significant changes in their expression pattern). Among those genes, we found that diurnal variation in transcript levels of VTC2 and GME1 correlated to leaf AsA content measured 8 h later. This study provides a new hypothesis on the role of GME1 in addition to VTC2 in light-regulated AsA biosynthesis
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Particle swarm optimization to design ideotypes for sustainable fruit production systems
auteur
Abdeslam Kadrani, Mohamed Mahmoud Ould Sidi, Bénédicte Quilot-Turion, Michel M. Génard, Francoise F. Lescourret
article
International Journal of Swarm Intelligence Research, 2012, 3 (2), pp.1-19. ⟨10.4018/jsir.2012040101⟩
resume
Designing peach ideotypes that satisfy the requirement of high fruit quality and low sensitivity to brown rot in a given environment was formulated as a multi-objective problem. The ‘Virtual Fruit’ model was used to perform virtual experiments. Particle swarm optimization (PSO) was interfaced to the ‘Virtual Fruit’ for solving the weighted optimization problem resulting by the linear aggregation of the criteria of the multi- objective problem. The comparison of the PSO with the Genetic Algorithm (GA) showed that the PSO method achieves better performance and outperforms the GA. The optimization results found by the PSO algorithm are considered to be satisfactory for the sustainable production systems of the peach fruit.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato
auteur
Sung-Chur Sim, Gregor Durstewitz, Joerg Plieske, Ralf Wieseke, Martin W. Ganal, Allen van Deynze, John P. Hamilton, C. Robin Buell, Mathilde M. Causse, Saranga Wijeratne, David M. Francis
article
PLoS ONE, 2012, 7 (7), ⟨10.1371/journal.pone.0040563⟩
resume
The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F-2 populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02650989/file/2012_Sim_PlosOne_1.pdf BibTex
titre
Genome-Wide Association Mapping in Tomato (Solanum lycopersicum) Is Possible Using Genome Admixture of Solanum lycopersicum var. cerasiforme
auteur
Nicolas N. Ranc, Stephane Munos, Jiaxin Xu, Marie-Christine Le Paslier, Aurelie A. Chauveau, Rémi Bounon, Sophie Rolland, Jean-Paul Bouchet, Dominique D. Brunel, Mathilde M. Causse
article
G3, 2012, 2 (8), pp.853 - 864. ⟨10.1534/g3.112.002667⟩
resume
Genome-wide association mapping is an efficient way to identify quantitative trait loci controlling the variation of phenotypes, but the approach suffers severe limitations when one is studying inbred crops like cultivated tomato (Solanum lycopersicum). Such crops exhibit low rates of molecular polymorphism and high linkage disequilibrium, which reduces mapping resolution. The cherry type tomato (S. lycopersicum var. cerasiforme) genome has been described as an admixture between the cultivated tomato and its wild ancestor, S. pimpinellifolium. We have thus taken advantage of the properties of this admixture to improve the resolution of association mapping in tomato. As a proof of concept, we sequenced 81 DNA fragments distributed on chromosome 2 at different distances in a core collection of 90 tomato accessions, including mostly cherry type tomato accessions. The 81 Sequence Tag Sites revealed 352 SNPs and indels. Molecular diversity was greatest for S. pimpinellifolium accessions, intermediate for S. l. cerasiforme accessions, and lowest for the cultivated group. We assessed the structure of molecular polymorphism and the extent of linkage disequilibrium over genetic and physical distances. Linkage disequilibrium decreased under r(2) = 0.3 within 1 cM, and minimal estimated value (r(2) = 0.13) was reached within 20 kb over the physical regions studied. Associations between polymorphisms and fruit weight, locule number, and soluble solid content were detected. Several candidate genes and quantitative trait loci previously identified were validated and new associations detected. This study shows the advantages of using a collection of S. l. cerasiforme accessions to overcome the low resolution of association mapping in tomato.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02652089/file/2012_Ranc_G3%20-%20Genes%20Genomes%20Genetics_1.pdf BibTex
titre
Variabilité génétique de réactivité aux stimulateurs de défense des plantes (SDP)
auteur
Brigitte B. Maisonneuve, Michel Pitrat
article
Vents du Sud (INRA - PACA), 2012, 11, 1 p
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02643221/file/Maisonneuve_Pitrat%202012%20Vents%20du%20sud_1.pdf BibTex
titre
Occidental diffusion of cucumber (Cucumis sativus) 500-1300 CE: two routes to Europe
auteur
Harry S. Paris, M-Christin Daunay, Jules Janick
article
Annals of Botany, 2012, 109 (1), pp.117-126. ⟨10.1093/aob/mcr281⟩
resume
Background The cucumber, Cucumis sativus, is one of the most widely consumed fruit vegetables the world over. The history of its dispersal to the Occident from its centre of origin, the Indian subcontinent, has been incorrectly understood for some time, due to the confusion of cucumbers with vegetable melons. Iconographic and literary evidence has shown that cucumber was absent in Roman times, up to 500 CE, but present in Europe by late medieval times, 1300. The objective of the present investigation was to determine more accurately when the cucumber arrived in Europe and by what route. Findings and Conclusions The evidence for the movement of C. sativus westward is entirely lexicographical until the 10th century. Syriac, Persian and Byzantine Greek sources suggest the presence of cucumbers, to the east and north-east of the Mediterranean Sea (modern Iran, Iraq and Turkey), by the 6th or 7th century. Arabic medical writings suggest the presence of cucumbers in Spain as early as the mid-9th century and in Tunisia by the early 10th century. Descriptive evidence in Arabic establishes the presence of cucumbers in Andalusia by the second half of the 10th century. Latin translations from Arabic sources indicate the presence of cucumbers in southern Italy by the second half of the 11th century. These writings, together with lexicographical discrepancies in names of cucurbits in late medieval Latin writings, suggest that cucumber was introduced to Europe by two independent diffusions. One diffusion appears to have been overland from Persia into eastern and northern Europe and preceded the Islamic conquests. The other, subsequent diffusion into western and southern Europe, was probably by a mostly maritime route from Persia or the Indian subcontinent into Andalusia.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The root-knot nematode resistance N-gene co-localizes in the Me-genes cluster on the pepper (Capsicum annuum L.) P9 chromosome
auteur
Ariane Fazari, Alain Palloix, Lihao Wang, Ming Yan Hua, Anne-Marie Sage-Palloix, Bao Xi Zhang, Caroline Djian-Caporalino
article
Plant Breeding, 2012, 131 (5), pp.665 - 673. ⟨10.1111/j.1439-0523.2012.01994.x⟩
resume
With 3 figures and 3 tables Abstract Root-knot nematodes (Meloidogyne spp.) are major plant pathognematicidesens, affecting several solanaceous crops worldwide including pepper (Capsicum spp.). Owing to the drastic reduction in the use of most , breeding for root-knot nematode resistance is a major challenge for pepper breeders. In pepper, resistance to this pathogen is dominant and controlled by several Me-genes, which were mapped on the pepper P9 chromosome using PCR-based markers, and by the N-gene which was shown to be linked to Me3 using allelism tests. In this study, we developed PCR-based markers and showed that the N-gene colocalized in the Me-genes cluster on the P9 chromosome on pepper reference maps using carthagene software (INRA: Institut National de la Recherche Agronomique, Toulouse, France). N was mapped at 7 cM from Me1 and 2 cM from Me3 which is confirmed to be allelic to Me7 according to allelism resistance tests. The tightly linked markers to Me and N-genes will be very useful for the marker-assisted selection of nematodes resistance in pepper and to study the durability of these R-genes, alone or pyramided in different genetic backgrounds.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic linkage map and diversity analysis of tahitian vanilla (Vanilla ×tahitensis, Orchidaceae)
auteur
Sandra Lepers-Andrzejewski, Sandrine Causse, Bernard Caromel, Maurice Wong, Michel Dron
article
Crop Science, 2012, 52 (2), pp.795-806. ⟨10.2135/cropsci2010.11.0634⟩
resume
The first vanilla genetic linkage map was constructed by analyzing the progeny of an interspecific cross between Vanilla ×tahitensis J. W. Moore (pro sp.) and Vanilla pompona Schiede. The two-way pseudotestcross mapping strategy was used and a total of 225 amplified fragment length polymorphism (AFLP) markers were mapped on 18 linkage groups covering 1035.85 cM. Thirteen tahitian vanilla morphotypes, one Vanilla planifolia Andrews and recent hybrids were compared by measuring seven morphological traits and by genotyping, with 539 AFLP fragments. The morphotypes studied showed relatively homogenous stem traits but differed in their bean and leaf traits as in their AFLP pattern. Genetic variability and AFLP genotyping comparison suggest a diversification in French Polynesia based on sexual reproduction and are consistent with the hypothesis of a single introduction event. These results are the first step for vanilla breeding program and will be also useful for tahitian vanilla resource preservation.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Co-localisation of host plant resistance QTLs affecting the performance and feeding behaviour of the aphid Myzus persicae in the peach tree
auteur
Marie-Hélène Sauge, Patrick Lambert, Thierry Pascal
article
Heredity, 2012, 108 (3), pp.292-301. ⟨10.1038/hdy.2011.74⟩
resume
The architecture and action of quantitative trait loci (QTL) contributing to plant resistance mechanisms against aphids, the largest group of phloem-feeding insects, are not well understood. Comparative mapping of several components of resistance to the green peach aphid (Myzus persicae) was undertaken in Prunus davidiana, a wild species related to peach. An interspecific F1 population of Prunus persica var. Summergrand × P. davidiana clone P1908 was scored for resistance (aphid colony development and foliar damage) and 17 aphid feeding behaviour traits monitored by means of the electrical penetration graph technique. Seven resistance QTLs were detected, individually explaining 6.1–43.1% of the phenotypic variation. Consistency was shown over several trials. Nine QTLs affecting aphid feeding behaviour were identified. All resistance QTLs except one co-located with QTLs underlying aphid feeding behaviour. A P. davidiana resistance allele at the major QTL was associated with drastic reductions in phloem sap ingestion by aphids, suggesting a phloem-based resistance mechanism. Resistance was also positively correlated with aphid salivation into sieve elements, suggesting an insect response to restore the appropriate conditions for ingestion after phloem occlusion. No significant QTL was found for traits characterising aphid mouthpart activity in plant tissues other than phloem vessels. Two QTLs with effects on aphid feeding behaviour but without effect on resistance were identified. SSR markers linked to the main QTLs involved in resistance are of potential use in marker-assisted selection for aphid resistance. Linking our results with the recent sequencing of the peach genome may help clarify the physiological resistance mechanisms
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02646555/file/42909_20111012022807911_1.pdf BibTex
titre
The tomato genome sequence provides insights into fleshy fruit evolution
auteur
Shusei Sato, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu, Kenta Shirasawa, Sachiko Isobe, Takakazu Kaneko, Yasukazu Nakamura, Daisuke Shibata, Koh Aoki, Michael Egholm, James Knight, Robert Bogden, Changbao Li, Yang Shuang, Xun Xu, Shengkai Pan, Shifeng Cheng, Xin Liu, Yuanuyan Ren, Jun Wang, Alessandro Albiero, Francesca Dal Pero, Sara Todesco, Joyce van Eck, Robert M. Buels, Aureliano Bombarely, Joseph R. Gosselin, Minyun Huang, Jonathan Leto, Naama Menda, Susan Strickler, Linyong Mao, Shan Gao, Isaak y Tecle, Thomas York, Yi Zheng, Julia T. Vrebalov, Jemin Lee, Silin Zhong, Lukas A. Mueller, Willem J Stiekema, Paolo Ribeca, Tyler Alioto, Wencai Yang, Sanwen Huang, Yongchen Du, Zhonghua Zhang, Jianchang Gao, Yanmei Guo, Xiaosuan Wang, Ying Li, Jun He, Chuanyou Li, Zhukuan Cheng, Jianru Zuo, Jianfeng Ren, Jiuhai Zhao, Liuhua Yan, Hongling Jiang, Bao Wang, Hongshuang Li, Zhenjun Li, Fuyou Fu, Bingtang Chen, Bin Han, Qi Feng, Danlin Fan, Ying Wang, Hongqing Ling, Yongbiao Xue, Doreen Ware, W. Richard Mccombie, Zachary B. Lippmamn, Jer-Ming Chia, Ke Jiang, Shiran Pastermak, Laura Gelley, Melissa Kramer, Lorinda K. Anderson, Song-Bin Chang, Suzanne Royer, Lindsay A. Shearer, Stephen M. Stack, Jocelyn K. C. Rose, Yimin Xu, Nancy Eannetta, Antonio J. Matas, Ryan Mcquinn, Steven D. Tanksley, Francisco Câmara, Mathilde M. Causse, Christophe Rothan, Thomas Schiex, Céline Noirot, Arnaud A. Bellec, Christophe Klopp, Helene H. Berges, Jérôme J. Mariette, - Tomato Genome Consortium
article
Nature, 2012, 485 (7400), pp.635-641. ⟨10.1038/nature11119⟩
resume
Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)
auteur
Maryse Nicolaï, Cedric Pisani, Jean-Paul Bouchet, M. Vuylsteke, Alain Palloix
article
Genetics and molecular research : GMR, 2012, 11 (3), pp.2295-2300. ⟨10.4238/2012.August.13.3⟩
resume
Genetic markers based on single nucleotide polymorphisms (SNPs) are in increasing demand for genome mapping and fingerprinting of breeding populations in crop plants. Recent advances in high-throughput sequencing provide the opportunity for whole-genome resequencing and identification of allelic variants by mapping the reads to a reference genome. However, for many species, such as pepper (Capsicum annuum), a reference genome sequence is not yet available. To this end, we sequenced the C. annuum cv. "Yolo Wonder" transcriptome using Roche 454 pyrosequencing and assembled de novo 23,748 isotigs and 60,370 singletons. Mapping of 10,886,425 reads obtained by the Illumina GA II sequencing of C. annuum cv. "Criollo de Morclos 334" to the "Yolo Wonder" transcriptome allowed for SNP identification. By setting a threshold value that allows selecting reliable SNPs with minimal loss of information, 11,849 reliable SNPs spread across 5919 isotigs were identified. In addition, 853 single sequence repeats were obtained. This information has been made available online.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02650422/file/2012_Nicolai_Genetics%20and%20Molecular%20Research_1.pdf BibTex
titre
Apricot cell wall composition: Relation with the intra-fruit texture heterogeneity and impact of cooking
auteur
Crepin Ella Missang, Jean Francois Maingonnat, Catherine M.G.C. Renard, Jean Marc Audergon
article
Food Chemistry, 2012, 133, pp.45-54. ⟨10.1016/j.foodchem.2011.12.059⟩
resume
The intra-fruit texture heterogeneity in fresh apricot fruit, the cell wall of the different tissue zones and those of cooked fruit were analysed in order to investigate the implication of cell wall in apricot texture. Firmness decreased gradually from the external to the internal tissue while from the peduncle to the pistil zone, the highest value in firmness was recorded in the peduncle zone, followed by the pistil zone and finally the equatorial zone. Texture was strongly correlated with water-soluble pectin (WSP), firmness being inversely proportional to WSP contents of the different tissue zones. CDTA-soluble pectin (CSP) underwent noticeable variation between tissues but no clear relationship was observed with firmness. Hemicelluloses extracted together with WSP also appeared to be implicated in tissue texture; highly positive correlation coefficients were observed between firmness and hemicellulosic sugars. After cooking, CSP was the only class of pectin which underwent substantial degradation, indicating that CSP was the pectin fraction most implicated in heat-induced softening in apricot fruit.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Cell wall glycosidase activities and protein content variations during fruit development and ripening in three texture contrasted tomato cultivars
auteur
Emadeldin Konozy, Mathilde M. Causse, Mireille Faurobert
article
Saudi Journal of Biological Sciences, 2012, 19 (3), pp.277 - 283. ⟨10.1016/j.sjbs.2012.04.006⟩
resume
Excessive softening is the main factor limiting fruit shelf life and storage. It is generally acceptable now that softening of fruit which occurs during the ripening is due to synergistic actions of several enzymes on cell wall polysaccharides. As a subject for this study, we have assayed some glycosidase activities using three tomato species (Lycopersicon esculentum) contrasted for their texture phenotypes; the cherry tomato line Cervil (Solanum lycopersicum var. cerasiforme), a common taste tomato line Levovil (S. lycopersicum Mill.) and VilB a modern line, large, firmer and with good storage capability. Four glycosidase activities namely alpha-galactosidase, beta-galactosidase, beta-mannosidase and beta-glucosidase were extracted from tomato's cell wall of the three species. Cell wall protein from fruits pericarp was extracted and compared among the three cultivars at the following stages; 14 days post anthesis (14DPA) fruit; 21 days post anthesis (21DPA), turning (breaker), red and over ripe. When glycolytic activities were also compared among these cultivars at the precited development stages, gross variations were noticed from stage to stage and also from species to species in accordance with the fruit firmness status. Interestingly, VilB cultivar, the firmer among the other two, though possessed the highest total protein content, exhibited the lowest enzymatic activities. Taken together, these results may therefore allow us to conclude that studies of glycolytic activities in a single tomato cultivar cannot be generalized to all species. On the other hand, relating fruit development to glycosidase activities should logically be coupled to these enzymes from cell wall compartment. (c) 2012 King Saud University. Production and hosting by Elsevier B.V. All rights reserved.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Comparison of the genetic determinism of two key phenological traits, flowering and maturity dates, in three Prunus species: peach, apricot and sweet cherry
auteur
Elisabeth Dirlewanger, José Quero-Garcia, Loick Le Dantec, Patrick Lambert, D. Ruiz, L. Dondini, E. Illa, Bénédicte Quilot-Turion, Jean Marc Audergon, S. Tartarini, P. Letourmy, P. Arus
article
Heredity, 2012, 109 (5), pp.280-292. ⟨10.1038/hdy.2012.38⟩
resume
The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five progenies from three Prunus species, peach, apricot and sweet cherry, during 3-8 years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs for flowering and maturity dates were highly stable, detected each year of evaluation, suggesting that they were not affected by climatic variations. For flowering date, major QTLs were detected on linkage groups (LG) 4 for apricot and sweet cherry and on LG6 for peach. QTLs were identified on LG2, LG3, LG4 and LG7 for the three species. For maturity date, a major QTL was detected on LG4 in the three species. Using the peach genome sequence data, candidate genes underlying the major QTLs on LG4 and LG6 were investigated and key genes were identified. Our results provide a basis for the identification of genes involved in flowering and maturity dates that could be used to develop cultivar ideotypes adapted to future climatic conditions.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02650383/file/hdy201237a_1.pdf BibTex
titre
Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence
auteur
Amandine Delteil, Melisande Blein-Nicolas, Odile Faivre-Rampant, Amira Guellim, Joan Estevan, Judith Hirsch, Rosangela Bevitori, Corinne Michel, Jean-Benoit J.-B. Morel
article
Molecular Plant Pathology, 2012, 13 (1), pp.72-82. ⟨10.1111/j.1364-3703.2011.00731.x⟩
resume
In Arabidopsis, gene expression studies and analysis of knock-out (KO) mutants have been instrumental in building an integrated view of disease resistance pathways. Such an integrated view is missing in rice where shared tools, including genes and mutants, must be assembled. This work provides a tool kit consisting of informative genes for the molecular characterization of the interaction of rice with the major fungal pathogen Magnaporthe oryzae. It also provides for a set of eight KO mutants, all in the same genotypic background, in genes involved in key steps of the rice disease resistance pathway. This study demonstrates the involvement of three genes, OsWRKY28, rTGA2.1 and NH1, in the establishment of full basal resistance to rice blast. The transcription factor OsWRKY28 acts as a negative regulator of basal resistance, like the orthologous barley gene. Finally, the up-regulation of the negative regulator OsWRKY28 and the down-regulation of PR gene expression early during M. oryzae infection suggest that the fungus possesses infection mechanisms that enable it to block host defences.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Regulation of the fruit-specific PEP Carboxylase SlPPC2 promoter at early stages of tomato fruit development
auteur
Carine Guillet, Mourad Aboul-Soud, Aline Le Menn, Nicolas Viron, Anne Pribat, Veronique Germain, Daniel Just, Pierre Baldet, Patrick Rousselle, Martine Lemaire, Christophe Rothan
article
PLoS ONE, 2012, 7 (5), pp.1-11. ⟨10.1371/journal.pone.0036795⟩
resume
The SlPPC2 phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) gene from tomato (Solanum lycopersicum) is differentially and specifically expressed in expanding tissues of developing tomato fruit. We recently showed that a 1966 bp DNA fragment located upstream of the ATG codon of the SlPPC2 gene (GenBank AJ313434) confers appropriate fruit-specificity in transgenic tomato. In this study, we further investigated the regulation of the SlPPC2 promoter gene by analysing the SlPPC2 cis-regulating region fused to either the firefly luciferase (LUC) or the beta-glucuronidase (GUS) reporter gene, using stable genetic transformation and biolistic transient expression assays in the fruit. Biolistic analyses of 5' SlPPC2 promoter deletions fused to LUC in fruits at the 8th day after anthesis revealed that positive regulatory regions are mostly located in the distal region of the promoter. In addition, a 5' UTR leader intron present in the 1966 bp fragment contributes to the proper temporal regulation of LUC activity during fruit development. Interestingly, the SlPPC2 promoter responds to hormones (ethylene) and metabolites (sugars) regulating fruit growth and metabolism. When tested by transient expression assays, the chimeric promoter: LUC fusion constructs allowed gene expression in both fruit and leaf, suggesting that integration into the chromatin is required for fruit-specificity. These results clearly demonstrate that SlPPC2 gene is under tight transcriptional regulation in the developing fruit and that its promoter can be employed to drive transgene expression specifically during the cell expansion stage of tomato fruit. Taken together, the SlPPC2 promoter offers great potential as a candidate for driving transgene expression specifically in developing tomato fruit from various tomato cultivars.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01136957/file/PLoS%20One%20SlPPC2%202012_%7B86E0B881-F91A-41A1-9579-A5A5B7F7D244%7D.pdf BibTex
titre
What do spring migrants reveal about sex and host selection in the melon aphid?
auteur
Sophie Thomas, Nathalie Boissot, Flavie Vanlerberghe-Masutti
article
BMC Evolutionary Biology, 2012, 12 (47), 16 p. ⟨10.1186/1471-2148-12-47⟩
resume
BACKGROUND: Host plants exert considerable selective pressure on aphids because the plants constitute their feeding, mating and oviposition sites. Therefore, host specialisation in aphids evolves through selection of the behavioural and chemical mechanisms of host-plant location and recognition, and through metabolic adaptation to the phloem content of the host plant. How these adaptive traits evolve in an aphid species depends on the complexity of the annual life cycle of that species. The purpose of this field study was to determine how winged spring-migrant populations contribute to the evolution and maintenance of host specialisation in Aphis gossypii through host-plant choice and acceptance. We also assessed whether host-specialised genotypes corresponded exclusively to anholocyclic lineages regardless of the environmental conditions. RESULTS: The spring populations of cotton-melon aphids visiting newly planted melon crops exhibited an unexpectedly high level of genetic diversity that contrasted with the very low diversity characterising the hostspecialised populations of this aphid species. This study illustrated in natura host-plant-selection pressure by showing the great differences in genetic diversity between the spring-migrant populations (alate aphids) and the melon-infesting populations (the apterous offspring of the alate aphids). Moreover, an analysis of the genetic composition of these alate and apterous populations in four geographic regions suggested differences in lifehistory strategies, such as host choice and reproductive mode, and questioned the common assertion that A. gossypii is an anholocyclic species throughout its distribution area, including Europe. CONCLUSIONS: Our results clearly demonstrate that the melon plant acts as a selective filter against the reproduction of non-specialised individuals. We showed that olfactory cues are unlikely to be decisive in natura for host recognition by spring-migrant aphid populations that are not specialised on Cucurbitaceae. The agroecosystem structure and history of the four studied regions may have partially shaped the genetic structure of the spring-migrant populations of A. gossypii. Cucurbitaceae-specialised genotypes corresponded exclusively to anholocyclic lineages, regardless of the environmental conditions. However, some genotypes that were genetically close to the host-specialised genotypes and some genotypes that probably originated from wild plants had never been previously sampled; both were holocylic.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02650759/file/Thomas-BMC-EvolBiol-2012_1.pdf BibTex
titre
Virus adaptation to quantitative plant resistance: erosion or breakdown?
auteur
Josselin Montarry, Elodie Cartier, Mireille Jacquemond, Alain Palloix, Benoît Moury
article
Journal of Evolutionary Biology, 2012, 25 (11), pp.2242-2252. ⟨10.1111/j.1420-9101.2012.02600.x⟩
resume
Adaptation of populations to new environments is frequently costly due to trade-offs between life history traits, and consequently, parasites are expected to be locally adapted to sympatric hosts. Also, during adaptation to the host, an increase in parasite fitness could have direct consequences on its aggressiveness (i.e. the quantity of damages caused to the host by the virus). These two phenomena have been observed in the context of pathogen adaptation to host's qualitative and monogenic resistances. However, the ability of pathogens to adapt to quantitative polygenic plant resistances and the consequences of these potential adaptations on other pathogen life history traits remain to be evaluated. Potato virus Y and two pepper genotypes (one susceptible and one with quantitative resistance) were used, and experimental evolutions showed that adaptation to a quantitative resistance was possible and resulted in resistance breakdown. This adaptation was associated to a fitness cost on the susceptible cultivar, but had no consequence either in terms of aggressiveness, which could be explained by a high tolerance level, or in terms of aphid transmission efficiency. We concluded that quantitative resistances are not necessarily durable but management strategies mixing susceptible and resistant cultivars in space and/or in time should be useful to preserve their efficiency.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Sensitivity of peach cultivars against a Dideron isolate of Plum pox virus
auteur
Manuel Rubio, Pedro Martínez-Gómez, Jesus Garcia-Brunton, Thierry Pascal, Ana Garcia-Ibarra, Federico Dicenta
article
Scientia Horticulturae, 2012, 144, pp.81 - 86. ⟨10.1016/j.scienta.2012.06.038⟩
resume
Sharka disease, caused by Plum pox virus (PPV), is one of the most significant limiting factors for Prunus production worldwide, and the cultivation of resistant cultivars is the only definitive solution to this problem. In this study, 40 cultivated peach cultivars with different origins, chill requirements and fruit type were evaluated against a PPV Dideron-type isolate in controlled conditions in greenhouse for three evaluation cycles. Cultivars were grafted onto PPV infected 'GF305' rootstocks and, in each cycle, the presence of symptoms on leaves was scored and ELISA and RT-PCR was applied to check the presence of PPV on rootstocks and cultivars. The results showed the resistance of 'Catherine' to this strain, for this cultivar never showed sharka symptoms and was ELISA and RT-PCR negative. Some cultivars without symptoms but ELISA or PCR positive were tolerant to PPV. Most cultivars were sensitive, and showed symptoms of sharka or were ELISA or RT-PCR positive. In these cultivars, different degrees of symptom expression among the three cycles and between replications of each cultivar were observed. (C) 2012 Elsevier B.V. All rights reserved.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus
auteur
Natalie H. Chapman, Julien Bonnet, Laurent Grivet, James Lynn, Neil Graham, Rebecca Smith, Guiping Sun, Peter G. Walley, Mervin Poole, Mathilde M. Causse, Graham J. King, Charles Baxter, Graham B. Seymour
article
Plant Physiology, 2012, 159 (4), pp.1644 - 1657. ⟨10.1104/pp.112.200634⟩
resume
Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Growth and proteomic analysis of tomato fruit under partial root-zone drying
auteur
Milena Marjanović, Radmila Stikic, Biljana Vucelic-Radovic, Sladjana Savic, Zorica Jovanovic, Nadia Bertin, Mireille Faurobert
article
OMICS, 2012, 16 (6), pp.343-356. ⟨10.1089/omi.2011.0076⟩
resume
The effects of partial root-zone drying (PRD) on tomato fruit growth and proteome in the pericarp of cultivar Ailsa Craig were investigated. The PRD treatment was 70% of water applied to fully irrigated (FI) plants. PRD reduced the fruit number and slightly increased the fruit diameter, whereas the total fruit fresh weight (FW) and dry weight (DW) per plant did not change. Although the growth rate was higher in FI than in PRD fruits, the longer period of cell expansion resulted in bigger PRD fruits. Proteins were extracted from pericarp tissue at two fruit growth stages (15 and 30 days post-anthesis [dpa]), and submitted to proteomic analysis including two-dimensional gel electrophoresis and mass spectrometry for identification. Proteins related to carbon and amino acid metabolism indicated that slower metabolic flux in PRD fruits may be the cause of a slower growth rate compared to FI fruits. The increase in expression of the proteins related to cell wall, energy, and stress defense could allow PRD fruits to increase the duration of fruit growth compared to FI fruits. Upregulation of some of the antioxidative enzymes during the cell expansion phase of PRD fruits appears to be related to their role in protecting fruits against the mild stress induced by PRD.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02649667/file/Faurobert%202012%20OMICS%20343-356_1.pdf BibTex
titre
Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis)
auteur
Fabien C. Lamaze, Christopher Sauvage, Amandine Marie, Dany Garant, Louis Bernatchez
article
Molecular Ecology, 2012, 21 (12), pp.2877-2895. ⟨10.1111/j.1365-294X.2012.05579.x⟩
resume
Salmonid fishes rank among species being most severely affected by introgressive hybridization as a result of a long tradition of stocking with hatchery-reared conspecifics. The objectives of this study were (i) to evaluate the genetic consequences of stocking and resulting introgression rates on the genetic integrity of natural populations of brook charr, (ii) to identify genomic regions potentially associated with adaptation to natural and artificial rearing environments, and (iii) to test the null hypothesis that introgression from domesticated brook charr into wild populations is homogeneous among loci. A total of 336 individuals were sampled from nine lakes, which were stocked at different intensities with domestic fish. Individuals were genotyped at 280 SNPs located in transcribed regions and developed by means of next-generation sequencing. As previously reported with microsatellites, we observed a positive relationship between stocking intensity and genetic diversity among stocking groups, and a decrease in population differentiation. Individual admixture proportions also increased with stocking intensity. Moreover, genomic cline analysis revealed 27 SNPs, seven of which were also identified as outliers in a genome scan, which showed an introgression rate either more restricted or enhanced relative to neutral expectations. This indicated that selection, mainly for growth-related biological processes, has favored or hampered the introgression of genomic blocks into the introgressed wild populations. Overall, this study highlights the usefulness of investigating the impact of stocking on the dynamics of introgression of potentially adaptive genetic variation to better understand the consequences of such practice on the genomic integrity of wild populations.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
1H-NMR metabolomics: Profiling method for a rapid and efficient screening of transgenic plants
auteur
Yosra Ben Akal-Ben Fatma, Katia Pianelli, Martine Dieuaide Noubhani, Aline Le Menn, Catherine Deborde, Mickael M. Maucourt, Marie-Hélène Andrieu, Dominique D. Rolin, Christophe Rothan, Annick Moing, Sadok Bouzid, Cécile Cabasson
article
African Journal of Biotechnology, 2012, 11 (52), pp.11386-11399. ⟨10.5897/AJB12.088⟩
resume
Metabolomics-based approaches are methods of choice for studying changes in fruit composition induced by environmental or genetic modulation of biochemical pathways in the fruit. Owing to enzyme redundancy and high plasticity of the metabolic network, transgenic alteration of the activity of the enzymes from the central metabolism very often results in only slight modifications of the fruit composition. In order to avoid costly and time-consuming plant analysis, we used a fast and sensitive 1H-NMR-based metabolomic profiling technique allowing discovery of slight metabolite variations in a large number of samples. Here, we describe the screening of transgenic tomato plants in which two genes from the central metabolism, phosphoenolpyruvate carboxylase (EC.3.4.1.1) and malate synthase (EC 2.3.3.9) were silenced by antisens and RNAi strategy. 1H-NMR metabolomic profiles of methanol-d4 D2O buffer extracts of tomato fruit flesh were acquired and subjected to unsupervised multivariate statistical analysis. 1H-NMR spectra were binned into variable-size spectral domains, making it possible to get an overall analysis of a large number of resonances, even in the case of uncontrolled variation of the chemical shift. Principal component analysis was used to separate groups of samples and to relate known and unknown metabolites to transgenic events. The screening of 100 samples, from extraction to data mining, took 36 h. Thus, this procedure allows the rapid selection of metabolic phenotypes of interest among about 30 transgenic lines.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02643145/file/2012_Ben%20Akal%20Ben%20Fatma_Afr%20J%20Biotechnol_1.pdf BibTex
titre
Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin
auteur
Hedia Bourguiba, Jean Marc Audergon, Lamia Krichen, Neila Trifi-Farah, Ali Mamouni, Samia Trabelsi, Claudio d'Onofrio, Bayram M Asma, Sylvain Santoni, Bouchaib Khadari
article
BMC Plant Biology, 2012, 12, ⟨10.1186/1471-2229-12-49⟩
resume
In order to reduce energy waste for artificial lights and subsequent air conditioning in plant growth chambers, the aim of this preliminary study was to evaluate the feasibility of growing the microvine under 100% of LED illumination. Plant growth under two different LED lights was compared amongst each other and with plants maintained in greenhouse conditions. Regarding the impact on the reproductive and vegetative systems, the study showed that LED light is suitable to grow microvines in confined environments. Plants exposed to LED light exhibited similar leaf emergence rate but reduced vegetative and reproductive organ size compared to plants grown in the greenhouse. Photosynthesis for plants exposed to LED light was higher than what is usually observed on grapevine under natural conditions.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01191293/file/Publis012-agap-030_Bourguiba_BMC%20PlantBiol_Loss%20genetic%20diversity%20Mediterranean%20Basin_%7B22D40E1C-CC1A-496F-8E60-CB5D34BA61A5%7D.pdf BibTex
titre
Application of a SUGAR model to analyse sugar accumulation in peach cultivars that differ in glucose–fructose ratio
auteur
B.H. Wu, Bénédicte Quilot-Turion, Michel M. Génard, S.H. Li, J.B. Zhao, J. Yang, Y.Q. Wang
article
Journal of Agricultural Science, 2012, 150, pp.53-63. ⟨10.1017/S0021859611000438⟩
resume
A SUGAR model, which was established to predict the partitioning of carbon into sucrose, glucose, fructose and sorbitol in fruit mesocarp of peach cultivars (Prunus persica (L.) Batch) with normal glucose: fructose ratio (G:F) of 0·8–1·5, was evaluated and extended for peach cultivars with a high G:F ratio of 1·5–7·8. The extended model (SUGARb) is more generic and assumes a high G:F ratio to be due to preferential transformation of sorbitol into glucose, preferential utilization of fructose or preferential conversion of fructose into glucose. The simulated seasonal variations in sugars via the SUGARb-model-matched experimental data for three normal and three high G:F cultivars well, and accurately exhibited G:F ratio characteristics. The relative rates of sucrose transformation into glucose and fructose differed according to cultivar but not according to G:F status. Compared with hexosephosphate interconversion, a lower production rate of fructose than glucose from sorbitol, and/or a higher utilization rate of fructose than that of glucose might be preferential alternatives for forming high G:F ratios in the high G:F cultivars studied in the present study, which is discussed in the light of recent results on enzyme activities
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02644745/file/44104_20110624111959148_1.pdf BibTex
titre
Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis)
auteur
Christopher Sauvage, Marie Vagner, Nicolas Derôme, Céline Audet, Louis Bernatchez
article
G3, 2012, 2 (6), pp.707 - 720. ⟨10.1534/g3.112.001990⟩
resume
Growth performance and reduced stress response are traits of major interest in fish production. Growth and stress-related quantitative trait loci (QTL) have been already identified in several salmonid species, but little effort has been devoted to charrs (genus Salvelinus). Moreover, most QTL studies to date focused on one or very few traits, and little investigation has been devoted to QTL identification for gene expression. Here, our objective was to identify QTL for 27 phenotypes related to growth and stress responses in brook charr (Salvelinus fontinalis), which is one of the most economically important freshwater aquaculture species in Canada. Phenotypes included 12 growth parameters, six blood and plasma variables , three hepatic variables, and one plasma hormone level as well as the relative expression measurements of five genes of interest linked to growth regulation. QTL analysis relied on a linkage map recently built from S. fontinalis consisting of both single-nucleotide polymorphism (SNP, n = 266) and microsatellite (n =81) markers in an F 2 interstrain hybrid population (n = 171). We identified 63 growth-related QTL and four stress-related QTL across 18 of the 40 linkage groups of the brook charr linkage map. Percent variance explained, confidence interval, and allelic QTL effects also were investigated to provide insight into the genetic architecture of growth-and stress-related QTL. QTL related to growth performance and stress response that were identified could be classified into two groups: (1) a group composed of the numerous, small-effect QTL associated with some traits related to growth (i.e., weight) that may be under the control of a large number of genes or pleiotropic genes, and (2) a group of less numerous QTL associated with growth (i.e., gene expression) and with stress-related QTL that display a larger effect, suggesting that these QTL are under the control of a limited number of genes of major effect. This study represents a first step toward the identification of genes potentially linked to phenotypic variation of growth and stress response in brook charr. The ultimate goal is to provide new tools for developing Molecular Assisted Selection for this species. KEYWORDS linkage mapping QTL detection single-nucleotide polymorphism growth stress response Salvelinus fontinalis Quantitative trait loci (QTL), the portions of a species' genome that affect the variation of heritable phenotypic traits, are revealed by the association of phenotypes with molecular markers. They provide insight into the number of loci affecting a trait and on the distribution of the QTL effects of each locus (Lynch and Walsh 1998). QTL analysis has become a popular method for studying the genetic basis of continuous variation in a variety of systems and is now an integral tool in medical genetics, livestock production, plant breeding, and population genetics of model organisms (Slate 2005). Thus, this approach is of great interest when studying experimental populations obtained from livestock species. Knowledge gained from these analyses can be used to improve traits of economic importance such as growth, resistance to pathogens, sexual maturation, or stress response through the clarification of their underlying genetic basis. Such information helps the development of selection programs aiming to improve efficiency,
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01251103/file/Sauvage%2C%20Vagner%20et%20al%202012b.pdf BibTex
titre
Hemicellulose fine structure is affected differently during ripening of tomato lines with contrasted texture
auteur
Marc Lahaye, Bernard Quemener, Mathilde M. Causse, Graham B. Seymour
article
International Journal of Biological Macromolecules, 2012, 53, pp.462-470. ⟨10.1016/j.ijbiomac.2012.05.024⟩
resume
The impact of genetic and fruit ripening on hemicelluloses fine structure was studied in twelve near isogenic lines of tomato fruits harboring firmness QTL. The sugar composition and the MALDI-TOF MS oligosaccharides profile after glucanase hydrolysis of the cell walls were determined from all green and red fruits pericarp tissue. MS profiles showed two major series of oligomers attributed to xyloglucan (XG) and glucomannan (GM) with minor peaks for xylan and ions attributed to galacto-oligomers. The oligosaccharides MS intensity varied significantly with the fruit genetic and ripening status. Correlations between MS intensity indicated structural regulations of both XG and GM structures with genetics and ripening. These results point to a region on the tomato chromosome 9 controlling cell wall galactose metabolism.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Anatomical and biochemical trait network underlying genetic variations in tomato fruit texture.
auteur
Rémy Aurand Aurand, Mireille Faurobert, David Page, Jean Francois Maingonnat, Béatrice Brunel, Mathilde M. Causse, Nadia Bertin
article
Euphytica, 2012
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Sensibilité variétale aux maladies et ravageurs. Fiche n° 5: la tavelure
auteur
Laurent Brun, Armand Guillermin, Guy Clauzel, Vincent Mercier, Jm Broquaire, Jean Marc Audergon
article
Arboriculture Fruitière, 2012, 662, 1 p
resume
Maladie observée lors de printemps humide. - dispositif expérimental abricotier sans protection fongicide. - De très fortes différences de sensibilité à la tavelure. - Tavelure, une maladie à ne pas négliger. - Contournement du gène de résistance Vf
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Apricot cell wall composition: Relation with the intra-fruit texture heterogeneity and impact of cooking.
auteur
Crepin Ella Missang, Jean Francois Maingonnat, Catherine C. Renard, Jean Marc Audergon
article
Food Chemistry, 2012
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Relative efficiency of morphological characters and molecular markers in the establishment of an apricot core collection
auteur
L. Krichen, Jean Marc Audergon, N. Trifi-Farah
article
Hereditas, 2012, 149 (5), pp.163 - 172. ⟨10.1111/j.1601-5223.2012.02245.x⟩
resume
In order to optimize the management of genetic resources, in most cases a representative sample of the germplasm collections needs to be developed. The establishment of a core collection is thus of major importance either to minimize the cost associated with the management of the associated germplasm or to apply analysis onto representative bases. In order to select a representative core collection among the Tunisian apricot germplasm of 110 accessions large, the Maximization strategy algorithm was used. This algorithm was shown to be the most convenient when using both morphological traits and molecular markers. Three core collections based on morphological characters, molecular markers or the combined data were compared. Our data indicate that both the molecular and the morphological markers have to be considered to obtain a core collection that represents the global diversity of the 110 accessions. Using this method, a subset of 34 selected accessions was found to represent accurately the 110 accessions present in the whole collection (75 to 100% for the morphological characters and 97% of the molecular markers). These results show that the combination of molecular and morphological markers is an efficient way to characterize the apricot core collection and provides an exhaustive coverage for the analyzed diversity on morphological and genetic bases.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02643301/file/2012_Krichen_Hereditas_1.pdf BibTex
titre
Inheritance of Fruit Quality Traits in Apricot Progenies
auteur
David Ruiz, Juan Alfonso Salazar, M.D Nortes, Pedro Martínez-Gómez, José Egea-Caballero, Jean Marc Audergon, Guy Clauzel, Alain Blanc, Patrick Lambert, Sylvie Bureau, Barbara Gouble, Maryse Reich, Patrice Reling, Catherine M.G.C. Renard, Luca Dondini, Stefano Tartarini
article
Acta Horticulturae, 2012, 966, pp.89-99. ⟨10.17660/ActaHortic.2012.966.14⟩
resume
The knowledge on the transmission of fruit quality traits has a great importance in order to optimize the inter-cultivar crosses design and to improve the efficiency of apricot breeding programmes. Four apricot progenies issued from different genetic origins were evaluated during two years; two apricot progenies cultivated in Avignon (France), one in Bologna (Italy), and other one in Murcia (Spain). Fruit quality characterization was based on physical measurements (fruit weight, colour, and firmness) and biochemical measurements (soluble solids content, and titratable acidity). Phenotypic datasets showed distribution of seedlings with regard to the parents, with a high variability for all analyzed quality parameters. An inter-annual variation was observed for the mean values of all the genotypes between the two years of the study, indicating the influence of the environmental conditions on fruit characteristics. Results indicated a quantitative inheritance of all quality traits in the apricot progenies indicating their polygenic nature. In general we observed in most cases a normal distribution of quality traits in the observed populations. However, in contrast to intermediate expected values between the parents, a large number of seedlings showed lower or higher values than their parents for many quality parameters. In this sense, results evidenced an extra genetic influence of the parents (the whole genetic background) on the transmission of fruit quality traits in apricot, which should be taken into consideration with inter-cultivar crosses design.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Association between Aphis gossypii genotype and phenotype on melon accessions
auteur
Sophie Thomas, Catherine Dogimont, Nathalie Boissot
article
Arthropod-Plant Interactions, 2012, 6 (1), pp.93-101. ⟨10.1007/s11829-011-9155-2⟩
resume
Development of molecular markers has allowed the characterization of several host–aphid interactions. We investigated the usefulness of microsatellite markers to characterize the plant resistance interaction in the model Aphis gossypii/Cucumis melo. Six aphid clones, collected in different localities and years and belonging to two multilocus genotypes (MLGs) based on eight microsatellite markers, were phenotyped on a set of 33 melon accessions, some of them known to carry the Vat gene. Three parameters were used: acceptance of plant, ability to colonize the plant and resistance to virus when inoculated by aphids. Concordance and correlation analyses showed that aphid clones sharing a same MLG exhibited a very agreeable phenotype on the set of accessions for acceptance of plant and resistance to virus when inoculated by aphids. From host point of view, melon accessions were grouped into four clear categories, resistant to aphids of both MLGs, only resistant to the NM1 MLG, only resistant to the C9 MLG, susceptible to both MLGs and another group of unclear characteristics. The four categories revealed different patterns of virulence for NM1 and C9 MLGs that are likely controlled by a single avirulence gene in accordance with a gene for gene interaction. In contrast, the ability to colonize the plant appeared slightly variable among clones sharing a same MLG. We hypothesize it is due to the putative polygenic control of this aphid trait. Because the phenotypic variability of A. gossypii matched the genetic variability revealed by eight microsatellite markers, these markers could be used to infer the frequency of biotypes in field experiments and help to elucidate the allele diversity of melon resistance genes
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02650233/file/2012_Thomas_Arthropod-Plant%20Interactions%20%28Postprint%29_2 BibTex
titre
Dossier pêche : Création variétale Inra. Transmissions du public au privé
auteur
Thierry Pascal, Fleur Masson
article
Arboriculture Fruitière, 2012, 666, pp.22-24
resume
Optimisation des moyens, enjeux environnementaux et progrès dans le champ des biotechnologies: l'Inra repositionne concrètement les orientations de son programme d'innovation variétale sur pêcher
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Obtention de laitues résistantes au chlorsulfuron par régénération de protoplastes irradiés aux UV
auteur
Marie Christine Chupeau, Yannick Bellec, Brigitte Maisonneuve, Yves Chupeau
article
Cahier des Techniques de l'INRA, 2012, 77, 7 p
resume
L'adaptation, à la laitue, de la mutagenèse par exposition aux UV de protoplastes a permis de sélectionner des colonies cellulaires résistantes au chlorsulfuron, puis de régénérer des plantes résistantes. L'analyse génétique des plantes a montré que les trois mutants régénérés possèdent la même mutation.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01019541/file/Maisonneuve_2012%20Le%20Cahier%20des%20Techniques%20de%20l%27INRA_1.pdf BibTex
titre
Mapping of the ms8 male sterility gene in sweet pepper (Capsicum annuum L.) on the chromosome P4 using PCR-based markers useful for breeding programmes
auteur
Grzegorz Bartoszewski, Cezary Waszczak, Piotr Gawronski, Iwona Stepien, Hanna Bolibok-Bragoszewska, Alain Palloix, Véronique Lefebvre, Aleksandra Korzeniewska, Katarzyna Niemirowicz-Szczytt
article
Euphytica, 2012, 186 (2), pp.453 - 461. ⟨10.1007/s10681-012-0637-9⟩
resume
The nuclear male sterility gene ms8 is expected to facilitate the production of sweet pepper (Capsicum annuum L.) hybrids as it provides means for hybridization without the labor-intensive hand emasculation of female inbred lines. The development of molecular markers linked to ms8 locus will help the breeding practice for the selection of hybrid parental lines. In this study, F-2 population resulting from a cross between the sweet pepper male sterile line 320 and the male fertile variety Elf was used to identify DNA markers linked to the ms8 locus. With the use of RAPD-BSA technique, seven markers linked to the ms8 locus were found. Four of them were converted into SCAR markers. In addition, two COSII/CAPS markers linked to the ms8 locus were identified. Comparative mapping with reference pepper maps indicated that the ms8 locus is located on the lower arm of the pepper chromosome P4. Identified markers are useful for molecular breeding, however, at present markers tightly linked to ms8 locus are still lacking. Identification of molecular markers linked to the ms8 locus and determination of its chromosomal localization are useful for fine mapping and also provide the perspective for ms8 gene cloning.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic diversity and differentiation of grafted and seed propagated apricot (Prunus armeniaca L.) in the Maghreb region
auteur
Hedia Bourguiba, Jean Marc Audergon, Lamia Krichen, Neila Trifi-Farah, Ali Mamouni, Samia Trabelsi, Bouchaib Khadari
article
Scientia Horticulturae, 2012, 142, pp.7-13. ⟨10.1016/j.scienta.2012.04.024⟩
resume
Apricots from Maghreb region (Algeria, Morocco and Tunisia) in North Africa are both clonally (by graft-ing) and seed propagated that are mainly grown in oasis agroecosystems. Are these two apricot groups genetically distinct or closely related, as previously suggested? We sought an answer to this question by analysing the genetic diversity and differentiation of 183 apricot accessions from Algeria, Morocco and Tunisia using 24 nuclear microsatellite markers distributed throughout the eight linkage groups of the Prunus genome. A total of 191 alleles were detected in the studied accessions. Similar high genetic diversity parameters were observed among all apricot geographic groups, revealing that there is high genetic variability in apricots from the Maghreb region. We conducted hierarchical clustering using the Neighbor-joining algorithm and showed that apricot can be classified according to its geographic origin and propagation mode in Maghreb. Despite this, we showed that both grafted and seed propagated apri-cots shared a common gene pool. Overall our results will help to improve management and conservation of Maghrebian apricot genetic resources.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The tomato genome sequence provides insights into fleshy fruit evolution
auteur
Shusei Sato, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu, Kenta Shirasawa, Sachiko Isobe, Takakazu Kaneko, Yasukazu Nakamura, Daisuke Shibata, Koh Aoki, Michael Egholm, James Knight, Robert Bogden, Changbao Li, Yang Shuang, Xun Xu, Shengkai Pan, Shifeng Cheng, Xin Liu, Yuanuyan Ren, Jun Wang, Alessandro Albiero, Francesca Dal Pero, Sara Todesco, Joyce van Eck, Robert M. Buels, Aureliano Bombarely, Joseph R. Gosselin, Minyun Huang, Jonathan Leto, Naama Menda, Susan Strickler, Linyong Mao, Shan Gao, Isaak y Tecle, Thomas York, Yi Zheng, Julia T. Vrebalov, Jemin Lee, Silin Zhong, Lukas A. Mueller, Willem J Stiekema, Paolo Ribeca, Tyler Alioto, Wencai Yang, Sanwen Huang, Yongchen Du, Zhonghua Zhang, Jianchang Gao, Yanmei Guo, Xiaosuan Wang, Ying Li, Jun He, Chuanyou Li, Zhukuan Cheng, Jianru Zuo, Jianfeng Ren, Jiuhai Zhao, Liuhua Yan, Hongling Jiang, Bao Wang, Hongshuang Li, Zhenjun Li, Fuyou Fu, Bingtang Chen, Bin Han, Qi Feng, Danlin Fan, Ying Wang, Hongqing Ling, Yongbiao Xue, Doreen Ware, W. Richard Mccombie, Zachary B. Lippmamn, Jer-Ming Chia, Ke Jiang, Shiran Pastermak, Laura Gelley, Melissa Kramer, Lorinda K. Anderson, Song-Bin Chang, Suzanne Royer, Lindsay A. Shearer, Stephen M. Stack, Jocelyn K. C. Rose, Yimin Xu, Nancy Eannetta, Antonio J. Matas, Ryan Mcquinn, Steven D. Tanksley, Francisco Câmara, Mathilde M. Causse, Christophe Rothan, Thomas Schiex, Céline Noirot, Arnaud A. Bellec, Christophe Klopp, Helene H. Berges, Jérôme J. Mariette, - Tomato Genome Consortium
article
Nature, 2012, 485 (7400), pp.635-641. ⟨10.1038/nature11119⟩
resume
Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Optimization of parameters of the ‘Virtual Fruit’ model to design peach genotype for sustainable production systems
auteur
Bénédicte Quilot-Turion, Mohamed Mahmoud Ould Sidi, Abdeslam Kadrani, Nadine Hilgert, Michel M. Génard, Francoise F. Lescourret
article
European Journal of Agronomy, 2012, 42, pp.34-38. ⟨10.1016/j.eja.2011.11.008⟩
resume
Designing sustainable production systems that are respectful of the environment and produce safe food of quality is a challenge for the future. A critical step is to find the best combinations of genetic resources and cultural practices adapted to target environments. The objective of this work is to illustrate how an ecophysiological process-based simulation model could be possibly used to design genotypes and to propose innovative production systems, by applying a methodology of optimization. As example, we studied the peach-brown rot system and used the ‘Virtual Fruit’, a process-based model that has been extensively tested, to perform virtual experiments. The challenge was to optimize the trade-off between antagonistic criteria of major importance for both fruit quality (increasing fruit mass and sweetness) and sensitivity to brown rot (decreasing skin density of cracks) in four different cultural scenarios. A multiobjective evolutionary algorithm, namely NSGA-II, was applied to solve this multiobjective optimization problem based on the ‘Virtual Fruit’. The optimized variables were six parameters of the ‘Virtual Fruit’, selected on the basis of a sensitivity analysis. This optimization method provided a large diversity of solutions among which the decision-maker can choose the best suited trade-off between criteria according to a particular objective. Most of the optimized solutions were distributed along Pareto fronts suggesting a good convergence of the algorithm. Moreover, it also provided some solutions located in non-crowded zones which constitute some original alternatives for the final decision-maker. The results confirmed the strong antagonism between the criteria considered. Large fruits had a weak sweetness and high crack density and for a given mass, those with improved sweetness had higher crack density. In a current breeding scheme, fruit mass would be the only criteria considered but alternative schemes could be considered for future, favoring organoleptic quality or environment friendly practices. In those cases, some interesting optimized solutions were identified. The work described in this paper supports that multiobjective evolutionary algorithms should be used to optimize parameters of process-based models and help identifying trade-off in complex systems. The use of the ‘Virtual Fruit’ to design sustainable production systems combining genotypes and innovative practices is further discussed.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02644612/file/50536_20120109110905425_1.pdf BibTex
titre
SPICY: towards automated phenotyping of large pepper plants in the greenhouse
auteur
Gerie van Der Heijden, Yu Song, Graham Horgan, Gerrit Polder, Anja Dieleman, Marco Bink, Alain Palloix, Fred van Eeuwijk, Chris Glasbey
article
Functional Plant Biology, 2012, 39 (10-11), pp.870 - 877. ⟨10.1071/FP12019⟩
resume
Most high-throughput systems for automated plant phenotyping involve a fixed recording cabinet to which plants are transported. However, important greenhouse plants like pepper are too tall to be transported. In this research we developed a system to automatically measure plant characteristics of tall pepper plants in the greenhouse. With a device equipped with multiple cameras, images of plants are recorded at a 5 cm interval over a height of 3 m. Two types of features are extracted: (1) features from a 3D reconstruction of the plant canopy; and (2) statistical features derived directly from RGB images. The experiment comprised 151 genotypes of a recombinant inbred population of pepper, to examine the heritability and quantitative trait loci (QTL) of the features. Features extracted from the 3D reconstruction of the canopy were leaf size and leaf angle, with heritabilities of 0.70 and 0.56 respectively. Three QTL were found for leaf size, and one for leaf angle. From the statistical features, plant height showed a good correlation (0.93) with manual measurements, and QTL were in accordance with QTL of manual measurements. For total leaf area, the heritability was 0.55, and two of the three QTL found by manual measurement were found by image analysis.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Anatomical and biochemical trait network underlying genetic variations in tomato fruit texture
auteur
Rémy Aurand, Mireille Faurobert, David Page, Jean Francois Maingonnat, Béatrice Brunel, Mathilde M. Causse, Nadia Bertin
article
Euphytica, 2012, 187 (1), pp.99 - 116. ⟨10.1007/s10681-012-0760-7⟩
resume
Firmness is an indicator of fruit freshness and a main component of tomato (Solanum lycopersicum) fruit texture. In this work, the genetic variability in fruit firmness and stiffness was analyzed in pre- and postharvest periods and underlying anatomical and biochemical traits were identified. Three tomato contrasted parental lines and six derived quantitative trait loci (QTL)-NILs harboring texture QTL on chromosome 4 (QTL4) and 9 (QTL9) were analyzed; the seasonal variability was assessed on two distant trusses. Firmness and stiffness were measured by compression and puncture tests at harvest and after 7-day storage at 20 A degrees C. QTL4 poorly influenced the textural variables, on the contrary to QTL9 which increased firmness measured by puncture test and had similar effects in the two genetic backgrounds. According to this test, firmness increased along the season, but ranks among genotypes and QTL effects were hardly affected. Only some of the QTL effects were still significant after storage and firmness losses were not predicted by firmness at harvest. Fruit firmness and stiffness measured by puncture tests correlated with both morphological (locular number, R = -0.89), histological (cell size, R < -0.80) and biochemical (dry matter (R > 0.82) and soluble sugar content (R < -0.74)) fruit traits. In contrast, compression test values hardly correlated with any of the measured traits. This work provided an original comprehensive approach to analyse fleshy fruit firmness and paves the way for a future predictive model.
typdoc
Journal articles
Accès au bibtex
BibTex

2011

Journal articles

titre
Isolation of C-glycosyl xanthones from Coffea pseudozanguebariae and their location.
auteur
Pascale Talamond, Geneviève Conejero, Jean-Luc Verdeil, Jean-Luc Poëssel
article
Natural Product Communications , 2011, 6 (12), pp.1885-8. ⟨10.1177/1934578X1100601223⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Histological study of organogenesis in Cucumis melo L. after genetic transformation: why is it difficult to obtain transgenic plants?
auteur
V Chovelon, V. Restier, N. Giovinazzo, Catherine Dogimont, J. Aarouf
article
Plant Cell Reports, 2011, 30 (11), pp.2001-2011. ⟨10.1007/s00299-011-1108-9⟩
resume
Melon (Cucumis melo L.) is widely considered as a recalcitrant species for genetic transformation. In this study, we developed different regeneration and transformation protocols and we examined the regeneration process at different steps by histological studies. The highest regener-ation rate (1.13 ± 0.02 plants per explant) was obtained using cotyledon explants of the ' Védrantais' genotype on Murashige and Skoog (MS) medium supplemented with 0.2 mg/l 6-benzylaminopurine (BAP) and 0.2 mg/l dim-ethylallylaminopurine (2-iP). Agrobacterium tumefaciens-mediated transformations with the uidA reporter gene were realized on cotyledon explants cultivated in these conditions: 70–90% of explants expressed a transient GUS activity during the early stages of regeneration, however, only few transgenic plants were obtained (1.8–4.5% of stable transformation with the GV2260pBI101 strain). These results revealed a low capacity of melon GUS-positive cells to regenerate transgenic plants. To evaluate the influence of the Agrobacterium infection on plant regeneration, histological analyses were conducted on explants 2, 7, 15, and 28 days after co-culture with the GV2260pBI101 strain. Genetic transformation occurred in epidermal and sub-epidermal cells and reached the meristematic structures expressing a high level of GUS activity during 14 days of culture; but after this period, most of the meristematic structures showed premature cell vacuolization and disorganization. This disruption of the GUS-positive meristematic areas could be responsible of the difficulties encountered to regenerate melon plants after genetic transformation.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01332269/file/2011_Chovelon_Plant%20Cell%20Reports%20%28Postprint%29_2 BibTex
titre
Salt and genotype impact on plant physiology and root proteome variations in tomato
auteur
Arafet Manaa, - Hela Ben Ahmed, Benoit B. Valot, Jean-Paul Bouchet, Samira Aschi-Smiti, Mathilde M. Causse, Mireille Faurobert
article
Journal of Experimental Botany, 2011, 62 (8), pp.2797-2813. ⟨10.1093/jxb/erq460⟩
resume
To evaluate the genotypic variation of salt stress response in tomato, physiological analyses and a proteomic approach have been conducted in parallel on four contrasting tomato genotypes. After a 14 d period of salt stress in hydroponic conditions, the genotypes exhibited different responses in terms of plant growth, particularly root growth, foliar accumulation of Na+, and foliar K/Na ratio. As a whole, Levovil appeared to be the most tolerant genotype while Cervil was the most sensitive one. Roma and Supermarmande exhibited intermediary behaviours. Among the 1300 protein spots reproducibly detected by two-dimensional electrophoresis, 90 exhibited significant abundance variations between samples and were submitted to mass spectrometry for identification. A common set of proteins (nine spots), up- or down-regulated by salt-stress whatever the genotype, was detected. But the impact of the tomato genotype on the proteome variations was much higher than the salt effect: 33 spots that were not variable with salt stress varied with the genotype. The remaining number of variable spots (48) exhibited combined effects of the genotype and the salt factors, putatively linked to the degrees of genotype tolerance. The carbon metabolism and energy-related proteins were mainly up-regulated by salt stress and exhibited most-tolerant versus most-sensitive abundance variations. Unexpectedly, some antioxidant and defence proteins were also down-regulated, while some proteins putatively involved in osmoprotectant synthesis and cell wall reinforcement were up-regulated by salt stress mainly in tolerant genotypes. The results showed the effect of 14 d stress on the tomato root proteome and underlined significant genotype differences, suggesting the importance of making use of genetic variability.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02646770/file/45048_20110224112420369_1.pdf https://hal.inrae.fr/hal-02646770/file/2011_Manaa_Journal%20of%20Experimental%20Botany_2.pdf BibTex
titre
Peach rusty spot is caused by the apple powdery mildew fungus, Podosphaera leucotricha
auteur
Tünde Jankovics, Nenad Dolovac, Aleksandra Bulajic, Branta Krstic, Thierry Pascal, Marc Bardin, Philippe C. Nicot
article
Plant Disease, 2011, 95 (6), pp.719-724. ⟨10.1094/PDIS-10-10-0711⟩
resume
Peach rusty spot, an economically important disease of peach (Prunus persica (L.) Batsch var. persica), appears as necrotic spots on fruit. The etiology of the disease is still not well understood although it has long been suspected that the causal agent is the apple powdery mildew pathogen, Podosphaera leucotricha. This work confirmed this hypothesis based on cross-inoculation experiments and analysis of rDNA ITS sequences PCR-amplified from rusty spot and peach powdery mildew lesions. Cross-inoculations of apple and peach leaves with P. leucotricha and P. pannosa, the causal agent of peach powdery mildew, showed that (i) young peach fruit, up to 5 cm diameter, developed symptoms typical of rusty spot following inoculation with P. leucotricha; (ii) leaves of apple seedlings, cv. Jonagold, developed powdery mildew infections when inoculated by touching young rusty spot lesions to their surfaces; (iii) P. leucotricha sporulated on young peach fruit, up to 5 cm diameter; and (iv) peach leaves and young shoots were not susceptible to P. leucotricha, whereas P. pannosa infected all the green parts of peach. A field experiment showed that there was only a 2-3 week period of time during early peach fruit development when the epidermis was susceptible to P. leucotricha. Based on these results, a clear distinction was made between the symptoms caused by P. pannosa and P. leucotricha on peach
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Application of EST-SSRs to examine genetic diversity in eggplant and its close relatives
auteur
Yeliz Tumbilen, Anne Frary, M-Christin Daunay, Sami Doganlar
article
Turkish Journal of Biology, 2011, 35, pp.125-136
resume
Within the genus Solanum, the term 'eggplant' encompasses several cultivated species that are used for food and, to a lesser extent, for medicine. The use of one common name to describe more than one species and the existence of many related wild species have led to taxonomic confusion which, in turn, have complicated analyses of evolutionary relationships and genetic diversity within this groups of species. A further challenge for eggplant research is that, despite the fact that the use of molecular markers for phylogenetic studies is well-established, very few studies have described the development of new markers for eggplant. In our work, genic microsatellite (SSR) markers were identified from an expressed sequence tag library of S. melongena and used for analysis of 47 accessions of eggplant and closely related species. The markers had very good polymorphism in the 18 species tested including 8 S. melongena accessions. Moreover, genetic analysis performed with these markers showed concordance with previous research and knowledge of eggplant domestication. These markers are expected to be a valuable resource for studies of genetic relationships, fingerprinting, and gene mapping in eggplant.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02650473/file/45089_20110719095943028_1.pdf BibTex
titre
Vers une horticulture à haute performance environnementale
auteur
Yves Lespinasse, Angélique Delahaye, M. Padilla, Daniel Plénet, Francoise Lescourret, Michel Génard, Mathilde Causse, Brigitte Navez, Francoise Dosba, Benoit Jeannequin
article
Comptes Rendus de l'Académie d'Agriculture de France, 2011, 97 (1), pp.81-94
resume
L’organisation de la filière Fruits et Légumes (F&L) et son fonctionnement très complexes connaissent actuellement des changements importants nécessités par les évolutions des marchés et une demande sociétale forte, notamment au niveau de la qualité des F&L. Comment concilier qualités de ces produits et contraintes environnementales de plus en plus soutenues? Comment analyser les composantes de la qualité et leur perception par les consommateurs et les prendre en compte dans les programmes d’amélioration génétique? Telles sont les questions qui seront abordées dans cette séance consacrée aux enjeux futurs de la qualité des F&L.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)
auteur
Aurora Díaz, Mohamed Fergany, Gelsomina Formisano, Peio Ziarsolo, José Blanca, Zhanjun Fei, Jack-E. Staub, Juan E. Zalapa, Hugo-E. Cuevas, Gayle Dace, Marc Oliver, Nathalie Boissot, Catherine Dogimont, Michel Pitrat, René Hofstede, Paul van Koert, Rotem Harel-Beja, Galil Tzuri, Vitaly Portnoy, Shahar Cohen, Arthur Schaffer, Nurit Katzir, Yong Xu, Haiying Zhang, Nobuko Fukino, Satoru Matsumoto, Jordi Garcia-Mas, Antonio J. Monforte
article
BMC Plant Biology, 2011, 11, pp.111. ⟨10.1186/1471-2229-11-111⟩
resume
Background: A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via markerassisted selection (MAS). Results: Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm. Conclusions: Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are Polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection).
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02652237/file/41297_20111005081648992_1.pdf BibTex
titre
Medieval herbal iconography and lexicography of Cucumis (cucumber and melon, Cucurbitaceae) in the Occident, 1300—1458
auteur
Harry S. Paris, Jules Janick, M-Christin Daunay
article
Annals of Botany, 2011, 108 (3), pp.471-484. ⟨10.1093/AOB/MCR182⟩
resume
Background The genus Cucumis contains two species of important vegetable crops, C. sativus, cucumber, and C. melo, melon. Melon has iconographical and textual records from lands of the Mediterranean Basin dating back to antiquity but cucumber does not. Our goal was to obtain an improved understanding of the history of these crops in the Occident. We examined medieval images purportedly of Cucumis, determined their specific identity, and compared them for originality, accuracy, and the lexicography of their captions. Findings The manuscripts having accurate, informative images are derived from Italy and France and were produced between 1300 and 1458. All have an illustration of cucumber but not all contain an image of melon. The cucumber fruits are green, unevenly cylindrical with an approximately 2:1 length-to-width ratio. Most of the images show the cucumbers marked by sparsely distributed, large dark dots, but images from northern France show them as having densely distributed, small black dots. The different size, color, and distribution reflects the different surface wartiness and spininess of modern American and French pickling cucumbers. The melon fruits are green, oval to serpentine, closely resembling the chate and snake vegetable melons, but not sweet melons. In nearly all manuscripts of Italian provenance, the cucumber image is labelled with the Latin caption citruli, or similar, plural diminuitive of citrus, citron (Citrus medica). However, in manuscripts of French provenance, the cucumber image is labelled cucumeres, which is derived from the classical Latin epithet cucumis for snake melon. The absence of melon in some manuscripts and the expropriation of the Latin cucumis/cucumer indicate replacement of vegetable melons by cucumbers during the medieval period in Europe. One image, from British Library ms. Sloane 4016, has a caption that allows tracing the word “gherkin” back to languages of the geographical nativity of C. sativus, the Indian subcontinent
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02647215/file/50217_20120116093152286_1.pdf BibTex
titre
Caracterisation of a loss-of-function mutant of gibberellin biosynthetic gene LsGA3ox1 in lettuce
auteur
Asami Umetsu, Yoshiaki Sawada, Wataru Mitsuhashi, Marianne Mazier, Tomonobu Toyomasu
article
Bioscience, Biotechnology and Biochemistry, 2011, 75 (12), pp.2398 - 2400. ⟨10.1271/bbb.110475⟩
resume
A previous study generated lettuce (Lactuca saliva) mutant lines tagged by retrotransposon Tnt1 from tobacco (Nicotiana tabacum) and identified a homozygous mutant, Tnt6a, that exhibited severe dwarf phenotype. Here we show that Tnt1 is inserted into the intron of gibberellin biosynthetic gene LsGA3ox1 in Tnt6a mutants. Expression analysis suggests that LsGA3ox1 is nearly knocked out in the Tnt6a mutants.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02642240/file/bioscience%20biotechnol%20biochem_1.pdf BibTex
titre
Mieux connaître le Bremia
auteur
Romain R. Valade, Claire C. Neema, Brigitte B. Maisonneuve
article
Réussir Fruits et Légumes, 2011, 311, pp.46
resume
absent
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Saturating the Prunus (Stone fruits) genome with candidate genes for fruit quality
auteur
Eudald Illa, Iban Eduardo, Jean Marc Audergon, Francesca Barale, Elisabeth Dirlewanger, - Xiongwei Li, Annick Moing, Patrick Lambert, Loick Le Dantec, - Zhongshan Gao, Jean-Luc Poessel, Carlo Pozzi, Laura Rossini, Alberto Vecchietti, Pere Arus, Werner Howad
article
Molecular Breeding, 2011, 28 (4), pp.667-682. ⟨10.1007/s11032-010-9518-x⟩
resume
To identify genes involved in the expression of a trait using the candidate gene (CG) approach, the genome positions of the maximum number of genes which potentially cause the observed phenotypic variability needs to be known. This position is compared with that of major genes or quantitative trait loci (QTLs) for this character, with co-location of the CG and major gene or QTL indicating possible cause and effect situations. In the present study we selected 273 sequences from EST collections, corresponding to CGs from metabolic pathways affecting fruit growth and maturity, texture, sugar and organic acid content, aroma and color, and mapped them in the Prunus reference map (TxE) based on an interspecific almond x peach F2 population. We used the bin-mapping approach, where only eight plants: six of the TxE progeny plus one of the parents and the F1 hybrid, are used to determine the position of a marker. This strategy was very efficient, with 206 CGs mapped, based mainly on the segregation of one or more single-nucleotide polymorphisms. These CGs were located throughout the Prunus genome and are a resource for genetic analysis in stone fruit (peach, plum, apricot and cherry) and almond. Co-locations between CGs and major genes or QTLs responsible for natural variability of fruit quality characters in Prunus were identified using the available information on their positions.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL
auteur
Stephane Munos, Nicolas N. Ranc, Emmanuel Botton, Aurélie A. Berard, Sophie Rolland, Philippe Duffe, Yolande Carretero, Marie-Christine Le Paslier, Corinne Delalande, Mondher Bouzayen, Dominique D. Brunel, Mathilde M. Causse
article
Plant Physiology, 2011, 156 (4), pp.2244-2254. ⟨10.1104/pp.111.173997⟩
resume
In tomato fruit, the number of locules (cavities containing seeds that are derived from carpels)varies from two to up to 10 or more. Locule number affects fruit shape and size, and is controlled by several Quantitative Trait Loci (QTLs). The large majority of the phenotypic variation is explained by two of these QTLs, fasciated and locule number (lc) that interact epistatically with one another. FASCIATED has been cloned, and mutations in the gene are described as key factors leading to the increase in fruit size in modern varieties. Here, we report the map-based cloning of lc. The lc QTL includes a 1600 bp region that is located 1080 bp from the 3’ end of WUSCHEL, which encodes a homeodomain protein that regulates stem cell fate in plants. The molecular evolution of lc showed a reduction in diversity in cultivated accessions with the exception of two SNPs. These two SNPs were shown to be responsible for the increase in locule number. An evolutionary model of locule number is proposed herein, suggesting that the fas mutation appeared after the mutation in the lc locus to confer the extreme high locule number phenotype.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02647706/file/2011_Munos_Plant%20Physiology_1.pdf BibTex
titre
Sensibilité au Monilia sur fleur de 16 variétés d'abricot : 4 années d'observation
auteur
Vincent Mercier, Laurent Brun, Guy Clauzel, Armand Guillermin, Jean Marc Audergon, J.M. Broquaire, Claude-Eric Parveaud, Christelle Gomez
article
Arbo Bio Infos, 2011, 159, pp.5-6
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Sensibilité variétale aux maladies et ravageurs - Fiche n° 1 Le chancre bactérien
auteur
Laurent Brun, Vincent Mercier, Armand Guillermin, Charlotte Arbona, Guy Clauzel, Vincent Delaunay, M Leon-Chapoux, Jean Marc Audergon
article
Arboriculture Fruitière, 2011, 659, pp.41
resume
Un dispositif expérimental a été implanté au printemps 2006 sur le domaine de l'INRA Gotheron pour évaluer la sensibilité au chancre bactérien de 16 variétés. Les attaques de chancre bactérien ont été importantes en 2009, 2010 et 2011. Un premier classement des sensibilités variétales a cette maladie a ainsi pu être réalisé.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Bacterial wilt resistance in tomato, pepper, and eggplant: genetic resources respond to diverse strains in the Ralstonia solanacearum species complex
auteur
Aurore Lebeau, M-Christin Daunay, Anne Frary, Alain Palloix, Jaw-Fen Wang, Jacques Dintinger, Frédéric Chiroleu, Emmanuel Wicker, Philippe Prior
article
Phytopathology, 2011, 101 (1), pp.154-165. ⟨10.1094/PHYTO-02-10-0048⟩
resume
Bacterial wilt, caused by strains belonging to the Ralstonia solanacearum species complex, inflicts severe economic losses in many crops worldwide. Host resistance remains the most effective control strategy against this disease. However, wilt resistance is often overcome due to the considerable variation among pathogen strains. To help breeders circumvent this problem, we assembled a worldwide collection of 30 accessions of tomato, eggplant and pepper (Core-TEP), most of which are commonly used as sources of resistance to R. solanacearum or for mapping quantitative trait loci. The Core-TEP lines were challenged with a core collection of 12 pathogen strains (Core-Rs2) representing the phylogenetic diversity of R. solanacearum. We observed six interaction phenotypes, from highly susceptible to highly resistant. Intermediate phenotypes resulted from the plants’ ability to tolerate latent infections (i.e., bacterial colonization of vascular elements with limited or no wilting). The Core-Rs2 strains partitioned into three pathotypes on pepper accessions, five on tomato, and six on eggplant. A “pathoprofile” concept was developed to characterize the strain clusters, which displayed six virulence patterns on the whole set of Core-TEP host accessions. Neither pathotypes nor pathoprofiles were phylotype specific. Pathoprofiles with high aggressiveness were mainly found in strains from phylotypes I, IIB, and III. One pathoprofile included a strain that overcame almost all resistance sources.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Amélioration des hôtes différentiels Bremia : obtention de lignées de laitue à résistance monogénique
auteur
Brigitte B. Maisonneuve
article
Innovations Agronomiques, 2011, 15, pp.9-14. ⟨10.17180/p5fk-s225⟩
resume
Several accessions of the actual set of Bremia differential hosts (BDH) are difficult to use to determine the virulence of Bremia isolates. This project was performed to create new BDH candidates of Lactuca sativa type with monogenic resistance. Some lines have been screened in the progenies from F3 [CGDM16 x F1 (Cg x LSE18/57)] as a susceptible BDH in one hand and as a Dm16-BDH in the other part; these lines would be used as substitute respectively of the actual susceptible BDH Cobham green (Cg) and the both actual BDH-Dm16 (L. serriola LSE18/57 or CGDM16, a Cobham green Dm16). The Cobham green resistance (Rcg) has been eliminated by tests with Serr84/99 strain. To replace Ninja (R36 = Dm3+Dm4+Dm11+Rsal-1) and Discovery (R37 = Dm7+Rsal-1), a breeding of a line Rsal1 has been made in the F3 (Discovery x Angie) by elimination of Dm7 from Discovery and Dm6 from Angie with adapted Bremia strains. The tests of resistance with the 14 UPOV Bremia strains of the obtained lines are up to expectation. The 7 partners are finishing the checking and the choice of the best lines. The three candidates, called FrDm0, FrDm16 and FrRsal-1, will be proposed to IBEB group at the end of 2011.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02643886/file/40624_20110905103420653_1.pdf BibTex
titre
Mid-infrared spectroscopy as a tool for rapid determination of internal quality parameters in tomato
auteur
Iwona Scibisz, Maryse Reich, Sylvie Bureau, Barbara Gouble, Mathilde M. Causse, Dominique D. Bertrand, Catherine M.G.C. Renard
article
Food Chemistry, 2011, 125 (4), pp.1390-1397. ⟨10.1016/j.foodchem.2010.10.012⟩
resume
The objective of this study was to investigate the possibility of predicting the quality parameters of tomato by mid-infrared spectroscopy. For 2 years, tomato samples, representing a large variability in the chemical composition, were scanned using the attenuated total reflectance accessory of a Fourier transform spectrometer in the wavenumber region between 4000 and 400 cm−1. Calibration models were developed using partial least squares (PLS) regression method and were tested with internal validation sample set in the first year. Different spectral preprocessing techniques were investigated and different spectral regions were selected to optimise the calibration models. In addition, the models obtained in 2007 were used to predict the soluble solids, dry matter and total acidity in tomato harvested in 2008. The regression models of the spectra showed reasonable ability to estimate the dry matter, soluble solids, total acidity, citric acid and individual sugars contents in tomatoes grown in 2007, with high coefficients of determination (from 0.98 for soluble solids to 0.92 for fructose) and low percentage errors of prediction (from 3% to 7% for soluble solids and citric acid, respectively). By contrast, the predictive capability of model for malic acid was unsatisfactory with error of prediction of 26%. When the best calibration models from 2007 were used to predict the selected parameters in tomato picked in 2008, very high correlations were obtained, confirmed by low errors of prediction, from 4% to 7% for dry matter and total acidity, respectively. Mid-infrared spectroscopy is an attractive alternative for standard methods for determination of internal quality parameters in tomato
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Cartographie des préférences des consommateurs européens et amélioration de la qualité de la tomate
auteur
Mathilde M. Causse, Brigitte Navez
article
Comptes Rendus de l'Académie d'Agriculture de France, 2011, 97 (1), pp.86-87
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Américano-japonaises cherchent pollinisateurs
auteur
Emile Koké, Henri Duval, Jean Michel Montagnon
article
Réussir Fruits et Légumes, 2011, 311, pp.34-37
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Distribution of SUN OVATE, LC and FAS in the tomato germplasm and the relationship to fruit shape diversity
auteur
Gustavo R Rodriguez, Stephane Munos, Claire Anderson, Sung-Chur Sim, Andrew Michel, Mathilde M. Causse, Brian B Mcspadden Gardener, Francis David, Esther van Der Knaap
article
Plant Physiology, 2011, 156 (1), pp.275-285
resume
Phenotypic diversity within cultivated tomato (Solanum lycopersicum) is particularly evident for fruit shape and size. Four genes that control tomato fruit shape have been cloned. SUN and OVATE control elongated shape whereas FASCIATED (FAS) and LOCULE NUMBER (LC) control fruit locule number and flat shape. We investigated the distribution of the fruit shape alleles in the tomato germplasm and evaluated their contribution to morphology in a diverse collection of 368 predominantly tomato and tomato var. cerasiforme accessions. Fruits were visually classified into eight shape categories that were supported by objective measurements obtained from image analysis using the Tomato Analyzer software. The allele distribution of SUN, OVATE, LC, and FAS in all accessions was strongly associated with fruit shape classification. We also genotyped 116 representative accessions with additional 25 markers distributed evenly across the genome. Through a model-based clustering we demonstrated that shape categories, germplasm classes, and the shape genes were nonrandomly distributed among five genetic clusters (P < 0.001), implying that selection for fruit shape genes was critical to subpopulation differentiation within cultivated tomato. Our data suggested that the LC, FAS, and SUN mutations arose in the same ancestral population while the OVATE mutation arose in a separate lineage. Furthermore, LC, OVATE, and FAS mutations may have arisen prior to domestication or early during the selection of cultivated tomato whereas the SUN mutation appeared to be a postdomestication event arising in Europe.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02642795/file/41028_20111125020158022_1.pdf BibTex
titre
Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits
auteur
Sarah Danan, Jean-Baptiste Veyrieras, Véronique Lefebvre
article
BMC Plant Biology, 2011, 11, 16 p. ⟨10.1186/1471-2229-11-16⟩
resume
Background: Integrating QTL results from independent experiments performed on related species helps to survey the genetic diversity of loci/alleles underlying complex traits, and to highlight potential targets for breeding or QTL cloning. Potato (Solanum tuberosum L.) late blight resistance has been thoroughly studied, generating mapping data for many Rpi-genes (R-genes to Phytophthora infestans) and QTLs (quantitative trait loci). Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits. Results: Nineteen QTL publications for late blight resistance were considered, seven of them reported maturity QTLs. Twenty-one QTL maps and eight reference maps were compiled to construct a 2,141-marker consensus map on which QTLs were projected and clustered into meta-QTLs. The whole-genome QTL meta-analysis reduced by six-fold late blight resistance QTLs (by clustering 144 QTLs into 24 meta-QTLs), by ca. five-fold maturity QTLs (by clustering 42 QTLs into eight meta-QTLs), and by ca. two-fold QTL confidence interval mean. Late blight resistance meta-QTLs were observed on every chromosome and maturity meta-QTLs on only six chromosomes. Conclusions: Meta-analysis helped to refine the genomic regions of interest frequently described, and provided the closest flanking markers. Meta-QTLs of late blight resistance and maturity juxtaposed along chromosomes IV, V and VIII, and overlapped on chromosomes VI and XI. The distribution of late blight resistance meta-QTLs is significantly independent from those of Rpi-genes, resistance gene analogs and defence-related loci. The anchorage of meta-QTLs to the potato genome sequence, recently publicly released, will especially improve the candidate gene selection to determine the genes underlying meta-QTLs. All mapping data are available from the Sol Genomics Network (SGN) database.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02650997/file/41561_20110228112444369_1.pdf BibTex
titre
Resistance induction and herbivore virulence in the interaction between Myzus persicae (Sulzer) and a major aphid resistance gene (Rm2) from peach
auteur
Marie-Hélène Sauge, Jean-Luc Poessel, Thomas Guillemaud, Laurent Lapchin
article
Arthropod-Plant Interactions, 2011, 5 (4), pp.369-377. ⟨10.1007/s11829-011-9141-8⟩
resume
In gene-for-gene host–enemy interactions, monogenic plant resistance results from pathogen recognition that initiates the induction of plant defense responses. Schematically, as the result of the on/off process of recognition, phenotypic variability in enemy virulence is expected to be qualitative, with either a failure or a success of host colonization. We focussed on a major gene from peach conferring avoidance resistance against the green peach aphid Myzus persicae. Measurements of herbivore density and time-dependent aspects of resistance induction were examined, as well as variability in the aphid’s ability to exploit the resistant host. Varying densities of infestation did not provoke differences in the aphid’s tendency to leave a plant, and a single aphid was sufficient to elicit a response. Similarly, the duration of infestation did not affect the aphid response. A brief aphid feeding time of 3 h triggered induced resistance, which became effective between 24 and 48 h after the initial attack. Induced resistance decayed over time in the absence of additional infestation. Thirty aphid genotypes collected from natural populations were tested in the laboratory. No clone could colonize the resistant host, suggesting that all of them triggered the induction of effective plant defense responses. However, we detected significant quantitative variation among clones in the tendency of aphids to leave plants. These results improve our understanding of induced resistance as a dynamic phenomenon and suggest that the potential for aphids to adapt to a major plant resistance gene may depend on factors other than the mere capacity to evade recognition.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02649450/file/2011_Sauge_Arthropod-Plant%20Interactions%20%28Preprint%29_2.pdf BibTex
titre
Vers des cultures fruitières et légumières à hautes performances environnementales
auteur
Benoit Jeannequin, Francoise Dosba, Daniel Plénet, Michel Pitrat, Jean-Eric Chauvin
article
Innovations Agronomiques, 2011, 12, pp.73-85. ⟨10.17180/m6da-zy06⟩
resume
In France, fruit and vegetable productions contribute 2% of the UAA and are characterised by a diversity of cultivated species and cropping systems with contrasting environmental impacts. Facing new stakes of implementing horticulture with high environment performance, Inra carries out researches targeting a reduction of the environmental impact of these crops and conc eption of innovative production systems. The main results achieved during the recent years concern optimisation of the management climatic conditions in greenhouses, optimised management of irrigation and fertilisation, creation of varieties with multiple resistance as well as durable management of resistances to pests and diseases, conception of production systems leading to reduced phytosanitary risks. Beyond researches in organic farming, the implementation of integrated pest management in fruit production and, more recently, integrated biological control in greenhouses are main contributions to environment preservation. Present approaches of Inra are more global and target low input production systems with high environmental and economic performances. They require modelling of complex systems and multiple partnerships. To feed and study these questions, Inra reinforces its collaborative structures, especially through Group of Scientific Interest (GIS) such as GIS PICLeg and, soon, GIS Fruits
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01512048/file/2011_Jeannequin_IA_%7BEEB8B5CB-4819-4165-92C8-C6AF4A895CFC%7D.pdf BibTex
titre
2011 Gene list for melon
auteur
Catherine Dogimont
article
Report - Cucurbit Genetics Cooperative, 2011, pp.104-133
resume
Melon (Cucumis melo L.) is an economically important, cross-pollinated species. Melon has 2n = 24 chromosomes and a relatively small genome (450 Mb), about three times larger than the Arabidopsis thaliana genome and similar to the rice genome (Arumanagathan and Earle, 1991). Melon has high intra-specific genetic variation and morphologic diversity. A great variety of genetic and molecular studies have been conducted on important agronomical traits, such as resistance to pathogens and insects, and floral and fruit traits. The following list is the latest version of the gene list for melon. Previous gene lists were organized by Pitrat: (Pitrat, 2006), (Pitrat, 2002), (Pitrat, 1998), (Pitrat, 1994), (Pitrat, 1990), (Pitrat, 1986), (Committee, 1982). This current list has been modified from previous lists in that (1) it provides an update of the known genes and QTLs, and (2) it adds an expanded description for reported genes including sources of resistance and resistance genes, phenotypes of mutants and traits related to seeds, seedlings, plant morphology and architecture, flowers and fruits. Locations of the reported genes on the melon genetic map and linked markers useful for marker assisted selection were reported where available. Since the first molecular marker-based melon map published in 1996 (Baudracco-Arnas and Pitrat, 1996), several genetic maps of melon have been published by several research teams, using several segregating populations. 2011 will be the year of the publication of an integrated map of melon in the framework of the International Cucurbit Genomic Initiative (Díaz et al., 2011). The integrated map has been constructed by merging data from eight independent mapping populations using genetically diverse parental lines. It spans 1150 cM distributed across the 12 melon linkage groups and comprises more than 1500 markers. Individual maps and the integrated map are available at www.icugi.org. The linkage groups were named according to Perin et al., 2002. The same nomenclature will be adopted hereafter. QTLs for 62 traits including virus resistance, fruit shape, fruit weight, sugar content have been located on this integrated map (Díaz et al., 2011). The list of melon sequences was not updated, as melon ESTs and full cDNAs are increasing extraordinarily (www.icugi.org). A physical map of the melon genome, anchored to the genetic map, has been established (Gonzalez et al., 2010) and the complete melon genome sequence is expected by the end of the year.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Sensibilité variétale aux maladies et ravageurs - Fiche n° 3 Monilioses sur fleur
auteur
Claude-Eric Parveaud, Christelle Gomez, Vincent Mercier, Laurent Brun, Armand Guillermin, Guy Clauzel, Jm Broquaire, Jean Marc Audergon
article
Arboriculture Fruitière, 2011, 661, 1 p
resume
Les monilioses sur fleur sont une des principales causes d'irrégularité de production en verger d'abricotier. Plusieurs espèces du champignon Monilia sont pathogènes. M. laxa et M. fructigena peuvent infecter les fleurs, les fruits et les pousses des arbres de fruits à noyaux et à pépins. M. furcicola a été observé dans la Vallée du Rhône pour la première fois en 2001.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02643268/file/44591_20111116030336176_1.pdf BibTex
titre
Which fruit selection for a sustainable agriculture with low inputs? Methodology for a decentralized plant breeding network
auteur
Laurent Brun, François Warlop, Vincent Mercier, Jm Broquaire, Guy Clauzel, Christelle Gomez, Claude-Eric Parveaud, Jean Marc Audergon
article
Innovations Agronomiques, 2011, 15, pp.105-115. ⟨10.17180/tjwc-sq36⟩
resume
In France, fruit production is cultivated on 140 thousand hectares, mainly conducted on intensive training system. Very few elements are available on low input training systems while they have to integrate the global rule under the frame of Ecophyto 2018. In order to evaluate if another system of cultivation is possible, a project was developed to highlight the main factors to be integrated in low input training system. A low input multilocal experimental design has thus been investigated on apricot in two main regions of production: Rhone valley and Roussillon. A set of 9 common cultivars with 20 replications each, planted in a complete single-tree randomization design was established. As already observed in apple orchard, a larger set of diseases has been observed in our experimental plots by comparison with conventional training orchards. A large genetic variability was evidenced among the observed cultivars, but if some of them expressed components of resistance against the observed diseases no one appeared widely resistant to all the diseases. Taking in consideration the longevity of the orchard, a huge concern exists with the tested germplasm because the observed dieback was in between 10 and 80% of the trees according to the cultivars after only 6 years of observation. On the methodological point of view, a clear optimization of the experimental design is expected on the base of the observed results.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02644350/file/51162_20120402085825516_1.pdf BibTex
titre
Salt-Stress Induced Physiological and Proteomic Changes in Tomato (Solanum lycopersicum) Seedlings
auteur
Arafet Manaa, Hela Ben Ahmed, Samira Smiti, Mireille Faurobert
article
OMICS, 2011, 15 (11), pp.801 - 809. ⟨10.1089/omi.2011.0045⟩
resume
Soil salinity is one of the major abiotic stress limiting crop productivity and the geographical distribution of many important crops worldwide. To gain a better understanding of the salinity stress responses at physiological and molecular level in cultivated tomato (Solanum lycopersicum. cv. Supermarmande), we carried out a comparative physiological and proteomic analysis. The tomato seedlings were cultivated using a hydroponic system in the controlled environment growth chamber. The salt stress (NaCl) was applied (0, 50, 100, 150 and 200 mM), and maintained for 14 days. Salt treatment induced a plant growth reduction estimated as fresh-dry weight. Photosynthetic pigments (chlorophyll a, b) content of NaCl-treated tomato plants was significantly decreased as the salinity level increased. Proline accumulation levels in leaf and root tissues increased significantly with increasing NaCl concentration. Relative electrolyte leakage known as an indicator of membrane damage caused by salt stress was increased proportionally according to the NaCl concentrations. Roots of control and salt-stressed plants were also sampled for phenol protein extraction. Proteins were separated by two-dimensional gel electrophoresis (2-DGE). Several proteins showed up-and downregulation during salt stress. MALDI-TOF/MS analysis and database searching of some of the identified proteins indicated that the proteins are known to be in a wide range of physiological processes, that is, energy metabolism, ROS (reactive oxygen species) scavenging and detoxification, protein translation, processing and degradation, signal transduction, hormone and amino acid metabolism, and cell wall modifications. All proteins might work cooperatively to reestablish cellular homeostasis under salt stress, water deficiency, and ionic toxicity.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Combining ecophysiological modelling and quantitative trait locus analysis to identify key elementary processes underlying tomato fruit sugar concentration
auteur
Marion Prudent, Alain Lecomte, Jean-Paul Bouchet, Nadia Bertin, Mathilde M. Causse, Michel M. Génard
article
Journal of Experimental Botany, 2011, 62 (3), pp.907-919. ⟨10.1093/jxb/erq318⟩
resume
A mechanistic model predicting the accumulation of tomato fruit sugars was developed in order (i) to dissect the relative influence of three underlying processes: assimilate supply (S), metabolic transformation of sugars into other compounds (M), and dilution by water uptake (D); and (ii) to estimate the genetic variability of S, M, and D. The latter was estimated in a population of 20 introgression lines derived from the introgression of a wild tomato species (Solanum chmielewskii) into S. lycopersicum, grown under two contrasted fruit load conditions. Low load systematically decreased D in the whole population, while S and M were targets of genotype×fruit load interactions. The sugar concentration positively correlated to S and D when the variation was due to genetic introgressions, while it positively correlated to S and M when the variation was due to changes in fruit load. Co-localizations between quantitative trait loci (QTLs) for sugar concentration and QTLs for S, M, and D allowed hypotheses to be proposed on the processes putatively involved at the QTLs. Among the five QTLs for sugar concentration, four co-localized with QTLs for S, M, and D with similar allele effects. Moreover, the processes underlying QTLs for sugar accumulation changed according to the fruit load condition. Finally, for some genotypes, the processes underlying sugar concentration compensated in such a way that they did not modify the sugar concentration. By uncoupling genetic from physiological relationships between processes, these results provide new insights into further understanding of tomato fruit sugar accumulation.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02647846/file/48133_20110224014702746_1.pdf BibTex
titre
Mapping Rm2 gene conferring resistance to the green peach aphid (Myzus persicae Sulzer) in the peach cultivar “Rubira®”
auteur
Patrick Lambert, Thierry Pascal
article
Tree Genetics and Genomes, 2011, 7 (5), pp.1057-1068. ⟨10.1007/s11295-011-0394-2⟩
resume
The green peach aphid (GPA), Myzus persicae (Sulzer), is a widespread pest insect that significantly reduces yield in peach orchards [Prunus persica (L.) Batsch]. Chemical control of the GPA population in the orchards showed little efficiency because of the development of resistance to most classes of insecticides. Biological control partially gave convincing results. Breeding for resistant peach cultivars is therefore a serious option to take into account for the development of sustainable pest management. Among the few available resistance cultivars, the rootstock peach “Rubira®” shows a strong induced antixenosis-type GPA resistance. This was demonstrated segregating as a single dominant gene. In order to investigate the genetic basis of resistance and develop molecular tools useful in breeding programs, a F2 population derived from “Rubira®” also segregating for leaf color was grown and scored for GPA resistance under contrasted environmental conditions. An SSR-based genetic linkage map composed of 120 SSR loci spanned over a distance of 497.8 cM was then established. The GPA resistance mapped to a single locus at the bottom end of linkage group 1. We propose to name Rm2 the dominant allele of the underlying gene. Additionally, a reciprocal translocation was identified near the Gr gene controlling leaf color. The red-leaf parent “Rubira®” was demonstrated responsible for the translocation. This study provides the basis for future molecular analysis for the use of Rm2 in peach breeding programs against GPA in peach orchards
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02652429/file/2011_Lambert_Tree%20Genetics%20and%20Genomes%20%28Postprint%29_2.pdf BibTex
titre
Combining major gene and QTL: potential for melon resistance to Aphis gossypii
auteur
Sophie Thomas, Nathalie Boissot, Pascale Mistral, Virginie Chareyron, Flavie Vanlerberghe-Masutti, Catherine Dogimont
article
Innovations Agronomiques, 2011, 15, pp.45-54. ⟨10.17180/59je-e042⟩
resume
The melon aphid, Aphis gossypii, is a major pest of many crops. Molecular markers have revealed a host race organization of the species and 8 microsatellite markers have allowed the identification of 21 multilocus genotypes (MLGs) among clones collected into colonies on Cucurbits. Aphid resistance have been identified in several melon accessions; it is controlled by a major gene, Vat, and some quantitative trait loci (QTLs). We built melon populations combining different loci of resistance, in a homogenous genetic background. They were cultivated in melon producing areas with contrasted aphid populations. Then, we showed a significant effect of the Vat gene on aphid density but non effect of the QTLs. One hundred and two MLGs were attributed to 2596 collected in trials, 54 MLGs were observed only once, five MLGs were only observed in the French West Indies, 19 MLGs were observed both in South eastern and South western France. Nevertheless, we did not observe a significant effect of the resistance loci on the diversity index of Shanon. Among clones collected into 125 colonies, we only identified 10 MLGs, five out of them were identified in clones collected on Vat-melon. The resistance loci might have an effect on the diversity of the South-eastern populations.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02643696/file/48084_20110905095639511_1.pdf BibTex
titre
Variation in melon (Cucumis melo) landraces adapted to the humid tropics of southern India
auteur
Mohamed Fergany, A.J. Balvir Kaur, A.J. Monforte, Michel Pitrat, Catherine Wipf-Scheibel, Hervé Lecoq, N. Dhillon, S.S. Dhaliwal
article
Genetic Resources and Crop Evolution, 2011, 58 (2), pp.225-243. ⟨10.1007/s10722-010-9564-6⟩
resume
We present here the first comprehensive genetic characterization of melon landraces from the humid tropics of southern India. The genetic diversity among 50 melon landraces collected from 3 agro-ecological regions of southern India (6 agro-ecological subregions)was assessed by variation at 17 SSR loci, morphological traits of plant habit and fruit, 2 yield-associated traits, pest and disease resistance, biochemical composition (ascorbic acid, carotenoids, titrable acidity) and mineral content (P, K, Fe, Zn). Differences among accessions were observed in plant and fruit traits. Melon germplasm with high titrable acidity, higher than average amounts of mineral content and resistance to Cucumber mosaic virus, Zucchini yellow mosaic virus, powdery mildew (races 1, 2, 3, 5), Fusarium wilt (races 1, 2), Aphis gossypii and leafminer was recorded in the collection. A high level of genetic variability in melon germplasm was suggested by the SSR analysis. Comparative analysis using SSRs of the genetic variability between Indian melons from north, south, and east regions and reference accessions of melon from Spain, France, Japan, Korea, Iraq, Zambia showed regional differentiation between Indian melon accessions and that Indian germplasm was weakly related to the melon accessions from other parts of the world, suggesting that an important portion of the genetic variability found within this melon collection has not been used yet for the development of new cultivars. Additional collections of acidulus melon germplasm should be made in southern India and adequate management of this important genetic resource is clearly a necessity.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02647391/file/2010_Fergany_Genetic%20Resources%20and%20Crop%20Evolution%20%28Postprint%29_2.pdf BibTex
titre
Knock-down of both eIF4E1 and eIF4E2 genes confers broad-spectrum resistance against potyviruses in tomato
auteur
Marianne Mazier, Fabrice Flamain, Maryse Nicolaï, Verane Sarnette, Carole Caranta
article
PLoS ONE, 2011, 6 (12), pp.1-10. ⟨10.1371/journal.pone.0029595⟩
resume
Background: The eukaryotic translation initiation factor eIF4E plays a key role in plant-potyvirus interactions. eIF4E belongs to a small multigenic family and three genes, eIF4E1, eIF4E2 and eIF(iso)4E, have been identified in tomato. It has been demonstrated that eIF4E-mediated natural recessive resistances against potyviruses result from non-synonymous mutations in an eIF4E protein, which impair its direct interaction with the potyviral protein VPg. In tomato, the role of eIF4E proteins in potyvirus resistance is still unclear because natural or induced mutations in eIF4E1 confer only a narrow resistance spectrum against potyviruses. This contrasts with the broad spectrum resistance identified in the natural diversity of tomato. These results suggest that more than one eIF4E protein form is involved in the observed broad spectrum resistance Methodology/Principal Findings: To gain insight into the respective contribution of each eIF4E protein in tomato-potyvirus interactions, two tomato lines silenced for both eIF4E1 and eIF4E2 (RNAi-4E) and two lines silenced for eIF(iso)4E (RNAi-iso4E) were obtained and characterized. RNAi-4E lines are slightly impaired in their growth and fertility, whereas no obvious growth defects were observed in RNAi-iso4E lines. The F1 hybrid between RNAi-4E and RNAi-iso4E lines presented a pronounced semi-dwarf phenotype. Interestingly, the RNAi-4E lines silenced for both eIF4E1 and eIF4E2 showed broad spectrum resistance to potyviruses while the RNAi-iso4E lines were fully susceptible to potyviruses. Yeast two-hybrid interaction assays between the three eIF4E proteins and a set of viral VPgs identified two types of VPgs: those that interacted only with eIF4E1 and those that interacted with either eIF4E1 or with eIF4E2 Conclusion/Significance: These experiments provide evidence for the involvement of both eIF4E1 and eIF4E2 in broad spectrum resistance of tomato against potyviruses and suggest a role for eIF4E2 in tomato-potyvirus interactions.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02649007/file/49600_20120208095120664_1.pdf BibTex
titre
The reproductive potential of root-knot nematodes Meloidogyne incognita is affected by selection for virulence against major resistance genes from tomato and pepper
auteur
Caroline Djian-Caporalino, Sergio Molinari, Alain Palloix, Aurelio Ciancio, Ariane Fazari, Nathalie Marteu, Nicolas Ris, Philippe Castagnone-Sereno
article
European Journal of Plant Pathology, 2011, 131, pp.431-440. ⟨10.1007/s10658-011-9820-4⟩
resume
Root-knot nematodes (RKNs, Meloidogyne spp.) are major plant pathogens of vegetables in most production areas, including the Solanaceous crops tomato and pepper. Due to the banning of chemical nematicides, current control strategies are mainly based on the deployment of resistance genes (R-genes), i.e., Mi(s) in tomato, Me(s) in pepper. These genes are effective against a wide range of RKN species, including M. arenaria, M. incognita and M. javanica, the most common species in temperate and tropical areas. However, the recent emergence of virulent populations able to overcome the resistance conferred by some of these R-genes may constitute a severe limitation to their use in the field. Research has been conducted to evaluate the durability of the Mi(s) and Me(s) R-genes, by comparing the reproduction of several laboratory-selected and wild virulent M. incognita isolates on both susceptible and resistant tomatoes and peppers. We first showed that the Me1 R-gene in pepper behaves as a robust R-gene controlling avirulent and virulent Me3 or Mi-1 isolates. We also confirm that virulence is highly specific to a determined R-gene on which selection has occurred, thus allowing the alternance of R-genes in the rotation as an effective mean to improve soil health. Another significant experimental result is the observation that a reproductive fitness cost is associated to nematode virulence. The adaptative significance of trade-offs between selected characters and fitness-related traits suggests that, although the resistance can be broken, it might prove durable in some conditions if the virulent nematodes are counterselected in susceptible plants, which has important consequences for the management of plant resistance in the field.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02646716/file/2011_Caporalino_European%20Journal%20of%20Plant%20Pathology%20%28Postprint%29_2 BibTex
titre
The Helper component proteinase cistron of Potato virus Y induces hypersensitivity and resistance in potato genotypes carrying dominant resistance genes on chromosome IV
auteur
Benoît Moury, Bernard Caromel, Elisabeth Ida Johansen, Vincent Simon, Laura Chauvin, Emmanuel Jacquot, Camille Kerlan, Véronique Lefebvre
article
Molecular Plant-Microbe Interactions, 2011, 24 (7), pp.787-797. ⟨10.1094/MPMI-10-10-0246⟩
resume
The Nctbr and Nytbr genes in Solanum tuberosum determine hypersensitive reactions, characterized by necrotic reactions and restriction of the virus systemic movement, toward isolates belonging to clade C and clade O of Potato virus Y (PVY), respectively. We describe a new resistance from S. sparsipilum which possesses the same phenotype and specificity as Nctbr and is controlled by a dominant gene designated Ncspl. Ncspl maps on potato chromosome IV close or allelic to Nytbr. The helper component proteinase (HC-Pro) cistron of PVY was shown to control necrotic reactions and resistance elicitation in plants carrying Ncspl, Nctbr, and Nytbr. However, inductions of necrosis and of resistance to the systemic virus movement in plants carrying Ncspl reside in different regions of the HC-Pro cistron. Also, genomic determinants outside the HC-Pro cistron are involved in the systemic movement of PVY after induction of necroses on inoculated leaves of plants carrying Nytbr. These results suggest that the Nytbr resistance may have been involved in the recent emergence of PVY isolates with a recombination breakpoint near the junction of HC-Pro and P3 cistrons in potato crops. Therefore, this emergence could constitute one of the rare examples of resistance breakdown by a virus which was caused by recombination instead of by successive accumulation of nucleotide substitutions.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Texture variation in apricot: Intra-fruit heterogeneity, impact of thinning and relation with the texture after cooking.
auteur
Crepin Ella Missang, Catherine C. Renard, Jean-Marc Audergon, Jean Francois Maingonnat
article
Foodservice Research International, 2011, 44 (1), pp.46-53. ⟨10.1016/j.foodres.2010.11.017⟩
resume
The rapid texture loss of apricot fruit during storage and transformation is a limiting factor for its commercialisation and use. Apricot flesh exhibits different tissue zones which differ in texture. To better understand texture in apricot fruit, we have studied (i) the intra-fruit heterogeneity of texture measured by puncture test (tissue firmness) (ii) the effect of thinning on whole fruit firmness (global firmness), measured by compression, and on tissue firmness and (iii) the evolution of texture upon steam cooking, on apricots of contrasted texture. Nine tissue zones were defined in fresh apricot fruits in order to study differences in texture from the peduncle to the pistil zones and from the external to the internal tissue. In the nine apricot varieties used, tissue firmness decreased gradually from the external to the internal tissue. However, from the peduncle to the pistil zone, the variation of texture seemed to be variety-dependent. Overall the textures measured for the nine tissue zones were highly correlated, indicative of the major differentiation between soft and firm fruits. However distinct heterogeneity patterns could be observed on axes 2 and 3 of a principal component analysis carried out on the textures of the nine zones. The effect of thinning on fruit firmness appeared variety-dependent. Tissue firmness of the raw apricots assessed by penetrometry explained about two-thirds of the variability of firmness of cooked apricots, versus only 40% for the compression test. High correlations between texture after cooking and prior to cooking were found for four (external equatorial, external pistil, median equatorial and median pistil) out of the nine tissue zones.
typdoc
Journal articles
Accès au bibtex
BibTex

2010

Journal articles

titre
Development and mapping of peach candidate genes involved in fruit quality and their transferability and potential use in other Rosaceae species
auteur
Loïck Le Dantec, Gaelle Cardinet, Julio Bonet, Mathieu Fouché, Karima Boudehri, Amparo Monfort, Jean-Luc Poëssel, Annick Moing, Elisabeth Dirlewanger
article
Tree Genetics and Genomes, 2010, 6 (6), pp.995-1012. ⟨10.1007/s11295-010-0308-8⟩
resume
The goal of the present study was to identify candidate genes (CGs) involved in fruit quality in peach that can be transferred to other Rosaceae species. Two cDNA libraries from fruit of the "Fantasia" peach cultivar, constructed at two stages of development, were used to generate a set of expressed sequence tag sequences. A total of 1,730 peach unigenes were obtained after clustering. Sequences and corresponding annotations were stored in a relational database and are available through a web interface. Fifty-nine CGs involved in fruit growth and development or fruit quality at maturity, focusing on sweetness, acidity, and phenolic compound content, were selected according to their annotation. Fifty-five primer pairs, designed from peach CG sequences and giving PCR products in peach, were tested in strawberry and 36 gave amplified products. Eight CGs were mapped in peach, 14 in strawberry, four in both species and confirmed the pattern of synteny already proposed using comparative mapping. In peach, the CGs are located in three linkage groups (3, 5, 7), and in strawberry they are distributed in all seven Fragaria linkage groups. Colocalization between some of these CGs and quantitative trait loci for fruit quality traits were identified and are awaiting confirmation in further analyses.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genotype-dependent response to carbon availability in growing tomato fruit
auteur
Marion Prudent, Nadia Bertin, Michel Génard, Stephane S. Munos, Sophie Rolland, Virginie Garcia, Johann Petit, Pierre Baldet, Christophe Rothan, Mathilde M. Causse
article
Plant, Cell and Environment, 2010, pp.33, 1186-1204. ⟨10.1111/j.1365-3040.2010.02139.x⟩
resume
Tomato fruit growth and composition depend on both genotype and environment. This paper aims (i) at studying how fruit phenotypic responses to changes in carbon availability can be influenced by genotype and (ii) at identifying genotype-dependent and -independent changes in gene expression underlying variations in fruit growth and composition. To this end, we grew a parental line (S. lycopersicum) and an introgression line from S. chmielewskii harboring QTL for fresh weight and sugar content under two fruit loads (FL). Lowering fruit load increased fruit cell number and reduced fruit developmental period in both genotypes. In contrast, fruit cell size was increased only in the parental line. Modifications in gene expression were monitored in expanding fruits using microarrays and RT-qPCR for a subset of genes. FL changes induced more deployments of regulation systems (transcriptional and post transcriptional) than massive adjustments of whole primary metabolism. Interactions between genotype and FL were especially noticeable for 99 genes mainly linked to hormonal and stress responses, and on gene expression kinetics during fruit development. Links between gene expression and fruit phenotype were found for aquaporin expression levels and fruit water content, and invertase expression levels and sugar content during fruit ripening phase. In summary, the present data emphasized age- and genotype-dependent responses of tomato fruit to carbon availability, at phenotypic as well as at gene expression level.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-00600426/file/PrudentPCE2009.pdf BibTex
titre
A SNP associated with alternative splicing of RPT5b causes unequal redundancy between RPT5a and RPT5b among Arabidopsis thaliana natural variation
auteur
Anouchka Guyon-Debast, Alain Lecureuil, Sandrine Bonhomme, Philippe Guerche, Jean-Luc Gallois
article
BMC Plant Biology, 2010, 10 (158), pp.1-10. ⟨10.1186/1471-2229-10-158⟩
resume
Background: The proteasome subunit RPT5, which is essential for gametophyte development, is encoded by two genes in Arabidopsis thaliana; RPT5a and RPT5b. We showed previously that RPT5a and RPT5b are fully redundant in the Columbia (Col-0) accession, whereas in the Wassilewskia accession (Ws-4), RPT5b does not complement the effect of a strong rpt5a mutation in the male gametophyte, and only partially complements rpt5a mutation in the sporophyte. RPT5bCol-0 and RPT5bWs-4 differ by only two SNPs, one located in the promoter and the other in the seventh intron of the gene. Results: By exploiting natural variation at RPT5b we determined that the SNP located in RPT5b intron seven, rather than the promoter SNP, is the sole basis of this lack of redundancy. In Ws-4 this SNP is predicted to create a new splicing branchpoint sequence that induces a partial mis-splicing of the pre-mRNA, leading to the introduction of a Premature Termination Codon. We characterized 5 accessions carrying this A-to-T substitution in intron seven and observed a complete correlation between this SNP and both a 10 to 20% level of the RPT5b pre-mRNA missplicing and the lack of ability to complement an rpt5a mutant phenotype. Conclusion: The accession-dependent unequal redundancy between RPT5a and RPT5b genes illustrates an example of evolutionary drifting between duplicated genes through alternative splicing.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01203865/file/39147_20101228091359389_1.pdf BibTex
titre
L’adaptation des virus de plantes aux résistances variétales
auteur
Benoît Moury, Frederic Fabre, Josselin Montarry, Bérenger Janzac, Valérie Ayme, Alain Palloix
article
Virologie, 2010, 14 (4), pp.227-239. ⟨10.1684/vir.2010.0311⟩
resume
Genetic resistances have allowed a large reduction of the impact of viral diseases in cultived plants. Their introduction into breeding programs was facilitated by the simple genetic control of many of them. However, as for any host-parasite couple, the targeted viruses can adapt rapidly to resistances even though the durability of resistances, i.e. the amount of time during which they remain efficient in crops, is highly variable. During these last two decades, the use of genetic analysis methods in plant viruses revealed the molecular mechanisms responsible for these adaptations and, hopefully, will allow a more precise prediction of the potential durability of resistances. If the mechanisms involved in virus adaptation at the plant scale have been unravelled, those responsible for the emergence of adapted viral populations at the agroecosystem scale are largely unknown. A better knowledge of the fitness of viral genotypes, adapted or not to the resistance, to infect their different host plants and to spread in the agro-ecosystem is needed. The difficulties linked to their experimental analysis require the development of mathematical modelling approaches of these phenomena, notably to define optimal spatiotemporal strategies of cultivar deployment.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Altes Gemüse
auteur
Elisabeth Raether, Michel Pitrat
article
Zeitmagazin, 2010, 48, pp.44-46
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02653348/file/37315_20101214091944793_1.pdf BibTex
titre
A point mutation in the polymerase of Potato virus Y confers virulence toward the Pvr4 resistance of pepper and a high competitiveness cost in susceptible cultivar
auteur
Bérenger Janzac, Josselin Montarry, Alain Palloix, Olivier Navaud, Benoît Moury
article
Molecular Plant-Microbe Interactions, 2010, 23 (6), pp.823-830. ⟨10.1094/MPMI-23-6-0823⟩
resume
To understand why the Pvr4 resistance of pepper against Potyvirus spp. remained durable in field conditions while virulent Potato virus Y (PVY) variants could be selected in the laboratory, we studied the molecular mechanisms which generated these variants and the consequences on viral fitness. Using a reverse genetics approach with an infectious cDNA clone of PVY, we found that the region coding for the NIb protein (RNA-dependent RNA polymerase) of PVY was the avirulence factor corresponding to Pvr4 and that a single nonsynonymous nucleotide substitution in that region, an adenosine to guanosine substitution at position 8,424 of the PVY genome (A8424G), was sufficient for virulence. This substitution imposed a high competitiveness cost to the virus against an avirulent PVY variant in plants devoid of Pvr4. In addition, during serial passages in susceptible pepper plants, the only observed possibility of the virulent mutant to increase its fitness was through the G8424A reversion, strengthening the high durability potential of the Pvr4 resistance. This is in accordance with the fact that the NIb protein is one of the most constrained proteins expressed by the PVY genome and, more generally, by Potyvirus spp., and with a previously developed model predicting the durability of virus resistances as a function of the evolutionary constraint applied on corresponding avirulence factors.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Engineering Melon Plants with Improved Fruit Shelf Life Using the TILLING Approach
auteur
Fatima Dahmani-Mardas, Christelle Troadec, Adnane Boualem, Sylvie Leveque, Abdullah A. Alsadon, Abdullah A. Aldoss, Catherine Dogimont, Abdelhafid A. Bendahmane
article
PLoS ONE, 2010, 5 (12), ⟨10.1371/journal.pone.0015776⟩
resume
Background: Fruit ripening and softening are key traits that have an effect on food supply, fruit nutritional value and consequently, human health. Since ethylene induces ripening of climacteric fruit, it is one of the main targets to control fruit over ripening that leads to fruit softening and deterioration. The characterization of the ethylene pathway in Arabidopsis and tomato identified key genes that control fruit ripening. Methodology/Principal Findings: To engineer melon fruit with improved shelf-life, we conducted a translational research experiment. We set up a TILLING platform in a monoecious and climacteric melon line, cloned genes that control ethylene production and screened for induced mutations that lead to fruits with enhanced shelf life. Two missense mutations, L124F and G194D, of the ethylene biosynthetic enzyme, ACC oxidase 1, were identified and the mutant plants were characterized with respect to fruit maturation. The L124F mutation is a conservative mutation occurring away from the enzyme active site and thus was predicted to not affect ethylene production and thus fruit ripening. In contrast, G194D modification occurs in a highly conserved amino acid position predicted, by crystallographic analysis, to affect the enzymatic activity. Phenotypic analysis of the G194D mutant fruit showed complete delayed ripening and yellowing with improved shelf life and, as predicted, the L124F mutation did not have an effect. Conclusions/Significance: We constructed a mutant collection of 4023 melon M2 families. Based on the TILLING of 11 genes, we calculated the overall mutation rate of one mutation every 573 kb and identified 8 alleles per tilled kilobase. We also identified a TILLING mutant with enhanced fruit shelf life. This work demonstrates the effectiveness of TILLING as a reverse genetics tool to improve crop species. As cucurbits are model species in different areas of plant biology, we anticipate that the developed tool will be widely exploited by the scientific community.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02660830/file/2010_%20Dahmani-Mardas_Plosone_1.pdf BibTex
titre
Under what circumstances can process-based simulation models link genotype to phenotype for complex traits? Case-study of fruit and grain quality traits
auteur
Nadia Bertin, Pierre Martre, Michel Génard, Bénédicte Quilot-Turion, Christophe Salon
article
Journal of Experimental Botany, 2010, 61 (4), pp.955-967. ⟨10.1093/jxb/erp377⟩
resume
Detailed information has arisen from research at gene and cell levels, but it is still incomplete in the context of a quantitative understanding of whole plant physiology. Because of their integrative nature, process-based simulation models can help to bridge the gap between genotype and phenotype and assist in deconvoluting genotype-by-environment (GxE) interactions for complex traits. Indeed, GxE interactions are emergent properties of simulation models, i.e. unexpected properties generated by complex interconnections between subsystem components and biological processes. They co-occur in the system with synergistic or antagonistic effects. In this work, different kinds of GxE interactions are illustrated. Approaches to link model parameters to genes or quantitative trait loci (QTL) are briefly reviewed. Then the analysis of GxE interactions through simulation models is illustrated with an integrated model simulation of peach (Prunus persica (L.) Batsch) fruit mass and sweetness, and with a model of wheat (Triticum aestivum L.) grain yield and protein concentration. This paper suggests that the management of complex traits such as fruit and grain quality may become possible, thanks to the increasing knowledge concerning the genetic and environmental regulation of organ size and composition and to the development of models simulating the complex aspects of metabolism and biophysical behaviours at the plant and organ levels.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Quantitative trait loci analysis of Plum pox virus resistance in Prunus davidiana P1908: new insights on the organization of genomic resistance regions
auteur
Manuel Rubio, Thierry Pascal, Alexandre Bachellez, Patrick Lambert
article
Tree Genetics and Genomes, 2010, 6 (2), pp.291-304. ⟨10.1007/s11295-009-0249-2⟩
resume
No valuable source of resistance to Plum pox virus (PPV), the causative agent of sharka disease, has been found in peach (Prunus persica), but polygenic resistance to PPV was described in Prunus davidiana clone P1908. Two previous studies using F1 and F2 populations derived from the nectarine cv. Summergrand and P. davidiana P1908 identified a total of six P. davidiana quantitative trait loci (QTLs) involved in PPV resistance (Marcus strain). In an effort to verify the QTL stability in a large progeny and to search for possible interactions of the genetic backgrounds, the current study evaluated the incidence of PPV infection in an F1 population derived from the susceptible peach cv. Rubira and P. davidiana P1908 over three growth periods using an improved method of PPV phenotyping referred to as “heavy test.” The phenotypic dataset was analyzed using similar methods as the previous studies and a newly developed simple-sequence-repeat-based P. davidiana map. Nine regions involved in differential symptom expression were identified among which six were common between studies. However, the level of resistance observed in the population was very low compared to the other studies, and the main QTL previously identified in linkage group 6 was not conserved, suggesting strong interaction of the genetic background of the susceptible parent with that of P. davidiana 1908. Consequently, this could be a limiting factor for developing resistant cultivars derived from P. davidiana P1908
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Single amino acid changes in the turnip mosaic virus viral genome-linked protein (VPg) confer virulence towards Arabidopsis thaliana mutants knocked out for eukaryotic initiation factors eIF(iso)4E and eIF(iso)4G
auteur
Jean-Luc J.-L. Gallois, Carine Charron, Flora Sanchez, Gaelle G. Pagny, Marie-Christine M.-C. Houvenaghel, André Moretti, Fernando Ponz, Frederic Revers, Carole Caranta, Sylvie S. German-Retana
article
Journal of General Virology, 2010, 91 (1), pp.288-293. ⟨10.1099/vir.0.015321-0⟩
resume
Previous resistance analyses of Arabidopsis thaliana mutants knocked out for eukaryotic translation initiation factors showed that disruption of the At-eIF(iso)4E or both the At-eIF(iso)4G1 and At-eIF(iso)4G2 genes resulted in resistance against turnip mosaic virus (TuMV). This study selected TuMV virulent variants that overcame this resistance and showed that two independent mutations in the region coding for the viral genome-linked protein (VPg) were sufficient to restore TuMV virulence in At-eIF(iso)4E and At-eIF(iso)4G1xAt-eIF(iso)4G2 knockout plants. As a VPg–eIF(iso)4E interaction has been shown previously to be critical for TuMV infection, a systematic analysis of the interactions between A. thaliana eIF4Es and VPgs of virulent and avirulent TuMVs was performed. The results suggest that virulent TuMV variants may use an eIF4F-independent pathway
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La revanche de la tomate
auteur
Frédéric Lewino, Rene Damidaux
article
Le Point, 2010, 1976, pp.66-68
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Pomological and nutraceutical properties in apricot fruit: cultivation systems and cold storage fruit management
auteur
Annamaria Leccese, Sylvie Bureau, Maryse Reich, Catherine M.G.C. Renard, Jean Marc Audergon, Carmelo Mennone, Susanna Bartolini, Raffaella Viti
article
Plant Foods for Human Nutrition, 2010, 65, pp.112-120
resume
We have investigated the effect of cultivation systems and fruit post-harvest management on the antioxidant properties of apricot fruits. Trees of five cultivars ‘Tyrinthos’, ‘Cafona’, ‘Bella d’Italia’, ‘Vitillo’ and ‘Pellecchiella’ were cultivated under integrated and organic systems. Fruits were collected at full maturity stage and analyzed either immediately or after storage at 4±0.5 °C and 85% of relative humidity for seven and 14 days. The main pomological traits (weight, colour, flesh firmness, total soluble sugars, titratable acidity) and antioxidant properties were analyzed. The total antioxidant capacity (TAC by TEAC method), total phenols content (TP by Folin-Ciocalteu method) and carotenoid content by HPLC-DAD were monitored. Cultivar characterization by principal component analysis (PCA) indicated a large variability on pomological and antioxidant properties of apricot fruits. ‘Bella d’Italia’ showed better TAC and TP values compared to the other cultivars. ANOVA interactions between cultivar and cultivation system (organic/integrated) were found for the antioxidant properties. These interactions may help to select a set of genotypes with better performances under organic system, which in our study might be indicated in ‘Cafona’ and ‘Bella d’Italia’
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Virtual profiling: a new way to analyse phenotypes
auteur
Michel M. Génard, Nadia Bertin, Hélène Gautier, Francoise F. Lescourret, Bénédicte Quilot
article
The Plant Journal, 2010, 62 (2), pp.344-355. ⟨10.1111/j.1365-313X.2010.04152.x⟩
resume
Simulation models can be used to perform virtual profiling in order to analyse eco-physiological processes controlling plant phenotype. To illustrate this, an eco-physiological model has been used to compare and contrast the status of a virtual fruit system under two situations of carbon supply. The model simulates fruit growth, accumulation of sugar, citric acid and water, transpiration, respiration and ethylene emission, and was successfully tested on peach (Prunus persica L. Batsch) for two leaf-to-fruit ratios (6 and 18 leaves per fruit). The development stage and the variation in leaf number had large effects of the fruit model variables dealing with growth, metabolism and fruit quality. A sensitivity analysis showed that changing a single parameter value, which could correspond to a genotypic change induced by a mutation, either strongly affects most of the processes, or affects a specific process or none. Correlation analysis showed that, in a complex system such as fruit, the intensity of many physiological processes and quality traits co-varies. It also showed unexpected co-variations resulting from emergent properties of the system. This virtual profiling approach opens a new route to explore the impact of mutations, or naturally occurring genetic variations, under differing environmental conditions.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Volatile organic compound emissions induced by the aphid Myzus persicae differ among resistant and susceptible peach cultivars and a wild relative
auteur
Michael Staudt, Benjamin Jackson, Hanane El Aouni, Bruno Buatois, Jean Philippe Lacroze, Jean-Luc Poessel, Marie-Hélène Sauge
article
Tree Physiology, 2010, 30 (10), pp.1320-1334. ⟨10.1093/treephys/tpq072⟩
resume
Little is known on aphid-induced emissions of volatile organic compounds (VOCs) from trees and particularly on their intraspecific variability in association with resistance traits. We compared VOC emissions from five peach cultivars (Prunus persica (L.) Batsch) and a wild relative (Prunus davidiana (Carrière) Franch) that differ in their level (susceptible/resistant) and type (antixenosis, antibiosis) of resistance to the green peach aphid, Myzus persicae (Sulzer). Additionally, the kinetics of VOC induction in response to aphids was compared with that by mechanical wounding. Qualitative and overall quantitative differences among peach genotypes were found in VOC emissions that were mainly composed of methyl-salicylate, farnesenes, (E)-β-ocimene and (E)-4,8-dimethyl-1,3,7-nonatriene. Irrespective of the type of resistance, all resistant genotypes had increased VOC emissions upon aphid attack, while in susceptible genotypes emissions remained low. Emission increases were highest in the genotypes that express increased aphid resistance during second infestations, which had also the highest proportions of methyl-salicylate in their emissions. VOC induction by aphids proceeded slowly with a delay of several hours. Artificial wounding of leaves did not result in emissions of aphid-induced VOCs but caused an immediate burst of green leaf volatiles and benzaldehyde. We conclude that VOC induction in resistant peach cultivars is part of a general defence syndrome that is being avoided or suppressed by M. persicae in the susceptible genotypes. The induction likely involves an aphid-specific elicitor and (methyl)-salicylate in the subsequent signalling and regulation processes that should include gene activation due to the marked delay in the emission response. The results are compared with those of the literature and discussed in view of their ecological and environmental significance
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Mapping and validation of QTLs for resistance to aphids and whiteflies in melon
auteur
Nathalie Boissot, Sophie Thomas, Nicolas Sauvion, Cécile Marchal, Claude Pavis, Catherine Dogimont
article
TAG Theoretical and Applied Genetics, 2010, 121 (1), pp.9-20. ⟨10.1007/s00122-010-1287-8⟩
resume
Aphis gossypii and Bemisia tabaci are severe hemipteran pests of melon crops and breeding for resistance to both insects is required to reduce pesticide use. Resistance was evaluated for its effect on behaviour and biotic potential of both hemipterans in a population of recombinant inbred lines (RILs) derived from the cross Védrantais x PI 161375. Insect variability was considered using two A. gossypii clones and two B. tabaci populations. Two additive QTLs affected the whiteflies. Four additive QTLs and two couples of epistatic QTLs affected the aphids. Amongst them, a major QTL affects both behaviour and biotic potential of A. gossypii and therefore a same R gene induces both antixenosis and antibiosis. This major QTL colocalizes with the Vat gene belonging to the NBS-LRR gene family. No loci affected both aphids and whiteflies contrary to what was observed for the Mi1.2 gene, a NBSLRR gene in tomato. Original populations with different allelic compositions at QTLs affecting A. gossypii were built by one inter-crossing of RILs used for the mapping process. The genetic background was shown homogeneous between these populations what allowed validating QTLs and investigating the effect of allelic combinations at QTLs. Effects of QTLs were stronger than expected and some QTLs had a wider spectrum than expected. This strategy of validation appeared rapid and low cost.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01927472/file/2010_Boissot_Theoretical%20and%20Applied%20Genetics%20%28Postprint%29_2 BibTex
titre
Grafting versus seed propagated apricot populations: two main gene pools in Tunisia evidenced by SSR markers and model-based Bayesian clustering
auteur
Hedia Bourguiba, Bouchaib Khadari, Lamia Krichen, Neila Trifi-Farah, Sylvain Santoni, Jean Marc Audergon
article
Genetica, 2010, 138 (9-10), pp.1023-1032. ⟨10.1007/s10709-010-9488-2⟩
resume
Apricot was introduced into the Mediterranean Basin from China and Asian mountains through the Middle-East and the Central Europe. Traditionally present in Tunisia, we were interested in accessing the origin of apricot species in the country, and in particular in the number and the location of its introductions. A set of 82 representative apricot accessions including 49 grafted cultivars and 33 seed propagated ‘Bargougs’ were genotyped using 24 microsatellite loci revealing a total of 135 alleles. The model-based Bayesian clustering analysis using both Structure and InStruct programs as well as the multivariate method revealed five distinct genetic clusters. The genetic differentiation among clusters showed that cluster 1, with only four cultivars, was the most differentiated from the four remaining genetic clusters, which constituted the largest part of the studied germplasm. According to their geographic origin, the five identified groups (north, centre, south, Gafsa oasis and other oases groups) enclosed a similar variation within group, with a low level of differentiation. Overall results highlighted the distinction of two apricot gene pools in Tunisia related to the different mode of propagation of the cultivars: grafted and seed propagated apricot, which enclosed a narrow genetic basis. Our findings support the assumption that grafting and seed propagated apricots shared the same origin.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01250497/file/Bourguiba-Genetica-2010-OA_%7BA26FBBBC-BC5C-49A5-9674-247A897EBD59%7D.pdf BibTex
titre
La tomate, les défis du goût (Dossier)
auteur
Géraud Chabriat, Magali Sarazin, Mathilde M. Causse
article
INRA Magazine, 2010, 13, pp.1-12
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02656158/file/33950_20100823115238478_1.pdf BibTex
titre
Horticulture and health in the Middle Ages: Images from the Tacuinum Sanitatis
auteur
Jules Janick, M-Christin Daunay, Harry Paris
article
HortScience, 2010, 45 (11), pp.1592-1596
resume
Lavishly illustrated late 14th century manuscripts known as the Tacuinum Sanitatis, a guide for healthy living, were based on an 11th century Arabic manuscript known as the Taqwim al-Sihha bi al-Ashab al-Sitta (Rectifying Health by Six Causes) written by the physician and philosopher Ibn Butlan (d. 1063). The expensive, illustrated Tacuinum Sanitatis tomes portray a utopian feudal society in which nobles are engaged in play and romance while feudal laborers work the estate. Rich in horticultural imagery, they include vivid scenes of the harvest of vegetables, fruits, flowers, and culinary and medicinal herbs. Each scene is accompanied by a brief summary of the health aspects of the subject. Although medieval medicine was based on ancient philosophical concepts of Greek sciences, particularly Hippocrates and Galen, these documents connect vegetables and fruits with human health and well-being, similar to modern medicine. Hence, the present-day focus on the connection between horticulture and health can be seen as an extension of ancient and medieval regimens for a healthy lifestyle
typdoc
Journal articles
Accès au bibtex
BibTex
titre
An induced mutation in tomato eIF4E leads to immunity to two potyviruses
auteur
Florence Piron, Maryse Nicolaï, Silvia Minoia, Elodie Piednoir, André Moretti, Aurélie Salgues, Dani Zamir, Carole Caranta, Abdelhafid A. Bendahmane
article
PLoS ONE, 2010, 5 (6), pp.e11313. ⟨10.1371/journal.pone.0011313⟩
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02658059/file/2010_Piron_Plosone_1.pdf BibTex
titre
Fluctuations in sugar content are not determinant in explaining variations in vitamin C in tomato fruit
auteur
Capucine Massot, Michel M. Génard, Rebecca Stevens, Hélène Gautier
article
Plant Physiology and Biochemistry, 2010, 48 (9), pp.751-757. ⟨10.1016/j.plaphy.2010.06.001⟩
resume
The present study aimed to clarify the relationship between sugars and vitamin C in fruit. The objective was to determine whether vitamin C content was regulated by sugar content due to the role of sugar as a precursor for vitamin C. During summer, maximal content in sugar and vitamin C were found in both genotypes tested Solanum lycopersicon ‘Cervil’ and ‘Levovil’. During autumn, fruit pruning increased fruit size and hexose content but fruit vitamin C content did not increase. Therefore sugar substrate was not limiting for vitamin C synthesis during autumn. We demonstrated for two cultivars, ‘Cervil’ and ‘Levovil’, with different sugar accumulation profiles during ripening, that sugar content was not determinant in the regulation of vitamin C content. The strong correlation observed between sugars and vitamin C in ‘Cervil’ was due to their concomitant increase during fruit ripening
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02667885/file/38552_20100915104837272_1.pdf BibTex
titre
Rouge de plaisir
auteur
Jean Luc Toula-Breysse, Mathilde M. Causse
article
Le Monde, 2010, 20328, p 45
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Response of the fruit antioxydant system to the post-chilling period in two different tomato lines
auteur
Noé Gest, David Page, Simona Birtic, Barbara Gouble, Louise Gilbert, Cecile Garchery, Mathilde M. Causse, Rebecca Stevens
article
Functional Plant Science and Biotechnology, 2010, 4 (1), pp.76-83
resume
Antioxidant systems play an important role in prevention of chilling injury, and chilling-tolerant fruit may initially contain more antioxidants or be able to maintain their antioxidant levels during stress. Tomato fruit are chilling sensitive and chilling symptoms generally appear after fruit are transferred to non chilling temperatures. The aim of this study was to characterise the events occurring at 20°C, immediately after a storage period at 4°C, and to establish the importance of tomato fruit ascorbic acid levels in the response to chilling. Two different tomato lines were used: a processing cultivar (M82) with low to average ascorbic acid levels and an introgression line (IL9.2.5) containing elevated ascorbic acid levels due to the introgression of wild Solanum pennellii alleles on chromosome 9. We show a rapid response (0.5 hours) of the antioxidant system in tomato to re-exposure to normal temperatures and light following chilling. The ascorbate redox state undergoes rapid changes and is followed by changes in the redox state of the glutathione pool. The response is different in the two tomato lines studied: fruits from IL9.2.5 have a higher ascorbic acid and glutathione redox state compared to the parent M82 where the pool of both antioxidants becomes oxidised. The redox state of the ascorbate pool is correlated with the activity of enzymes involved in ascorbate regeneration (monodehydroascorbate reductase and dehydroascorbate reductase) in the fruit. Furthermore the ability of IL9.2.5 to maintain reduced antioxidant levels is correlated with a decreased loss of fruit firmness when compared to M82.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02654203/file/Gest.N._FPSB_4%28SI1%2976-83o%282%29_1.pdf BibTex
titre
Impact of mapped SSR markers on the genetic diversity of apricot (Prunus armeniaca L.) in Tunisia
auteur
Hedia Bourguiba, Lamia Kirchen, Jean Marc Audergon, Bouchaib Khadari, Neïla Trifi-Farah
article
Plant Molecular Biology Reporter, 2010, 28, pp.578-587. ⟨10.1007/s11105-010-0189-x⟩
resume
The impact of mapped microsatellites on the study of genetic diversity of Tunisian apricot accessions was assessed. The genetic variability of 47 traditional apricot cultivars originating from several areas in Tunisia was investigated with 32 polymorphic microsatellite loci selected for their location throughout the eight linkage groups of Prunus genome. The higher polymorphism and greater transportability of these markers among Prunus species were proved by the expected heterozygosity (He=0.56) and Shannon’s index of diversity (I=1.05), indicating that Tunisian apricot germplasm maintained a substantial level of genetic diversity. According to their geographical origin, the genetic differentiation among groups (north, center, and south; Fst=0.04) was lower, while the gene flow among groups was consequent (Nm=4.79), attesting a narrow genetic background of apricot in the country. Both unweighted pair-group method with arithmetic mean dendrogram, based on Nei’s genetic distances and factorial correspondence analysis, separated northern cultivars from central and southern cultivars, revealing the same molecular basis of apricot material in the Center and the South of Tunisia. These results revealed the efficiency of mapped markers for genetic variability measurements compared to randomly ones, however, no advantage was observed considering the genetic relationships among studied accessions.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Development and mapping of peach candidate genes involved in fruit quality and their transferability and potential use in other Rosaceae species
auteur
Loick Le Dantec, Gaëlle Cardinet, Julio Bonet, Mathieu Fouché, Karima Boudehri, Amparo Monfort, Jean-Luc Poessel, Annick Moing, Elisabeth Dirlewanger
article
Tree Genetics and Genomes, 2010, 6 (6), pp.995-1012. ⟨10.1007/s11295-010-0308-8⟩
resume
The goal of the present study was to identify candidate genes (CGs) involved in fruit quality in peach that can be transferred to other Rosaceae species. Two cDNA libraries from fruit of the “Fantasia” peach cultivar, constructed at two stages of development, were used to generate a set of expressed sequence tag sequences. A total of 1,730 peach unigenes were obtained after clustering. Sequences and corresponding annotations were stored in a relational database and are available through a web interface. Fifty-nine CGs involved in fruit growth and development or fruit quality at maturity, focusing on sweetness, acidity, and phenolic compound content, were selected according to their annotation. Fifty-five primer pairs, designed from peach CG sequences and giving PCR products in peach, were tested in strawberry and 36 gave amplified products. Eight CGs were mapped in peach, 14 in strawberry, four in both species and confirmed the pattern of synteny already proposed using comparative mapping. In peach, the CGs are located in three linkage groups (3, 5, 7), and in strawberry they are distributed in all seven Fragaria linkage groups. Colocalization between some of these CGs and quantitative trait loci for fruit quality traits were identified and are awaiting confirmation in further analyses.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Comparative analysis of genetic diversity in Tunisian apricot germplasm using AFLP and SSR markers
auteur
Lamia Krichen, Hedia Bourguiba, Jean Marc Audergon, Neïla Trifi-Farah
article
Scientia Horticulturae, 2010, 127 (1), pp.54-63. ⟨10.1016/j.scienta.2010.09.012⟩
resume
Eighty-one accessions representing apricot germplasm in Tunisia were collected from different areas of cultivation and fingerprinted using amplified fragment length polymorphism (AFLP) and microsatellites (SSR) markers. A total of 339 polymorphic markers were revealed using 5 AFLP primers combinations and 24 SSR loci. AFLP and SSR markers expressed a high level of polymorphism allowing the distinction of the accessions with an efficiency coefficient of discrimination of 100% for AFLP and 97% for SSR markers. Genetic diversity structure was assessed with AFLPs and SSRs markers separately then with combined matrix data by the help of hierarchical clustering elaborated using Wards method based on Nei and Li (1979) distances. Comparison of the obtained dendrograms revealed a phylogeographic structure into two major groups with significant conservation between the observed subgroups in relation with the geographic origin of the accessions. The relative efficiency of the markers in determining the genetic relationships among apricot accessions has been assessed and a combination of AFLPs and SSRs markers was the most effective. In addition, Mantel test based on genetic distances indicated highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with Pearson correlation values of r = 0.873 and r = 0.692, respectively, revealing the higher efficiency of the combination of both molecular techniques (AFLP and SSR) to estimate the levels of genetic variability among apricot germplasm.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Prunus microsatellite marker transferability across rosaceous crops
auteur
Mourad Mnejja, Jordi Garcias-Mas, Jean Marc Audergon, Pere Arus
article
Tree Genetics and Genomes, 2010, 6 (5), pp.689-700. ⟨10.1007/s11295-010-0284-z⟩
resume
A total of 145 microsatellite primer pairs from Prunus DNA sequences were studied for transferability in a set of eight cultivars from nine rosaceous species (almond, peach, apricot, Japanese plum, European plum, cherry, apple, pear, and strawberry), 25 each of almond genomic, peach genomic, peach expressed sequence tags (EST), and Japanese plum genomic, 22 of almond EST, and 23 of apricot (13 EST and 10 genomic), all known to produce single-locus and polymorphic simple-sequence repeats in the species where they were developed. Most primer pairs 83.6%) amplified bands of the expected size range in other Prunus. Transferability, i.e., the proportion of microsatellites that amplified and were polymorphic, was also high in Prunus (63.9%). Almond and Japanese plum were the most variable among the diploid species (all but the hexaploid European plum) and peach the least polymorphic. Thirty-one microsatellites amplified and were polymorphic in all Prunus species studied, 12 of which, covering its whole genome, are proposed as the “universal Prunus set”. In contrast, only 16.3% were transferable in species of other Rosaceae genera (apple, pear, and strawberry). Polymorphic Prunus microsatellites also detected lower levels of variability in the non-congeneric species. No significant differences were detected in transferability and the ability to detect variability between microsatellites of EST and genomic origin.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Production de souches monospores d’un oomycète, parasite obligatoire, Bremia lactucae Regel
auteur
Loic Jean, Brigitte B. Maisonneuve
article
Cahier des Techniques de l'INRA, 2010, 69, pp.29-34
resume
Pour disposer de souches pures de Bremia, nous avons adapté au mildiou de la laitue une méthode d’obtention de souches monospores. Des prélèvements de spores isolées sont effectués avec un cil sous loupe binoculaire ; ces spores sont cultivées sur cotylédons détachés en atmosphère humide. Après 8 à 12 jours de culture, une sporulation apparaît sur certains cotylédons. Ces cotylédons sont isolés, les spores obtenues sont inoculées à des plantules afin d’obtenir une souche monospore. Cette méthode est utilisée avec succès au laboratoire avec deux objectifs : obtenir une souche monospore à partir de vingt cotylédons inoculés par des spores isolées, et isoler plusieurs souches à partir d’un isolat correspondant à un mélange de souches.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02661026/file/37948_20100701082657019_1.pdf BibTex
titre
Sensory quality of fresh french and dutch market tomatoes: a preference mapping study with italian consumers
auteur
Fiorella Sinesio, Maria Cammareri, Elisabetta Moneta, Brigitte Navez, Marina Peparaio, Mathilde M. Causse, Silvana Grandillo
article
Journal of Food Science, 2010, 75 (1), pp.S55-S67. ⟨10.1111/j.1750-3841.2009.01424.x⟩
resume
Sensory properties are important elements to evaluate the qualities of vegetable products and are also determinant factors in purchasing decision. Here we report the Italian results of a preference mapping study conducted within a larger European project with the aim of describing the preferences of European consumers in regard to the diversity of traditional and modern tomato varieties, available on the market. This study has allowed the assessment of fruit quality at 3 levels: objective description of sensory properties, consumer preference tests, and physicochemical measurements. A set of 16 tomato cultivars, with different fruit sizes and shapes, was described and classified according to 18 sensory attributes including flavor, appearance, and texture characteristics. The same cultivars were evaluated by 179 consumers in a “preference mapping” experiment with the goal of identifying the preferred varieties and the reasons for the choice. The consumer data are referred to hedonic ratings (aspect liking and overall liking), familiarity for the analyzed cultivars, and individual features collected by a questionnaire. A hierarchical analysis of the clusters allowed to distinguish, within the sampled Italian consumers, 4 segments with different preferences which represented 19%, 25%, 41%, and 15% of the population, respectively. A partial least square regression model allowed the identification of the sensory attributes that best described consumer cluster preferences for tomato cultivars. Both texture and flavor descriptors were important drivers of consumer preferences, but the relevance (predictive value) of individual descriptors to model tomato liking was different for each consumer segment. Information on demographic and behavioral characteristics, usage habits, and factors relevant for purchasing were also provided on the 4 groups of consumers.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Protective proteins are differentially expressed in tomato genotypes differing for their tolerance to low-temperature storage
auteur
David Page, Barbara Gouble, Benoit B. Valot, Jean-Paul Bouchet, Caroline Callot, Andre Kretzschmar, Mathilde M. Causse, Catherine M.G.C. Renard, Mireille Faurobert
article
Planta, 2010, 232 (2), pp.483-500. ⟨10.1007/s00425-010-1184-z⟩
resume
When stored at low temperature, tomato fruits exhibit chilling-injury symptoms such as rubbery texture and irregular ripening. In order to identify proteins related to chilling tolerance, we compared two tomato near isogenic lines differing for their texture phenotype at harvest in a fruit-storage trial including two temperatures (4 and 20°C) along several days of conservation. Fruit evolution was followed by assessing fruit color, ethylene emission and texture parameters. The most contrasted samples were submitted to proteomic analysis including two-dimensional electrophoresis and mass spectrometry of protein spots in order to identify the proteins whose expression varied according to the genotype or the storage conditions. Unexpectedly the most firm genotype at harvest, was the most sensitive to cold storage. The other genotype exhibited a delay in fruit firmness loss leading to the texture differences observed after 20 days of 4°C storage. The proteome analysis of these contrasted fruit identified 85 proteins whose quantities varied with temperature or genotype. As expected, cold storage decreased expression of proteins related to maturation process such as acidic invertase, possilby controlled post-translational regulation of polygalacturonase, and up-regulated proteins related to freezing tolerance. But the study point out proteins involved in the differential resistance to chilling conditions of the two lines. This include specific isoforms among the large family of small heat shocked proteins (sHSP), and a ste of proteins involved in the defense against of the reticulum endoplasmic stress.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Le projet QualiTomFil Trois ans de recherche pour la filière
auteur
Brigitte Navez, Mathilde M. Causse
article
Infos CTIFL, 2010, 258, pp.30-33
resume
Le projet QualiTomFil a été retenu en 2006 dans le cadre de l'appel à projet ANR PNRA, "Programme national de recherche en alimentation et nutrition humaine". Il est arrivé à son terme en 2009. Le projet Qualitomfil a regroupé neuf équipes de recherche et des entreprises autour de travaux contribuant à la compréhension des mécanismes impliqués dans l'élaboration de la qualité de la tomate et dans sa valorisation pour répondre au mieux aux demandes des consommateurs. L'article présente les travaux engagés autour de cinq axes de recherche: attentes du consommateur, impact des signaux de qualité, analyse de la qualité organoleptique, conditions de culture, prototypes variétaux. Les résultats font l'objet de publications scientifiques ou dans la presse professionnelle. Co-organisée par le Ctifl et l'lnra, une journée de restitution sera par ailleurs prévue sous forme de rencontre technique (le 4 février 2010
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La tomate un fruit d'été
auteur
Pascale Mosnier, Mathilde M. Causse
article
Cuisine et Vins de France, 2010, 134, pp.112
typdoc
Journal articles
Accès au bibtex
BibTex
titre
You say tomato and I say potato
auteur
René Klein Lankhorst, Mathilde M. Causse, Christian Bachem, . International Innovation Food
article
International Innovation, 2010, May, pp.19-21
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Les bases génétiques de la composition biochimique et des qualités organoleptiques de la tomate
auteur
Mathilde M. Causse
article
Innovations Agronomiques, 2010, 9, pp.59-66. ⟨10.17180/nvw9-x112⟩
resume
In order to help breeders in their attempt at improving organoleptic quality of fresh market tomato, a QTL mapping experiment was performed, followed by marker-assisted breeding. The detection of QTLs controlling the variation of several fruit quality traits was performed in the progeny of a cross between a cherry tomato chosen for its good flavour and a line with bigger but less tasty fruits. The lines were evaluated for physical, chemical and sensorial traits. A marker-assisted selection scheme was then set up to transfer into elite lines the chromosome regions carrying the most important QTLs for fruit quality. A backcross scheme was optimised taking into account both theoretical aspects and practical constraints. Three recurrent lines were chosen in order to study the effect of genetic background on QTL expression. After three backcrosses and two selfing generations, lines carrying one to five introgressed regions were selected and evaluated. About half of the QTLs appeared to be stable over genetic backgrounds and generations. A positive improvement of quality components was observed, but fruit weight could not be recovered as expected. Several interactions among QTLs were shown, which limit the possible progress.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02665417/file/35647_20101124082212872_1.pdf BibTex
titre
Consumer Preferences for Fresh Tomato at the European Scale: A Common Segmentation on Taste and Firmness
auteur
Mathilde M. Causse, Chloé Friguet, Clément Coiret, Mélanie Lépicier, Brigitte Navez, Monica Lee, Nancy Holthuysen, Fiorella Sinesio, Elisabetta Moneta, Silvana Grandillo
article
Journal of Food Science, 2010, 75 (9), pp.S531-S541. ⟨10.1111/j.1750-3841.2010.01841.x⟩
resume
Although tomato flavor has not been a major goal for breeders, nowadays it becomes important as it is a subject of consumer complaint. A better knowledge of tomato consumer preferences, at the European level, should provide the basis for improvement of fruit quality and for market segmentation. In the framework of a large European project, 806 consumers from 3 countries, The Netherlands, France, and Italy, were presented with a set of 16 varieties representing the diversity of fresh tomato offer in order to evaluate their preferences. In parallel, sensory profiles were constructed by expert panels in each country. Preference maps were then constructed in each country revealing the structure of consumer preferences and allowing identification of the most important characteristics. Then a global analysis revealed that preferences were quite homogeneous across countries. This study identified the overall flavor and firmness as the most important traits for improving tomato fruit quality. It showed that consumer preferences from different European countries, with different cultures and food practices, are segmented following similar patterns when projected onto a common referential plan. Moreover, the results clearly showed that diversification of taste and texture is required to satisfy all consumers' expectations as some consumers preferred firm tomatoes, while others preferred melting ones and were more or less demanding in terms of sweetness and flavor intensity. Detailed comparisons also showed the importance of the fruit appearance in consumer preference. Practical Application: The consumer preferences for fresh market tomato were studied in 3 European countries. The main descriptors for further breeding for consumer satisfaction were identified. Four clusters of consumers were identified in the overall analysis, the 3 countries contributing the same way to each cluster. The impact of appearance in the preferences was also underlined.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-00910339/file/Causse_prefMap_3_countries_preprint.pdf BibTex
titre
Host plant resistance to aphids in cultivated crops: Genetic and molecular bases, and interactions with aphid populations
auteur
Catherine Dogimont, Abdelhafid A. Bendahmane, Veronique Chovelon, Nathalie Boissot
article
Comptes Rendus. Biologies, 2010, 333 (6-7), pp.566-573
resume
Host plant resistance is an efficient and environmentally friendly means of controlling insects, including aphids, but resistant-breaking biotypes have occurred in several plant–aphid systems. Our review of the genetic and molecular bases of aphid resistance in crop species emphasizes the limited number of aphid resistance genes and alleles. Inheritance of aphid resistance may be monogenic (dominant or recessive genes) or polygenic. Two dominant, aphid resistance genes have been isolated to date. They both encode NBS-LRR proteins involved in the specific recognition of aphids. Strategies to ensure aphid resistance effectiveness and durability are discussed. Innovative research activities are proposed.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing
auteur
Paul Arens, Carmen Mansilla, Daniël Deinum, Laetitia Cavellini, André Moretti, Sophie Rolland, Hanneke van Der Schoot, David Calvache, Fernando Ponz, Cecile C. Collonnier, Rene Mathis, Diederick Smilde, Carole Caranta, Ben Vosman
article
TAG Theoretical and Applied Genetics, 2010, 120 (3), pp.655-664. ⟨10.1007/s00122-009-1183-2⟩
resume
Abstract Molecular markers linked to phenotypically important traits are of great interest especially when traits are diYcult and/or costly to be observed. In tomato where a strong focus on resistance breeding has led to the introgression of several resistance genes, resistance traits have become important characteristics in distinctness, uniformity and stability (DUS) testing for Plant Breeders Rights (PBR) applications. Evaluation of disease traits in biological assays is not always straightforward because assays are often inXuenced by environmental factors, and diYculties in scoring exist. In this study, we describe the development and/or evaluation of molecular marker assays for the Verticillium genes Ve1 and Ve2, the tomato mosaic virus Tm1 (linked marker), the tomato mosaic virus Tm2 and Tm22 genes, the Meloidogyne incognita Mi1-2 gene, the Fusarium I (linked marker) and I2 loci, which are obligatory traits in PBR testing. The marker assays were evaluated for their robustness in a ring test and then evaluated in a set of varieties. Although in general, results between biological assays and marker assays gave highly correlated results, marker assays showed an advantage over biological tests in that the results were clearer, i.e., homozygote/heterozygote presence of the resistance gene can be detected and heterogeneity in seed lots can be identiWed readily. Within the UPOV framework for granting of PBR, the markers have the potential to fulWl the requirements needed for implementation in DUS testing of candidate varieties and could complement or may be an alternative to the pathogenesis tests that are carried out at present.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02664660/file/2010_Arens_Theoretical%20and%20Applied%20Genetics_1 BibTex
titre
Reaction of an F1 apricot hybrid population to artificial and natural inoculation of Plum pox virus
auteur
I. Karayiannis, T. Tomidis, Z. Michailides, Jean Marc Audergon
article
New Zealand Journal of Crop and Horticultural Science, 2010, 38 (4), pp.283-288. ⟨10.1080/01140671.2010.524147⟩
resume
The reaction to plum pox virus (PPV) inoculation is investigated in 163 F1 hybrids ‘Polonais’ x ‘Stark Early Orange’, susceptible and resistant to ‘Sharka’ disease, respectively. The hybrids are inoculated with PPV by grafting and planting in the field where the disease is endemic. Visual symptoms of ‘Sharka’ on the leaves of the hybrids are recorded eight months post-inoculation as well as in the second and fourth year. Mild disease symptoms are recorded in almost all hybrids in the first year. The ratio of hybrids presenting symptoms versus those not presenting is 9:1. This ratio changes to 1:1 in the second year and remains stable in the fourth year. The ELISA test applied to the leaves of the asymptomatic hybrids is negative, confirming the monogenic control of resistance to PPV conferred by cv. ‘Stark Early Orange’. The phenomenon of ‘recovery’ from infection accounts for the reduction in infection levels after the first year
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Nitrogen fertilization effects on Myzus persicae aphid dynamics on peach: vegetative growth allocation or chemical defence?
auteur
Marie-Hélène Sauge, Isabelle Grechi, Jean-Luc Poessel
article
Entomologia Experimentalis et Applicata, 2010, 136 (2), pp.123-133
resume
Plant nitrogen (N) fertilization is a common cropping practice that is expected to serve as a pest management tool. Its effects on the dynamics of the aphid Myzus persicae (Sulzer) (Hemiptera: Aphididae) were examined on young peach [Prunus persica (L.) Batsch (Rosaceae)] trees grown under five N treatments, ranging from N shortage to supra-optimal supply for growth. Aphid population increased over time at the three intermediate N levels. It remained stable at the lowest N level and decreased at the highest N level. Four weeks after the start of infestation, the number of aphids displayed a parabolic response to N level. The relationships between N status and parameters of plant vegetative growth (stem diameter) or biomass allocation (lateral-total leaf area and root-shoot ratio) were consistent with responses proposed by models of adaptive plasticity in resource allocation patterns. However, the variation in plant growth predicted aphid population dynamics only partially. Whereas aphid number was positively correlated with plant N status and vegetative growth up to the intermediate N level, it was negatively correlated with plant N status above this level, but not with vegetative growth. The concentrations of primary and secondary (plant defence-related) metabolites in the plant shoots weremodified by Ntreatments: amino acids (main nutritional resource of aphids) and prunasin increased, whereas chlorogenic acid decreased with increasing N availability. Constitutive changes in plant chemistry in response to N fertilization could not directly explain the reduced aphid performance for the highest N level. Nevertheless, the indirect effect of N on the induction of plant defence compounds by aphid feeding warrants further investigation. The study focuses on the feasibility of handling N fertilization to control M. persicae in orchards, but findingsmay also be relevant for our understanding of the physiological relationships between the host’s nutritional status and the requirements of the insect.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Apricot genetic resource management. New prospects offered by phylo-geographic and association genetic approaches. Application in the mediterranean basin germplasm
auteur
Hedia Bourguiba, Lamia Krichen, Neïla Trifi-Farah, Bouchaib Khadari, Sylvain S. Santoni, Jean Marc Audergon
article
Acta Horticulturae, 2010, 862, pp.167-172
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Powdery mildew resistance in the peach cultivar Pamirskij 5 is genetically linked with the Gr gene for leaf color
auteur
Thierry Pascal, Georges Pfeiffer, Jocelyne Kervella
article
HortScience, 2010, 45 (1), pp.150-152
resume
Peach powdery mildew (Podosphaera pannosa var. persicae) is a major disease of peach trees [Prunus persica (L.) Batsch]. Various studies on powdery mildew resistance have been conducted in peach. The present study was initiated to determine the inheritance of powdery mildew resistance found in the green leaf peach rootstock ‘Pamirskij 5’. Crosses were carried out between ‘Pamirskij 5’ and the susceptible red leaf peach rootstock ‘Rubira’®. Segregation analysis performed in F1 (1:0), F2 (3:1), and test cross (1:1) progenies indicated single dominant gene control of peach powdery mildew resistance in ‘Pamirskij 5’. Cosegregation analysis provided clear evidence that the loci for powdery mildew resistance and the leaf color trait are very closely linked in ‘Pamirskij 5’. The estimated distance between these loci was 0 ± 3.26 cM for the F2 and 0 ± 0.00 cM for the test cross populations.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Ajuster la qualité de la tomate aux attentes des consommateurs
auteur
Mathilde M. Causse, . Végétable Echo Edition
article
Végétable : l'écho de la planète fruits et légumes, 2010, 268, p 21
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The influence of fruit load on the tomato pericarp metabolome in a Solanum chmielewskii introgression line population
auteur
Phuc Thi Do, Marion Prudent, Ronan Sulpice, Mathilde M. Causse, Alisdair R. Fernie
article
Plant Physiology, 2010, 154 (3), pp.1128-1142
resume
It has been recently demonstrated, utilizing interspecific introgression lines of tomato, generated from the cross between Solanum lycopersicum and the wild species Solanum pennellii, that the efficiency of photosynthate partitioning exerts a considerable influence on the metabolic composition of tomato fruit pericarp. In order to further evaluate the influence of source-sink interaction, metabolite composition was determined by gas chromatography-mass spectrometry in a different population. For this purpose, we used 23 introgression lines resulting from an interspecific cross between S. lycopersicum and the wild species Solanum chmielewskii under high (unpruned trusses) and low (trusses pruned to one fruit) fruit load conditions. Following this strategy, we were able to contrast the metabolite composition of fruits from plants cultivated at both fruit loads as well as to compare the network behavior of primary metabolism in the introgression line population. The study revealed that while a greater number of metabolic quantitative trait loci were observed under high fruit load (240) than under low fruit load (128) cultivations, the levels of metabolites were more highly correlated under low fruit load cultivation. Finally, an analysis of genotype x fruit load interactions indicated a greater influence of development and cultivation than genotype on fruit composition. Comparison with previously documented transcript profiles from a subset of these lines revealed that changes in metabolite levels did not correlate with changes in the levels of genes associated with their metabolism. These findings are discussed in the context of our current understanding of the genetic and environmental influence on metabolic source-sink interactions in tomato, with particular emphasis given to fruit amino acid content.
typdoc
Journal articles
Accès au bibtex
BibTex

2009

Journal articles

titre
An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato
auteur
Virginie Garcia, Rebecca Stevens, Laurent Gil, Louise Gilbert, Noé Gest, Johann Petit, Mireille Faurobert, Mickael Maucourt, Catherine Deborde, Annick Moing, Jean-Luc Poessel, Daniel Jacob, Jean-Paul Bouchet, Jean-Luc Giraudel, Barbara Gouble, David Page, Moftah Alhagdow, Capucine Massot, Hélène Gautier, Martine Lemaire-Chamley, Antoine de Daruvar, Dominique Rolin, Bjoern Usadel, Marc Lahaye, Mathilde Causse, Pierre Baldet, Christophe Rothan
article
Comptes Rendus. Biologies, 2009, 332, pp.1007 - 1021. ⟨10.1016/j.crvi.2009.09.013⟩
resume
Very few reports have studied the interactions between ascorbate and fruit metabolism. In order to get insights into the complex relationships between ascorbate biosynthesis/recycling and other metabolic pathways in the fruit, we undertook a fruit systems biology approach. To this end, we have produced tomato transgenic lines altered in ascorbate content and redox ratio by RNAitargeting several key enzymes involved in ascorbate biosynthesis (2 enzymes) and recycling (2 enzymes). In the VTC (ViTamin C) Fruit project, we then generated phenotypic and genomic (transcriptome, proteome, metabolome) data from wild type and mutant tomato fruit at two stages of fruit development, and developed or implemented statistical and bioinformatic tools as a web application (named VTC Tool box) necessary to store, analyse and integrate experimental data in tomato. By using Kohonen's self-organizing maps (SOMs) to cluster the biological data, pair-wise Pearson correlation analyses and simultaneous visualization
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A transposon-induced epigenetic change leads to sex determination in melon
auteur
Antoine Martin, Christelle Troadec, Adnane Boualem, Mazen Rajab, Ronan Fernandez, Halima Morin, Michel Pitrat, Catherine Dogimont, Abdelhafid Bendahmane
article
Nature, 2009, 461, pp.1135-1139. ⟨10.1038/nature08498⟩
resume
Sex determination in plants leads to the development of unisexual flowers from an originally bisexual floral meristem. This mechanism results in the enhancement of outcrossing and promotes genetic variability, the consequences of which are advantageous to the evolution of a species. In melon, sexual forms are controlled by identity of the alleles at the andromonoecious (a) and gynoecious (g) loci. We previously showed that the a gene encodes an ethylene biosynthesis enzyme, mACS-7, that represses stamen development in female flowers. Here we show that the transition from male to female flowers in gynoecious lines results from epigenetic changes in the promoter of a transcription factor, CmWIP1. This natural and heritable epigenetic change resulted from the insertion of a transposon, which is required for initiation and maintenance of the spreading of DNA methylation to the CmWIP1 promoter. Expression of CmWIP1 leads to carpel abortion, resulting in the development of unisexual male flowers. Moreover, we show that CmWIP1 indirectly represses the expression of the andromonoecious gene, CmACS-7, to allow tamen development. Together our data indicate a model in which CmACS-7 and CmWIP1 interact to control the development of male, female and hermaphrodite flowers in melon.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic and physiological analysis of tomato fruit weight and composition: influence of carbon availability on QTL detection
auteur
Marion Prudent, Mathilde M. Causse, Michel Génard, Pasquale Tripodi, Silvana Grandillo, Nadia Bertin
article
Journal of Experimental Botany, 2009, 60 (3), Vol. 60, No. 3, pp. 923-937. ⟨10.1093/jxb/ern338⟩
resume
Throughout tomato domestication, a large increase in fruit size was associated with a loss of dry matter and sugar contents. This study aims to dissect the contributions of genetic variation and the physiological processes underlying the relationships between fruit growth and the accumulation of dry matter and sugars. Fruit quality traits and physiological parameters were measured on 20 introgression lines derived from the introgression of Solanum chmielewskii into S. lycopersicum, under high (HL, unpruned trusses) and low (LL, trusses pruned to one fruit) fruit load conditions. Inter- and intra-genotypic correlations among traits were estimated and quantitative trait loci (QTL) for size, composition, and physiological traits were mapped. LL increased almost all traits, but the response of sugar content was genotype-dependent, involving either dilution effects or differences in carbon allocation to sugars. Genotype3fruit load interactions were significant for most traits and only 30% of the QTL were stable under both fruit loads. Many QTL for fresh weight and cell or seed numbers co-localized. Eleven clusters of QTL for fresh weight and dry matter or sugar content were detected, eight with opposite allele effects and three with negative effects. Two genotypic antagonistic relationships, between fresh weight and dry matter content and between cell number and cell size, were significant only under HL; the second could be interpreted as a competition for carbohydrates among cells. The role of cuticular conductance, fruit transpiration or cracking in the relationship between fruit fresh weight and composition was also emphasized at the genetic and physiological levels.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-00600425/file/Prudentetal_Rev2.pdf BibTex
titre
Allele mining in the pepper gene pool provided new complementation effects between pvr2-eIF4E alleles and pvr6-eIF(iso)4E for resistance to the Pepper veinal mottle virus
auteur
Manuel Rubio, Maryse Nicolaï, Carole Caranta, Alain Palloix
article
Journal of General Virology, 2009, 90 (11), pp.2808-2814. ⟨10.1099/vir.0.013151-0⟩
resume
Molecular cloning of recessive resistance genes to potyviruses in a large range of host species identified the eukaryotic translation initiation factor 4E (eIF4E) as an essential determinant in the outcome of potyvirus infection. Resistance results from a few amino acid changes in the eIF4E protein encoded by the recessive resistance allele that disrupt the direct interaction with the potyviral protein VPg. In plants, several loci encode two protein subfamilies, eIF4E and eIF(iso)4E. While most eIF4E-mediated resistance to potyviruses depends on mutations in a single eIF4E protein, simultaneous mutations in eIF4E (corresponding to the pvr2 locus) and eIF(iso)4E (corresponding to the pvr6 locus) are required to prevent pepper veinal mottle virus (PVMV) infection in pepper. We used this model to look for additional alleles at the pvr2-eIF4E locus that result in resistance when combined with the pvr6-eIF(iso)4E resistant allele. Among the 12 pvr2-eIF4E resistance alleles sequenced in the pepper gene pool, three were shown to have a complementary effect with pvr6-eIF(iso)4E for resistance. Two amino acid changes were exclusively shared by these three alleles and were systematically associated with a second amino acid change, suggesting that these substitutions are associated with resistance expression. The availability of new resistant allele combinations increases the possibility for the durable deployment of resistance against this pepper virus which is prevalent in Africa
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02659560/file/32299_20091012012606702_1.pdf BibTex
titre
Key determinants of resistance durability to plant viruses: insights from a model linking within- and between-host dynamics
auteur
Frederic Fabre, Claude Bruchou, Alain Palloix, Benoît Moury
article
Virus Research, 2009, 141 (2), pp.140-149. ⟨10.1016/j.virusres.2008.11.021⟩
resume
The emergence of new genotypes of parasites involves several evolutionary, epidemiological and ecological processes whose individual effects and interactions are difficult to disentangle using experimental approaches. Here, a model is proposed to investigate how these processes lead to the emergence of plant viral genotypes breaking down qualitative resistance genes. At the individual plant scale, selection, drift and mutation processes shape the evolution of viral populations from a set of differential equations. The spatial segregation of virus genotypes in their hosts is also considered. At the host population scale, the epidemiological dynamics is given by an individual-based algorithm. Global sensitivity analyses allowed ranking the ten demo-genetic and epidemiological parameters of the model according to their impact on the mean and variance of the risk of breakdown of a plant resistance. Demo-genetic parameters (number and nature of mutations involved in breakdown, fitness of mutant genotypes) had the largest impact on the mean breakdown risk, whereas epidemiological parameters had more influence on its standard deviation. It is discussed how these results can be used to choose the potentially most durable resistance genes among a pool of candidates. Finally, our analyses point out the parameters which should be estimated more precisely to improve durability predictions
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02666453/file/29088_20090203012841255_1.pdf BibTex
titre
Baseline sensitivity of Botrytis cinerea to pyrrolnitrin, an antibiotic produced by several biological control agents
auteur
Sakhr Ajouz, Marc Bardin, Claire Troulet, Gisèle Riqueau, Véronique Decognet, Christel Leyronas, Anne-Sophie Walker, Pierre Leroux, Philippe C. Nicot
article
IOBC WPRS Bulletin, 2009, Integrated control in protected crops, mediterranean climate, 49, pp.51-56
resume
To establish a distribution of baseline sensitivity of Botrytis cinerea to pyrrolnitrin, an antibiotic produced by several biological control agents, 166 isolates collected from different crops were tested for sensitivity to pyrrolnitrin using a spore germination assay. Baseline EC50 (effective concentration to reduce spore germination by 50% comparing to the control) was determined. The results showed that the isolates exhibited a wide range of sensitivity to pyrrolnitrin, with a 8.4-fold difference in EC50 values between the least and the most sensitive isolates (from 0.0038 µg.ml-1 to 0.032 µg.ml-1). For all the isolates tested, the conidial germination was completely inhibited by pyrrolnitrin at doses above 0.1µg/ml. The efficacy of the pyrrolnitrin-producing Pseudomonas chlororaphis PhZ24 strain was tested in vitro on Petri plates and on tomato plants with isolates of B. cinerea having different EC50 values. Whatever the EC50 value of the isolates tested, no significant differences in sensitivity were observed towards this bacterium suggesting an absence of resistance to this biological control agent within B. cinerea isolates
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02757078/file/2009-Ajouz-IOBC.pdf BibTex
titre
Constraints on evolution of virus avirulence factors predict the durability of corresponding plant resistances
auteur
Bérenger Janzac, Frederic Fabre, Alain Palloix, Benoît Moury
article
Molecular Plant Pathology, 2009, 10 (5), pp.599-610. ⟨10.1111/j.1364-3703.2009.00554.x⟩
resume
Understanding the factors driving pathogen emergence and re-emergence is a major challenge, particularly in agriculture, where the use of resistant plant cultivars imposes strong selective pressures on plant pathogen populations and leads frequently to 'resistance breakdown'. Presently, durable resistances are only identified after a long period of large-scale cultivation of resistant cultivars. We propose a new predictor of the durability of plant resistance. Because resistance breakdown involves modifications in the avirulence factors of pathogens, we tested for correlations between the evolutionary constraints acting on avirulence factors or their diversity and the durability of the corresponding resistance genes in the case of plant–virus interactions. An analysis performed on 20 virus species–resistance gene combinations revealed that the selective constraints applied on amino acid substitutions in virus avirulence factors correlate with the observed durability of the corresponding resistance genes. On the basis of this result, a model predicting the potential durability of resistance genes as a function of the selective constraints applied on the corresponding avirulence factors is proposed to help breeders to select the most durable resistance genes
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02666562/file/37843_20100416125454166_2.pdf https://hal.inrae.fr/hal-02666562/file/37843_20100416125524948_3.pdf https://hal.inrae.fr/hal-02666562/file/37843_20100416125551882_4.pdf BibTex
titre
Diversité génétique des populations de Bremia, premiers résultats sur des collectes en Provence
auteur
Brigitte B. Maisonneuve
article
Culture légumière, 2009, septembre 2009, 22p
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Cultivars hybrides chez les espèces légumières
auteur
M-Christin Daunay
article
Sélectionneur Français, 2009, 60, pp.73-90
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic dissection of resistance to root-knot nematodes Meloidogyne spp. in plum, peach, almond, and apricot from various segregating interspecific Prunus progenies
auteur
Daniel Esmenjaud, Roger R. Voisin, Cyril van Ghelder, Nathalie Bosselut, Bernard Lafargue, M. Di Vito, Elisabeth Dirlewanger, Jean-Luc Poessel, Marc M. Kleinhentz
article
Tree Genetics and Genomes, 2009, 5 (2), pp.279-289. ⟨10.1007/s11295-008-0173-x⟩
resume
Sources of resistance in Prunus spp. exhibit different spectra to the root-knot nematodes (RKN) Meloidogyne incognita, Meloidogyne javanica and Meloidogyne floridensis. In this Prunus genus, two dominant genes, Ma with a complete spectrum from the heterozygous Myrobalan plums P.2175 and P.2980 (section Euprunus; subgenus Prunophora) and RMia with a more restricted spectrum from the peaches Nemared and Shalil (subgenus Amygdalus), have been identified. This study characterizes the resistance spectra of interspecific crosses involving (1) previous Myrobalan and peach sources, (2) two Alnem almonds (subgenus Amygdalus) resistant to M. javanica, and (3) the apricot A.3923, representing a species considered RKN-resistant (section Armeniaca; Prunophora). For both latter species, genetic data could be obtained through F1 crosses with genetically characterized Myrobalans that conferred their rooting ability for clonal multiplication of the hybrids and permitted their simultaneous evaluation to the three RKN. Crosses involving either Ma or RMia or both generated the expected resistance spectra. Nemared confirmed the species-specific resistance to M. incognita conferred by RMia. This rootstock, also previously considered resistant to M. javanica, was susceptible to the M. javanica isolate used, what illustrates an isolate-specific resistance to this species. Alnem accessions were shown homozygous resistant to M. javanica. In the progeny P.2980 × A.3923, Ma markers allowed to distinguish resistant individuals carrying that gene from resistant individuals lacking it. Distribution of non-Ma individuals in this cross suggested, in the apricot parent, (1) the absence of a major gene allelic to Ma and (2) the presence of a non RKN specific polygenic resistance.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Tacuinum Sanitatis: medieval horticulture and health
auteur
Jules Janick, M-Christin Daunay, Harry Paris
article
HortScience, 2009, 44 (4), pp.984-985
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Characterization of Genetic Components Involved in Durable Resistance to Stripe Rust in the Bread Wheat ‘Renan’.
auteur
Françoise Dedryver-Person, Sophie S. Paillard, Stephanie Mallard, Olivier Robert, Maxime M. Trottet, Sylvie Negre, Gwenn Verplancke, Joseph J. Jahier
article
Phytopathology, 2009, 99 (8), pp.968-973. ⟨10.1094/PHYTO-99-8-0968⟩
resume
Stripe rust, caused by Puccinia striiformis f. tritici, is one of the most widespread and destructive wheat diseases in areas where cool temperatures prevail. The wheat cv. Renan, carrying the specific gene Yr17, has shown effective resistance for a long time, even though some pathotypes overcame the Yr17 gene. The objectives of this study were to locate and map genetic loci associated with adult-plant resistance (APR) to stripe rust in a recombinant inbred line population derived from a cross between Renan (resistant) and Recital (susceptible). Field assays were performed for 4 years (1995, 1996, 2005, and 2006) to score disease-progress data and identify APR quantitative trait loci (QTLs). Three QTLs, QYr.inra-2BS, QYr.inra-3BS, and QYr.inra-6B, with resistance alleles derived from Renan were detected in 1995 to 1996 with the 237E141 pathotype, which is avirulent against genotypes carrying Yr17. These QTLs were stable and explained a major part of the phenotypic variation seen in 2005 to 2006, when the 237E141 V17 pathotype was used. Each of these QTLs contributed approximate to 4 to 15% of the phenotypic variance and was effective at different adult plant stages. Interactions were observed between some markers of the Yr17 gene and three Renan QTLs: QYr.inra-2BS, QYr.inra-3BS, and QYr.inra-6B. Resistance based on the combination of different APR types should provide durable resistance to P. striiformis.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Tacuinum Sanitatis: horticulture and health in the late Middle Ages
auteur
M-Christin Daunay, Jules Janick, Harry Paris
article
Chronica Horticulturae, 2009, 49 (3), pp.22-29
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Durability of plant major resistance genes to pathogens depends on the genetic background, experimental evidence and consequences for breeding strategies
auteur
Alain Palloix, Valérie Ayme, Benoît Moury
article
New Phytologist, 2009, 183 (1), pp.190-199. ⟨10.1111/j.1469-8137.2009.02827.x⟩
resume
The breakdown of plant resistance by pathogen populations is a limit to the genetic control of crop disease. Polygenic resistance is postulated as a durable alternative to defeated major resistance genes. We tested this postulate in the pepper-Potato virus Y interaction. • The virus was selected for virulence towards monogenic and polygenic host resistance, using serial inoculations in laboratory and in natural epidemic conditions. The frequency of resistance breakdown and the genetic changes in the virus avirulence gene were analysed. • The monogenic resistance due to the pvr23 gene was defeated at high frequency when introgressed in a susceptible genetic background whereas it was not when combined to partial resistance quantitative trait loci. The suppression of emergence of virulent mutants due to the genetic background resulted both from a differential selection effect and the necessity for the virus to generate multiple mutations. The virus adaptation to the polygenic resistance required a step-by-step selection with a primary selection for virulence towards the major gene, followed by selection for adaptation to the genetic background. • Polygenic resistance proved more durable than monogenic, but breeding strategies giving priority to major resistance factors may jeopardize the progress in durability expected from polygenic resistance.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02665455/file/32440_20090624110701025_2.pdf BibTex
titre
The Arabidopsis proteasome RPT5 subunits are essential for gametophyte development and show accession-dependent redundancy
auteur
Jean-Luc J.-L. Gallois, Anouchka Guyon-Debast, Alain A. Lecureuil, Daniel Vezon, Virginie Carpentier, Sandrine S. Bonhomme, Philippe Guerche
article
The Plant cell, 2009, 21 (2), pp.442-459
resume
We investigated the role of the ubiquitin proteasome system (UPS), which allows proteins to be selectively degraded, during gametophyte development in Arabidopsis thaliana. Three mutant alleles altering the UPS were isolated in the Wassilewskija (Ws) accession: they affect the Regulatory Particle 5a (RPT5a) gene, which (along with RPT5b) encodes one of the six AAAATPases of the proteasome regulatory particle. In the heterozygous state, all three mutant alleles displayed 50% pollen lethality, suggesting that RPT5a is essential for male gametophyte development. However, a fourth mutant in the Columbia (Col) accession did not display such a phenotype because the RPT5b Col allele complements the rpt5a defect in the male gametophyte, whereas the RPT5b Ws allele does not. Double rpt5a rpt5b mutants showed a complete male and female gametophyte lethal phenotype in a Col background, indicating that RPT5 subunits are essential for both gametophytic phases. Mitotic divisions were affected in double mutant gametophytes correlating with an absence of the proteasome-dependent cyclinA3 degradation. Finally, we show that RPT5b expression is highly increased when proteasome functioning is defective, allowing complementation of the rpt5a mutation. In conclusion, RPT5 subunits are not only essential for both male and female gametophyte development but also display accession-dependent redundancy and are crucial in cell cycle progression.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Local adaptation in European populations of Arabidopsis lyrata (Brassicaceae)
auteur
Païvi Leinonen, Saskia Sandring, Bénédicte Quilot, Maria J. Clauss, Thomas Mitchell-Olds, Jon Agren, Outi Savolainen
article
American Journal of Botany, 2009, 96 (6), pp.1129-1137. ⟨10.3732/ajb.0800080⟩
resume
We studied local adaptation to contrasting environments using an emerging model organism of evolutionary plant biology – the outcrossing, perennial herb Arabidopsis lyrata ssp. petraea (Brassicaceae). We found variation in cumulative fitness, indicating significant adaptive differentiation among populations. Non-local populations did not exhibit higher fitness than the local population. Sites for reciprocal transplant experiments were located in Norway (alpine), Sweden (coastal) and Germany (continental). At all sites after one year, the local populations also had higher cumulative fitness, as quantified by survival combined with rosette area, than at least one of the non-local populations. At the Norwegian site, measurements were done for two additional years and fitness differences were found to persist. Fitness components contributing most to differences in cumulative fitness varied among sites. Relatively small rosette area combined with large number of inflorescences produced by German plants may reflect differentiation in life history. The results of the present study demonstrate that A. lyrata harbours considerable variation in several characters contributing to adaptive population differentiation. The wealth of genetic information available for this species makes A. lyrata a highly attractive system for examining also the functional and genetic basis of local adaptation in plants.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02668501/file/29041_20090624025225731_1.pdf BibTex
titre
A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites
auteur
Christophe Sallaud, Denis Rontein, Sandrine Onillon, Francoise Jabes, Philippe Duffe, Cécile Giacalone, Samuel Thoraval, Camille Escoffier, Gaëtan Herbette, Nathalie Leonhardt, Mathilde M. Causse, Alain Tissier
article
The Plant cell, 2009, 21, pp.301-307. ⟨10.1105/tpc.107.057885⟩
resume
In the wild tomato Solanum habrochaites, the Sst2 locus on chromosome 8 is responsible for the biosynthesis of several class II sesquiterpene olefins by glandular trichomes. Analysis of a trichome-specific EST collection from S. habrochaites revealed two candidate genes for the synthesis of Sst2-associated sesquiterpenes. zFPS encodes a protein with homology to Z-isoprenyl pyrophosphate synthases and SBS (for Santalene and Bergamotene Synthase) encodes a terpene synthase with homology to kaurene synthases. Both genes were found to cosegregate with the Sst2 locus. Recombinant zFPS protein catalyzed the synthesis of Z,Z-FPP from isopentenylpyrophosphate (IPP) and dimethylallylpyrophosphate (DMAPP), while coincubation of zFPS and SBS with the same substrates yielded a mixture of olefins identical to the Sst2-associated sesquiterpenes, including (+)-a-santalene, (+)-endo-b-bergamotene, and (2)-endo-a-bergamotene. In addition, headspace analysis of tobacco (Nicotiana sylvestris) plants expressing zFPS and SBS in glandular trichomes afforded the same mix of sesquiterpenes. Each of these proteins contains a putative plastid targeting sequence that mediates transport of a fused green fluorescent protein to the chloroplasts, suggesting that the biosynthesis of these sesquiterpenes uses IPP and DMAPP from the plastidic DXP pathway. These results provide novel insights into sesquiterpene biosynthesis and have general implications concerning sesquiterpene engineering in plants.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La sélection assistée par marqueurs (SAM) chez les arbres fruitiers: une approche prometteuse au service de l’innovation variétale
auteur
Patrick Lambert, Elisabeth Dirlewanger, François Laurens
article
Innovations Agronomiques, 2009, 7, pp.139-152. ⟨10.17180/51ce-f154⟩
resume
Fruit tree breeding has to face numerous constraints which strongly slow down development and release of new varieties. The breeding methods are often empirical, as a result of the low genetic knowledge on the main agronomic traits, to which is added the influence of environment. Thus, breeders are looking for new methods to speed up selection process to release new cultivars. In the last ten years, significant development have been made in molecular biology applied to perennial crops in particular in genetic mapping of major genes and QTLs. This technical improvement makes it possible to develop a new approach: the marker assisted breeding or MAB. It is based on the researches from upstream and on the techniques allowing the high throughput genotyping of large numbers of individuals. It is already exploited for traits showing simple heredity in several fruit breeding programs, in particular in peach tree. Even if it is less obvious and more complex to implement on quantitative inherited traits, it is a real improvement compared to traditional breeding methods. MAB thus appears a promising approach to fruit tree breeding
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02658321/file/2009_Lambert_Innovations%20Agronomiques_1.pdf BibTex
titre
LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers
auteur
Sheh May Tam, Véronique Lefebvre, Alain Palloix, Anne-Marie Sage-Palloix, Corinne Mhiri, Marie Angele Grandbastien
article
TAG Theoretical and Applied Genetics, 2009, 119 (6), pp.973-989. ⟨10.1007/s00122-009-1102-6⟩
resume
Plant genetic resources often constitute the foundation of successful breeding programs. Pepper (Capsicum annuum L.) is one of the most economically important and diversely utilized Solanaceous crop species worldwide, but less studied compared to tomato and potato. We developed and used molecular markers based on two copia-type retrotransposons, Tnt1 and T135, in a set of Capsicum species and wild relatives from diverse geographical origins. Results showed that Tnt1 and T135 insertion polymorphisms are very useful for studying genetic diversity and relationships within and among pepper species. Clusters of accessions correspond to cultivar types based on fruit shape, pungency, geographic origin and pedigree. Genetic diversity values, normally reflective of past transposition activity and population dynamics, showed positive correlation with the average number of insertions per accession. Similar evolutionary relationships are observed to that inferred by previous karyosystematics studies. These observations support the possibility that retrotransposons have contributed to genome inflation during Capsicum evolution
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01203848/file/2009_May%20Tam_Theoretical%20and%20Applied%20Genetics%20%28Postprint%29_2 BibTex
titre
La pomme de terre entre en résistance
auteur
Sylvain Fournet, Eric Grenier, Marie-Claire Kerlan, Bernard Caromel
article
Réussir Fruits et Légumes, 2009, 284, pp.34-35
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Rapid and non-destructive analysis of apricot fruit quality using FT-near-infrared spectroscopy
auteur
Sylvie Bureau, David Ruiz, Maryse Reich, Barbara Gouble, Dominique D. Bertrand, Jean Marc Audergon, Catherine M.G.C. Renard
article
Food Chemistry, 2009, 113 (4), pp.1323-1328. ⟨10.1016/j.foodchem.2008.08.066⟩
resume
A non-destructive optical method based on near-infrared spectroscopy has been used for the evaluation of apricot fruit quality. Diffuse reflectance measurements (800–2500 nm), physical, physiological and biochemical measurements were performed individually on 877 apricot fruits from eight contrasted cultivars harvested at different ripening stages. Relationships between spectral wavelengths and quality attributes were evaluated by application of chemometric techniques based on partial least squares (PLS) on fruit set divided randomly into two groups: 598 fruits for calibration and 279 for validation. Good prediction performance was obtained for soluble solids and titratable acidity with correlation coefficients of 0.92 and 0.89 respectively and root mean square errors of prediction of 0.98% Brix and 3.62 meq 100 g−1 FW respectively. For the other quality traits such as firmness, ethylene, individual sugars and organic acids, the prediction models were not satisfactorily accurate due to the high error of calibration and prediction
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Linkage map saturation, construction, and comparison in four populations of Prunus
auteur
E. Illa, Patrick Lambert, Bénédicte Quilot, Jean Marc Audergon, Elisabeth Dirlewanger, W. Howad, L. Dondini, Stefano Tartarini, O. Lain, R. Testolin, Daniele Bassi, Pere Arus
article
Journal of Horticultural Science and Biotechnology, 2009, pp.168-175
resume
One of the objectives of the ISAFRUIT Project was to perform genetic analyses in four populations of Prunus, two of peach (P. persica) and two of apricot (P. armeniaca), in order to identify major genes and quantitative trait loci (QTLs) for characters related to fruit quality.This required the construction of saturated marker maps in each of these populations. Marker maps were available for an intra-specific peach x peach F2, a BC2 peach x P. davidiana (using peach as the recurrent parent), and an apricot x apricot F1.We have further saturated these maps mainly with SSR (simple sequence repeat) markers. A new map, constructed uniquely from SSRs was prepared for a fourth apricot x apricot F1 population. Using anchor markers, we compared these four maps with the reference Prunus map, constructed using an almond x peach F2 population. As previously observed, conservation of synteny and co-linearity were the general rule, providing additional evidence of the high level of similarity between all Prunus genomes. Comparisons of genetic distances between the maps suggested that those involving similar genomes had higher levels of recombination than those with more distant genomes, particularly the inter-specific crosses.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Progress in mapping and cloning qualitative and quantitative resistance against Phytophthora infestans in potato and its wild relatives
auteur
Ingo Hein, Paul R.J. Birch, Sarah Danan, Véronique Lefebvre, Damaris Achieng Odeny, Christiane Gebhart, Friederike Trognitz, Glenn J. Bryan
article
Potato Research, 2009, 52 (3), pp.215-227. ⟨10.1007/s11540-009-9129-2⟩
resume
Cultivated potato is susceptible to many pests and pathogens, none of which is more of a threat to potato agriculture than the late blight disease, caused by the oomycete Phytophthora infestans (Mont.) de Bary. To date all efforts to thwart this most adaptive of pathogens have failed, and early attempts to deploy ‘R genes’ introgressed from the wild Mexican hexaploid Solanum demissum ended in abject failure. With the advent of facile gene mapping and cloning, allied to knowledge of plant resistance gene structure, renewed efforts are leading to mapping and isolation of new sources of late blight resistance in potato wild species, many of which are being performed under the auspices of the BIOEXPLOIT project (Sub-project 2). We document recent advances in late blight resistance gene mapping and isolation, and postulate how these genes, allied to knowledge of pathogen effectors and their recognition specificity, may greatly enhance our chances of halting the progress of late blight disease in potato crops worldwide.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Quantitative resistance to Plum pox virus in Prunus davidiana P1908 linked to components of the eukaryotic translation initiation complex
auteur
Grégoire Marandel, Thierry Pascal, Thierry Candresse, Véronique Decroocq
article
Plant Pathology, 2009, 58 (3), pp.425-435. ⟨10.1111/j.1365-3059.2008.02012.x⟩
resume
A complex, polygenic resistance to Plum pox virus (PPV) was previously described in a wild peach-related species, Prunus davidiana clone P1908. In the current study, an analysis of quantitative trait loci (QTL) was performed on an F2 population comprising 99 individuals obtained by selfing the F1 individual #40 of an interspecific cross between susceptible nectarine cv. Summergrand and the resistant P. davidiana clone P1908. Six QTL were identified using both parametric and non-parametric methods of detection, individually explaining 5–28% of the phenotypic variance. The total phenotypic variation explained ranged from 29 to 58%. Alignment of the genetic map of the F2 cross with the P. davidiana parent map showed consistency of QTL over generations, with three of the six QTL co-localizing at the 1-LOD interval and another one at the 2-LOD interval. Two of the QTL were mapped onto linkage group one, where resistance to PPV was previously mapped in apricot. Development and mapping of new microsatellite markers linked to candidate genes revealed a striking co-localization of three of the detected QTL with gene copies coding for eukaryotic translation initiation factors eIF4E and eIF(iso)4G. As co-localization of one QTL with candidate gene eIF(iso)4E was previously reported in the F1 population, the results reported here strongly reinforce the idea that components of the eukaryotic translation initiation complex are correlated with resistance to PPV in P. davidiana P1908.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic diversity of the melon aphid Aphis gossypii Glover in different melon growing areas of France
auteur
Sophie Thomas, Pascale Mistral, Virginie Chareyron, Bastien Barral, Nathalie Boissot, Flavie Vanlerberghe-Masutti
article
Redia, 2009, XCII, pp.47-50
resume
In melon, the Vat gene confers resistance to colonization by the Cotton-Melon aphid species, Aphis gossypii Glover. The Vat gene has been present in several melon varieties produced in south-eastern France for the past fifteen years, although as time goes by, the risk of the aphids overcoming such resistance is increasing. The study of the genetic structure of Cotton-Melon aphid populations is important in order to understand the efficacy and durability of methods to control pests through the use of resistant plants. Therefore, as outlined in the present paper, we set up field trials in geographically distant melon-producing areas in France and the French West Indies (FWI) using melon plants with the resistant allele or with the susceptible allele at the Vat locus. Samples of A. gossypii were collected from these crops in the different regions and their genetic diversity analyzed at eight microsatellite loci. We identified 33 multilocus genotypes (MLGs) that were present in multiple copies, of which five were observed in several regions of France whilst two were restricted to the FWI. The genetic diversity was high in south-eastern France, moderate in south-western and western France, and low in Guadeloupe (FWI). Differentiation between pairs of geographical populations in mainland France estimated by multilocus FST was not significant. Some MLGs (NM1 and C9) were significantly less frequent on melon with the resistant allele at the Vat locus than on melon with the susceptible allele at the Vat locus, while the frequencies of others (C6, CUC1, CUC13 and CUC25) increased significantly on melon plants with the resistant allele at the Vat locus.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02662676/file/Thomas-Redia%281%29_1.pdf BibTex
titre
Identification of growth processes involved in QTLs for tomato fruit size and composition
auteur
Nadia Bertin, Mathilde M. Causse, Béatrice Brunel, David Tricon, Michel M. Génard
article
Journal of Experimental Botany, 2009, 60 (1), pp.237-248. ⟨10.1093/jxb/ern281⟩
resume
Many quantitative trait loci (QTLs) for quality traits have been located on the tomato genetic map, but introgression of favourable wild alleles into large fruited species is hampered by co-localizations of QTLs with antagonist effects. The aim of this study was to assess the growth processes controlled by the main QTLs for fruit size and composition. Four nearly isogenic lines (NILs) derived from an intraspecific cross between a tasty cherry tomato (Cervil) and a normal-tasting large fruit tomato (Levovil) were studied. The lines carried one (L2, L4, and L9) or five (Lx) introgressions from Cervil on chromosomes 1, 2, 4, and 9. QTLs for fruit size could be mainly associated with cell division processes in L2 and L9, whereas cell expansion was rather homogeneous among the genotypes, except Cervil for which the low expansion rate was attributed to low cell plasticity. The link between endoreduplication and fruit size remained unclear, as cell or fruit sizes were positively correlated with the cell DNA content, but not with the endoreduplication factor. QTLs for fruit composition reflected differences in water accumulation rather than in sugar accumulation, except in L9 for which the up-regulation of sucrose unloading and hexose transport and/or starch synthesis was suggested. This may explain the increased amount of carbon allocated to cell structures in L9, which could be related to a QTL for fruit texture. In Lx, these effects were attenuated, except on fruit size and cell division. Finally, the region on top of chromosome 9 may control size and composition attributes in tomato, by a combination of QTL effects on cell division, cell wall synthesis, and carbon import and metabolism.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02656740/file/28682_20091104090742272_1.pdf BibTex
titre
Major-effect QTLs for stem and foliage resistance to late blight in the wild potato relatives Solanum sparsipilum and S. spegazzinii are mapped to chromosome X
auteur
Sarah Danan, Jean-Eric Chauvin, Bernard Caromel, Jean Denis Moal, Roland Pellé, Véronique Lefebvre
article
TAG Theoretical and Applied Genetics, 2009, 119 (4), pp.705-719. ⟨10.1007/s00122-009-1081-7⟩
resume
To find out new resistance sources to late blight in the wild germplasm for potato breeding, we examined the polygenic resistance of Solanum sparsipilum and S. spegazzinii by a quantitative trait locus (QTL) analysis. We performed stem and foliage tests under controlled conditions in two diploid mapping progenies. Four traits were selected for QTL detection. A total of 30 QTLs were mapped, with a large-effect QTL region on chromosome X detected in both potato relatives. The mapping of literature-derived markers highlighted colinearities with published late blight QTLs or R-genes. Results showed (a) the resistance potential of S. sparsipilum and S. spegazzinii for late blight control, and (b) the efficacy of the stem test as a complement to the foliage test to break down the complex late blight resistance into elementary components. The relationships of late blight resistance QTLs with R-genes and maturity QTLs are discussed.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Metabolic characterization of loci affecting sensory attributes in tomato allows an assessment of the influence of the levels of primary metabolites and volatile organic contents
auteur
Maria Inés Zanor, José-Luis Rambla, Jamila Chaïb, Agnes Steppa, Aurore Medina, Antonio Grannell, Alisdair Fernie, Mathilde M. Causse
article
Journal of Experimental Botany, 2009, 60 (7), pp.2139-2154. ⟨10.1093/jxb/erp086⟩
resume
Numerous studies have revealed the extent of genetic and phenotypic variation between both species and cultivars of tomato. Using a series of tomato lines resulting from crosses between a cherry tomato and three independent large fruit cultivar (Levovil, VilB, and VilD), extensive profiling of both central primary metabolism and volatile organic components of the fruit was performed. In this study, it was possible to define a number of quantitative trait loci (QTLs) which determined the levels of primary metabolites and/or volatile organic components and to evaluate their co-location with previously defined organoleptic QTLs. Correlation analyses between either the primary metabolites or the volatile organic compounds and organoleptic properties revealed a number of interesting associations, including pharmaceutical aroma–guaiacol and sourness–alanine, across the data set. Considerable correlation within the levels of primary metabolites or volatile organic compounds, respectively, were also observed. However, there was relatively little association between the levels of primary metabolites and volatile organic compounds, implying that they are not tightly linked to one another. A notable exception to this was the strong association between the levels of sucrose and those of a number of volatile organic compounds. The combined data presented here are thus discussed both with respect to those obtained recently from wide interspecific crosses of tomato and within the framework of current understanding of the chemical basis of fruit taste.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02668215/file/26045_20090904023824202_1.pdf BibTex
titre
Phenotype and spectrum of action of the Pvr4 resistance in pepper against potyviruses, and selection for virulent variants
auteur
Bérenger Janzac, Marie-Françoise Fabre, Alain Palloix, Benoît Moury
article
Plant Pathology, 2009, 58 (3), pp.443-449. ⟨10.1111/j.1365-3059.2008.01992.x⟩
resume
The dominant Pvr4 gene identified in Capsicum annuum cv. Criollo de Morelos 334 (CM334) is frequently used in pepper cultivars because it possesses one of the largest spectra of action among plant virus resistance genes. This gene was previously shown to confer efficient resistance to all known Potato virus Y isolates, to Pepper mottle virus, to Pepper yellow mosaic virus and to Ecuadorian rocoto virus. This study showed that the W4 line, derived from CM334 and carrying Pvr4, was also resistant to Peru tomato mosaic virus and Pepper severe mosaic virus, but not to Pepper veinal mottle virus, Chilli veinal mottle virus or Tobacco etch virus. It was noticed that the phenotype of the resistance was atypical since, in the W4 line, hypersensitive reaction or extreme resistance could be observed, depending on virus isolates and inoculated organs. Despite the large deployment of Pvr4 in hybrid cultivars, the numerous tests performed in controlled conditions and the use of W4 serial back-inoculations with potyvirus isolates controlled by this line, no virulent variant isolates were obtained. However, it was shown that the use of graft inoculation experiments allow PVY virulent variants to be selected.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The Cucurbitaceae and Solanaceae illustrated in medieval manuscripts known as the Tacuinum sanitatis
auteur
Harry Paris, M-Christin Daunay, Jules Janick
article
Annals of Botany, 2009, 103 (8), pp.1187-1205. ⟨10.1093/aob/mcp055⟩
resume
Background and Aims: Beginning in the last two decades of the 14th century, richly illuminated versions of the Tacuinum sanitatis, the latin translation of an 11th-century arabic manuscript known as Taqwim al-Sihha bi al-Ashab al-Sitta, were produced in northern Italy. These illustrated manuscripts provide a window on late medieval life in that region by containing some 200 full-page illustrations, many of which vividly depict the harvest of vegetables, fruits, flowers, grains, aromatics and medicinal plants. Our objective was to search for and identify the images of taxa of Cucurbitaceae and Solanaceae. Methods: We have located all reported illustrated Tacuinum sanitatis and similar or related manuscripts, searched through printed or electronic reproductions of them, categorized six of them that display full-page illustrations as archetypic, and established the identity of the Cucurbitaceae and Solanaceae appearing in these six manuscripts. Key Results and Conclusions: Of the Cucurbitaceae, Cucumis sativus (short-fruited cucumbers), Cucumis melo (including round as well as elongate melons), Citrullus lanatus (both sweet watermelons and citrons), and Lagenaria siceraria (including bottle-shaped as well as long gourds), are illustrated. Of the Solanaceae, Solanum melongena (egg-shaped purple aubergines) and Mandragora sp. (mandrake) are illustrated. These depictions include some of the earliest known images of cucumber, casaba melon (Cucumis melo Inodorous Group) and aubergine, each of which closely resembles an extant cultivar-group or market type. Overall, the botanically most accurate images are in the version of the Tacuinum located in the Osterreichische Nationalbibliothek, Vienna, cod. ser. n. 2644. Similarities and differences in botanical accuracy among the images of Cucurbitaceae and Solanaceae in the six archetypal Tacuinum manuscripts suggest to us that another illustrated Tacuinum, now lost, may have antedated and served as a model or inspiration for the six surviving archetypic manuscripts
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Regulation of tomato fruit ascorbate content is more highly dependent on fruit irradiance than leaf irradiance
auteur
Hélène Gautier, Capucine Massot, Rebecca Stevens, Sylvie Serino, Michel M. Génard
article
Annals of Botany, 2009, 103 (3), pp.495-504. ⟨10.1093/aob/mcn233⟩
resume
Background and Aims: The mechanisms involving light control of vitamin C content in fruits are not yet fully understood. The present study aimed to evaluate the impact of fruit and leaf shading on ascorbate (AsA) accumulation in tomato fruit and to determine how fruit sugar content (as an AsA precursor) affected AsA content. Methods: Cherry tomato plants were grown in a glasshouse. The control treatment (normally irradiated fruits and irradiated leaves) was compared with the whole-plant shading treatment and with leaf or fruit shading treatments in fruits harvested at breaker stage. In a second experiment, the correlation between sugars and AsA was studied during ripening. Key Results: Fruit shading was the most effective treatment in reducing fruit AsA content. Under normal conditions, AsA and sugar content were correlated and increased with the ripening stage. Reducing fruit irradiance strongly decreased the reduced AsA content (–74 %), without affecting sugars, so that sugar and reduced AsA were no longer correlated. Leaf shading delayed fruit ripening: it increased the accumulation of oxidized AsA in green fruits (+98 %), whereas it decreased the reduced AsA content in orange fruits (–19 %), suggesting that fruit AsA metabolism also depends on leaf irradiance. Conclusions: Under fruit shading only, the absence of a correlation between sugars and reduced AsA content indicated that fruit AsA content was not limited by leaf photosynthesis or sugar substrate, but strongly depended on fruit irradiance. Leaf shading most probably affected fruit AsA content by delaying fruit ripening, and suggested a complex regulation of AsA metabolism which depends on both fruit and leaf irradiance and fruit ripening stage
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Application of ATR-FTIR for a rapid and simultaneous determination of sugars and organic acids in apricot fruit
auteur
Sylvie Bureau, David Ruiz, Maryse Reich, Barbara Gouble, Dominique D. Bertrand, Jean Marc Audergon, Catherine M.G.C. Renard
article
Food Chemistry, 2009, 115 (3), pp.1133-1140. ⟨10.1016/j.foodchem.2008.12.100⟩
resume
A simple, fast and accurate Fourier transform mid-infrared spectroscopy method was developed for simultaneously determining sugar and organic acid contents in apricot fruit slurries using the attenuated total reflectance. The potential of this method coupled with chemometric techniques based on partial least squares was assessed by comparison with currently used enzymatic determination of sucrose, glucose, fructose, malic acid and citric acid. Fruits of eight contrasted cultivars harvested at different ripening stages were used in this study and randomly divided in a calibration set (505 apricots) and in a validation set (252 apricots). The most suitable region was found in the range between 1500 and 900 cm-1. Good prediction performances were obtained (R2 >= 0.74 and RMSEP <=18%). Results concerning the prediction of other quality traits such as firmness, skin colour, ethylene production, soluble solids content and titratable acidity were discussed.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A high-resolution map of the Grp1 locus on chromosome V of potato harbouring broad-spectrum resistance to the cyst nematode species Globodera pallida and Globodera rostochiensis
auteur
Anna Finkers-Tomczak, Sarah Danan, Thijs van Dijk, Amelework Beyene, Liesbeth Bouwman, Hein Overmars, Herman van Eck, Aska Goverse, Jaap Bakker, Erin Bakker
article
TAG Theoretical and Applied Genetics, 2009, 119 (1), pp.165-173. ⟨10.1007/s00122-009-1026-1⟩
resume
The Grp1 locus confers broad-spectrum resistance to the potato cyst nematode species Globodera pallida and Globodera rostochiensis and is located in the GP21-GP179 interval on the short arm of chromosome V of potato. A high-resolution map has been developed using the diploid mapping population RHAM026, comprising 1,536 genotypes. The flanking markers GP21 and P179 have been used to screen the 1,536 genotypes for recombination events. Interval mapping of the resistances to G. pallida Pa2 and G. rostochiensis Ro5 resulted in two nearly identical LOD graphs with the highest LOD score just north of marker TG432. Detailed analysis of the 44 recombinant genotypes showed that G. pallida and G. rostochiensis resistance could not be separated and map to the same location between marker SPUD838 and TG432. It is suggested that the quantitative resistance to both nematode species at the Grp1 locus is mediated by one or more tightly linked R genes that might belong to the NBS-LRR class.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02661493/file/2009_Finkers-Tomczak_Theoretical%20and%20Applied%20Genetics_1 BibTex
titre
Changes in volatiles and glycosides during fruit maturation of two contrasted tomato (Solanum lycopersicum) lines
auteur
Simona Birtic-Pindat, Christian Ginies, Mathilde M. Causse, Catherine M.G.C. Renard, David Page
article
Journal of Agricultural and Food Chemistry, 2009, 57 (2), pp.591-598. ⟨10.1021/jf8023062⟩
resume
The relationship between fruit maturation and volatile contents was investigated in two contrasted Cervil (CER) and Levovil (LEV) tomato (Solanum lycopersicum) lines. As fruits ripened, their volatile contents mainly increased. Although some compounds displayed contrasting patterns, overall, volatiles were clearly more abundant and conferred stronger aromas to CER than to LEV fruits. This intervarietal difference in volatile contents yielding much lower volatile contents in LEV was further investigated to determine whether it is due to a higher capacity of volatile glycosylation within LEV as compared to CER. Again, glycosides mainly increased during fruit maturation and were more abundant within CER than within LEV. Overall glycoside findings were indicative of a superior capacity to biosynthesize rather than an inferior capacity to glycosylate volatiles of CER. Eugenol and 2-methoxyphenol volatiles were exceptional compounds as they remained at higher levels in maturing LEV than in CER. 2-Methylthioacetaldehyde was for the first time identified as putatively related to differences of aroma between lines, as it was abundant in Cervil but absent in Levovil. Considering the described odor value of these three products, they should contribute differently to the particular olfactive features of LEV and CER fruits
typdoc
Journal articles
Accès au bibtex
BibTex
titre
GDP-d-mannose 3,5-epimerase (GME) plays a key role at the intersection of ascorbate and non-cellulosic cell-wall biosynthesis in tomato
auteur
Louise Gilbert, Moftah Alhagdow, Adriano Nunes-Nesi, Bernard Quemener, Fabienne Guillon, Brigitte B. Bouchet, Mireille Faurobert, Barbara Gouble, David Page, Virginie V. Garcia, Johann J. Petit, Rebecca Stevens, Mathilde M. Causse, Alisdair Fernie, Marc Lahaye, Christophe Rothan, Pierre Baldet
article
The Plant Journal, 2009, 60 (3), pp.499-508. ⟨10.1111/j.1365-313X.2009.03972.x⟩
resume
P>The GDP-d-mannose 3,5-epimerase (GME, EC 5.1.3.18), which converts GDP-d-mannose to GDP-l-galactose, is generally considered to be a central enzyme of the major ascorbate biosynthesis pathway in higher plants, but experimental evidence for its role in planta is lacking. Using transgenic tomato lines that were RNAi-silenced for GME, we confirmed that GME does indeed play a key role in the regulation of ascorbate biosynthesis in plants. In addition, the transgenic tomato lines exhibited growth defects affecting both cell division and cell expansion. A further remarkable feature of the transgenic plants was their fragility and loss of fruit firmness. Analysis of the cell-wall composition of leaves and developing fruit revealed that the cell-wall monosaccharide content was altered in the transgenic lines, especially those directly linked to GME activity, such as mannose and galactose. In agreement with this, immunocytochemical analyses showed an increase of mannan labelling in! stem and fruit walls and of rhamnogalacturonan labelling in the stem alone. The results of MALDI-TOF fingerprinting of mannanase cleavage products of the cell wall suggested synthesis of specific mannan structures with modified degrees of substitution by acetate in the transgenic lines. When considered together, these findings indicate an intimate linkage between ascorbate and non-cellulosic cell-wall polysaccharide biosynthesis in plants, a fact that helps to explain the common factors in seemingly unrelated traits such as fruit firmness and ascorbate content.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTL analysis of plant development and fruit traits in pepper and performance of selective phenotyping
auteur
Lorenzo Barchi, Véronique Lefebvre, Anne-Marie Sage-Palloix, Sergio Lanteri, Alain Palloix
article
TAG Theoretical and Applied Genetics, 2009, 118 (6), pp.1157-1171. ⟨10.1007/s00122-009-0970-0⟩
resume
A QTL analysis was performed to determine the genetic basis of 13 horticultural traits conditioning yield in pepper (Capsicum annuum). The mapping population was a large population of 297 recombinant inbred lines (RIL) originating from a cross between the large fruited bell pepper cultivar ‘Yolo Wonder’ and the small fruited chilli pepper ‘Criollo de Morelos 334’. A total of 76 QTLs were detected for 13 fruit and plant traits, grouped in 28 chromosome regions. These QTLs explained together between 7% (internode growth time) and 91% (fruit diameter) of the phenotypic variation. The QTL analysis was also performed on two subsets of 141 and 93 RILs sampled using the MapPop software. The smaller populations allowed for the detection of a reduced set of QTLs and reduced the over all percentage of trait variation explained by QTLs. The frequency of false positives as well as the individual effect of QTLs increased in reduced population sets as a result of reduced sampling. The results from the QTL analysis permitted an overall glance over the genetic architecture of traits considered by breeders for selection. Colinearities between clusters of QTLs controlling fruit traits and/or plant development in distinct pepper species and in related solanaceous crop species (tomato and eggplant) suggests that shared mechanisms control the shape and growth of different organs throughout these species
typdoc
Journal articles
Accès au bibtex
BibTex

2008

Journal articles

titre
A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons
auteur
Adnane Boualem, Mohamed Fergany, Ronan Fernandez, Christelle Troadec, Antoine Martin, Halima H. Morin, Marie-Agnès Sari, Fabrice Collin, Jonathan Flowers, Michel Pitrat, Michael Purugganan, Catherine Dogimont, Abdelhafid A. Bendahmane
article
Science, 2008, 321 (5890), pp.836-838. ⟨10.1126/science.1159023⟩
resume
Andromonoecy is a widespread sexual system in angiosperms characterized by plants carrying both male and bisexual flowers. In melon, this sexual form is controlled by the identity of the alleles at the andromonoecious (a) locus. Cloning of the a gene reveals that andromonoecy results from a mutation in the active site of 1-aminocyclopropane-1-carboxylic acid synthase. Expression of the active enzyme inhibits the development of the male organs and is not required for carpel development. A causal single-nucleotide polymorphism associated with andromonoecy was identified, which suggests that the a allele has been under recent positive selection and may be linked to the evolution of this sexual system
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Is competition between mesocarp cells of peach fruits affected by the percentage of wild species (Prunus davidiana) genome
auteur
Bénédicte Quilot-Turion, Michel M. Génard
article
Journal of Plant Research, 2008, 121 (1), pp.55-63. ⟨10.1007/s10265-007-0125-9⟩
resume
The number of cells and the mean cell volume in the mesocarps of fruits from peach genotypes with different percentages of the genome of Prunus davidiana, a wild, related, species, were evaluated. The mesocarp mass varied greatly between the four groups of genotypes. The mean cell volume and the number of cells were negatively correlated within each group. This correlation can be interpreted as a relationship of competition between cells. In order to describe the type of competition in the different groups, we tried to adjust a model of competition for resources proposed by Lescourret and Génard (Ecoscience 10:334–341, 2003). To estimate the values of the three parameters of the model for the different groups, we applied model selection. Within nested models, we identified a single best model with six parameter values. This model was roughly accurate, but it allowed us to describe the general relationship for each group. The parameter values revealed a strong and under-compensating density-dependence effect for all groups. The percentage of P. davidiana genome appeared to influence the maximal number of cells and the strength of the competition, but no effect was found on the maximal mean volume of cells
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Functional markers for selection of potyvirus resistance alleles at the pvr2-eIf4e locus in pepper using tetra-primer ARMS-PCR
auteur
Manuel Rubio, Carole Caranta, Alain Palloix
article
Genome, 2008, 51 (9), pp.767-771. ⟨10.1139/G08-056⟩
resume
Functional markers targeted on single nucleotide polymorphisms (SNPs) responsible for phenotypic variation constitute optimal tools for marker-assisted selection (MAS) of resistance alleles with different specificities. Here, we used the tetra-primer ARMS–PCR procedure to assay SNP signatures of four distinct alleles at the pvr2-eIF4E locus, which controls pepper resistance to several potyviruses. These simple, economical, and codominant markers open the way for MAS of pepper genotypes resistant to the potyviral strains and species that are prevalent in distinct cultivation areas across the world.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Phenotypic diversity and relationships of fruit quality traits in apricot (Prunus armeniaca L.) germplasm
auteur
David Ruiz, José Egea
article
Euphytica, 2008, 163 (1), pp.143-158. ⟨10.1007/s10681-007-9640-y⟩
resume
Fruit quality attributes were studied for two consecutive years in forty-three apricot cultivars and selections grown in a Mediterranean climate. Physical parameters (weight, size, flesh and skin colour, percentage of blush, firmness and percentage of dry matter), chemical parameters (total soluble solids content and acidity) and sensory parameters (attractiveness, taste, aroma and texture) were evaluated. A high variability was found in the set of the evaluated apricot genotypes and significant differences were found among them in all studied quality attributes. Year-by-year variations were observed for some pomological traits such as harvest date, flesh colour, fruit weight, firmness and soluble solids content. A high correlation was found among some apricot quality attributes. In addition, principal component analysis (PCA) made it possible to establish similar groups of genotypes depending on their quality characteristics as well as to study relationships among pomological traits in the set of apricot genotypes evaluated
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La lutte contre les nématodes à kyste de la pomme de terre Globodera rostochiensis et Globodera pallida
auteur
Laura Chauvin, Bernard Caromel, Marie-Claire Kerlan, Elsa Rulliat, Sylvain Fournet, Jean-Eric Chauvin, Eric Grenier, Daniel Ellisèche, Didier Mugniery
article
Cahiers Agricultures, 2008, 17 (4), pp.368-374. ⟨10.1684/agr.2008.0217⟩
resume
Inscrits parmi les parasites de quarantaine, les nématodes à kyste, Globodera rostochiensis et Globodera pallida sont présents dans de nombreux bassins de production de pomme de terre où les dégâts sont parfois considérables. La lutte contre ces ravageurs est préventive dans les zones de culture indemnes, condition indispensable à la production de plant de pomme de terre. Des pratiques agronomiques adéquates et l’utilisation de variétés résistantes conduisent à la réduction du taux d’infestation des terrains contaminés. Dans certaines situations géographiques, le traitement du sol par solarisation peut remplacer efficacement l’emploi de nématicides destinés à être interdits. La résistance génétique représente le moyen de lutte le plus efficace. L’introgression de nouvelles formes de résistance a été entreprise à partir d’autres espèces tubéreuses, notamment Solanum vernei. La récente caractérisation moléculaire de nouveaux facteurs génétiques de la résistance chez les espèces Solanum spegazzinii et Solanum sparsipilum et l’étude de leur association devraient faire progresser le travail de sélection variétale. La combinaison des différents moyens de lutte présentés en fonction des situations devrait aboutir à la mise en pratique d’une véritable lutte intégrée en culture de pomme de terre de consommation.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Using AFLP markers for the analysis of the genetic diversity of apricot cultivars in Tunisia
auteur
Lamia Krichen, Joao M.S. Martins, Patrick Lambert, Abderrazzak Daaloul, Neïla Trifi-Farah, Mohamed Marrakchi, Jean Marc Audergon
article
Journal of the American Society for Horticultural Science, 2008, 133 (2), pp.204-212
resume
Apricot (Prunus armeniaca L.) culture is present in a wide range of areas and microclimates in Tunisia. Each of them contains several specific cultivars and shows a high level of morphological diversity. To characterize the related diversity, surveys were performed in the four main apricot cultivation areas, where 31 cultivars representing apricot landraces were sampled. DNA was extracted and amplified with five different EcoRI–MseI AFLP primer combinations. Autoradiographs revealed 203 polymorphic markers in a total of 295 detected fragments. A set of redundant marker patterns was identified and deleted from the binary data matrix, data analysis being performed on a total of 167 polymorphic markers. In a dendrogram calculated by the Ward clustering technique, two major groups were identified, separating nine cultivars from the other 22. Three subgroups have been revealed in each of the main groups. The groups and subgroups identified on the genetic basis are closely related to the geographic origin of the cultivars. Analysis of the actual repartition suggested at least the introduction of two independent gene funds in the northern and central prospected areas, followed by a local diversification and then a dissemination phase. Their interaction occurred at least in the two sites of Testour and Sbikha
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Gamme variétale d'abricotiers : évaluation de la sensibilité au monilia
auteur
Vincent Mercier, Christelle Gomez, François Warlop, Guy Clauzel, Laurent Brun, Jm Broquaire, F. Gilles, Jean Marc Audergon
article
Arboriculture Fruitière, 2008, 626-627, pp.20-23
resume
L ’abricotier est une des espèces fruitières les plus aisées à conduire en agriculture biologique, étant donné le faible nombre de bioagresseurs à maîtriser dans les conditions de production. Mais le principal d ’entre eux reste le monilia (Monilinia laxa essentiellement)qui constitue une impasse technique majeure,de par la sensibilité de l’espèce aux attaques sur fleurs,rameaux et fruits. Les conditions climatiques à la floraison peuvent entraîner une contamination primaire importante et des pertes de récolte considérables. La levée d ’un tel verrou,tout comme l’analyse objective des risques encourus,permettraient un développement de la production d’abricots biologiques en France, mais les pistes de lutte sont encore limitées.La sensibilité variétale reste l’alternative la plus pertinente à long terme.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Analysis of the variability and correlations of floral biology factors affecting fruit set in apricot in a mediterranean climate
auteur
David Ruiz, J. Egea
article
Scientia Horticulturae, 2008, 115 (2), pp.154-163. ⟨10.1016/j.scienta.2007.08.016⟩
resume
Floral biology factors which affect fruiting in apricot, such as flower bud production, flower production, flower bud drop, flowering time, percentage pollen germination, height difference between the stigma and the superior plane of the anthers, percentage of aborted pistils, autogamy level, fruit set and fruit production, have been studied for 3 consecutive years in 43 apricot cultivars and selections grown in a Mediterranean climate. An important genetic diversity has been found in the set of evaluated apricot genotypes and significant differences were found among them in all attributes studied. Significant year-by-year variation has been shown for flower bud production, flower bud drop, flowering time, autogamy level, fruit production and fruit set. High correlation existed between some floral biology factors. Flower bud drop and pollen germination were correlated significantly with flowering time. Flower production influenced significantly fruit production, which was highly correlated with fruit set. Significant negative correlation was found between autogamy level and height difference between the stigma and the superior plane of the anthers. Significant negative correlation between percentage of flower bud drop and flower production was observed, while late-flowering genotypes with high chilling requirements showed higher percentages of flower bud drop than early-flowering genotypes.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Isolation of genes potentially related to fruit quality by subtractive selective hybridization in tomato
auteur
David Page, Isabelle Marty, Jean-Paul Bouchet, Barbara Gouble, Mathilde M. Causse
article
Postharvest Biology and Technology, 2008, 50 (2-3), pp.117-124. ⟨10.1016/j.postharvbio.2008.05.017⟩
resume
Improved understanding of the genetic and physiological control of quality traits could be helpful for identifying new technological or genetic targets to improve tomato fresh fruit quality and shelf life. This study aimed at screening for genes whose expression varied between lines genetically close but differing for fruit quality, using subtractive and selective hybridization (SSH). A set of 310 unigenes was isolated. The differential expression pattern of the SSH clones between LCx and Levovil, the two lines of the trial, was assessed by macroarray screening, and for 14 of them, by real-time PCR. Their putative functions were identified by BLAST comparison with public EST databases, and were classified on the basis of their function. Thirty nine percent of the unigenes corresponded to proteins which had never been isolated in fruit or with functions in fruit that were not clear or unknown. Among the others, proteins related to oxidative stress responses, calcium-binding proteins, a few cell-wall-related proteins, and several transcription regulators were identified. The SSH unigenes were then compared to the EST set of the tomato array Tom2 developed from public resources. The BLAST comparison revealed that 41% of the unigenes were not included in this set. This result revealed that our study emphasizes genes that would not have been considered with commercially available microarrays, and that constitute new targets for fruit quality control
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The Arabidopsis proteasome RPT5 subunits are essential for gametophyte development
auteur
Jean-Luc J.-L. Gallois, Anouchka Guyon-Debast, Alain A. Lecureuil, Daniel Vezon, V Carpentier, Mathilde Grelon, Sandrine S. Bonhomme, Philippe Guerche
article
Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology, 2008, 150 (3), pp.S 178. ⟨10.1016/j.cbpa.2008.04.474⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A clarified position for Solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (Solanaceae)
auteur
Nicolas N. Ranc, Stephane Munos, Sylvain S. Santoni, Mathilde M. Causse
article
BMC Plant Biology, 2008, 8, pp.130. ⟨10.1186/1471-2229-8-130⟩
resume
The natural phenotypic variability present in the germplasm of cultivated plants can be linked to molecular polymorphisms using association genetics. However it is necessary to consider the genetic structure of the germplasm used to avoid false association. The knowledge of genetic structure of plant populations can help in inferring plant evolutionary history. In this context, we genotyped 360 wild, feral and cultivated accessions with 20 simple sequence repeat markers and investigated the extent and structure of the genetic variation. The study focused on the red fruited tomato clade involved in the domestication of tomato and confirmed the admixture status of cherry tomatoes (Solanum lycopersicum var. cerasiforme). We used a nested sample strategy to set-up core collection maximizing the genetic diversity with a minimum of individuals. Results Molecular diversity was considerably lower in S. lycopersicum i.e. the domesticated form. Model-based analysis showed that the 144 S. lycopersicum var. cerasiforme accessions were structured into two groups: one close to the domesticated group and one resulting from the admixture of the S. lycopersicum and S. pimpinellifolium genomes. SSR genotyping also indicates that domesticated and wild tomatoes have evolved as a species complex with intensive level of hybridization. We compiled genotypic and phenotypic data to identify sub-samples of 8, 24, 32 and 64 cherry tomato accessions that captured most of the genetic and morphological diversity present in the entire S. lycopersicum var. cerasiforme collection. Conclusion The extent and structure of allelic variation is discussed in relation to historical events like domestication and modern selection. The potential use of the admixed group of S. lycopersicum var. cerasiforme for association genetics studies is also discussed. Nested core collections sampled to represent tomato diversity will be useful in diversity studies. Molecular and phenotypic variability of these core collections is defined. These collections are available for the scientific community and can be used as standardized panels for coordinating efforts on identifying novel interesting genes and on examining the domestication process in more detail.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02668658/file/27337_20090421011547154_1.pdf BibTex
titre
Natural variation and functional analyses provide evidence for co-evolution between plant eIF4E and potyviral VPg
auteur
Carine Charron, Maryse Nicolaï, Jean-Luc J.-L. Gallois, Christophe Robaglia, Benoît Moury, Alain Palloix, Carole Caranta
article
The Plant Journal, 2008, 54 (1), pp.56-68. ⟨10.1111/j.1365-313X.2008.03407.x⟩
resume
Amino acid substitutions in the eukaryotic translation initiation factor 4E (eIF4E) result in recessive resistance to potyviruses in a range of plant species, including Capsicum spp. Correspondingly, amino acid changes in the central part of the viral genome-linked protein (VPg) are responsible for the potyvirus’s ability to overcome eIF4E-mediated resistance. A key observation was that physical interaction between eIF4E and the VPg is required for viral infection, and eIF4E mutations that cause resistance prevent VPg binding and inhibit the viral cycle. In this study, polymorphism analysis of the pvr2-eIF4E coding sequence in a worldwide sample of 25 C. annuum accessions identified 10 allelic variants with exclusively non-synonymous variations clustered in two surface loops of eIF4E. Resistance and genetic complementation assays demonstrated that pvr2 variants, each with signature amino acid changes, corresponded to potyvirus resistance alleles. Systematic analysis of the interactions between eIF4E proteins encoded by the 10 pvr2 alleles and VPgs of virulent and avirulent potato virus Y (PVY) and tobacco etch virus (TEV) strains demonstrated that resistance phenotypes arose from disruption of the interaction between eIF4E and VPg, and that viral adaptation to eIF4E-mediated resistance resulted from restored interaction with the resistance protein. Complementation of an eIF4E knockout yeast strain by C. annuum eIF4E proteins further shows that amino acid changes did not impede essential eIF4E functions. Altogether, these results argue in favour of a co-evolutionary ‘arms race’ between Capsicum eIF4E and potyviral VPg
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Immunolocalization and histocytopathological effects of Xanthomonas arboricola pv. pruni on naturally infected leaf and fruit tissues of peach (Prunus persica L. Batsch)
auteur
Alexandra Garcin, Jawad Aarrouf, Y. Lizzi, Mohamed El Maataoui
article
Journal of Phytopathology, 2008, 156, pp.338-345. ⟨10.1111/j.1439-0434.2007.01364.x⟩
resume
Immunofluorescence and cytohistochemical studies have been performed to understand the host–parasite relationships in the pathosystem: peach–Xanthomonas arboricola pv. pruni (Xap). Using a commercial immunodetection kit, Xap cells were specifically identified in tissues from infected leaves and fruits. Sections from infected leaves showed that the pathogen penetrates the mesophyll via stomata and develops in the intercellular spaces where it degrades the cell wall components. This leads to cell collapse and consequently to the formation of necrotic lesions. The same events have been noted in sections from infected fruits. However, the contaminated zones of mesocarp parenchyma exhibited cell dedifferentiation and generated somatic embryo-like structures. Sections from midrib samples collected at different distances from infected lamina revealed the presence of Xap cells in the sieve tubes and xylem suggesting a systemic trafficking of the pathogen. The results are discussed in terms of cytological effects and epidemiology of Xap.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Flanking the major Plum pox virus resistance locus in apricot with co-dominant markers (SSRs) derived from candidate resistance genes
auteur
Ophélie Sicard, Grégoire Marandel, J.M. Soriano, D.A. Lalli, Patrick Lambert, J. Salava, M.L. Badenes, Albert Abbott, Véronique Decroocq
article
Tree Genetics and Genomes, 2008, 4 (2), pp.359-365. ⟨10.1007/s11295-007-0114-0⟩
resume
Plum pox virus (PPV) is a potyvirus that causes sharka disease in infested stone fruit trees (Prunus species, peach, apricot, plum). In apricots, the resistance is controlled by a major quantitative trait locus that explains up to 70% of the phenotypic variance; it is localised in the upper part of linkage group 1. In this report, we transformed candidate genes that mapped in the region of the apricot resistance locus into polymerase chain reaction markers (SSCP and SSR) and tested for their co-localisation with the major PPV resistance locus in related and unrelated populations. Three populations of F1 and F2 individuals issued from crosses between the PPV-resistant cultivar ‘Stark Early Orange’ or ‘Goldrich’ and three susceptible parents were used in this study. Molecular-marker data were collected to determine the linkage relationship between the PPV resistance locus in apricots and markers that target candidate disease-resistance genes. In addition, SSR markers linked to resistance-gene candidates were mapped to positions flanking the PPV resistance locus in different apricot populations. Therefore, we demonstrate that this strategy helps to saturate the major genomic region controlling resistance to PPV in apricot with valuable codominant markers
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Molecular, biological and serological variability of Zucchini yellow mosaic virus in Tunisia.
auteur
Soumaya Yakoubi, Cecile Desbiez, Hatem Fakhfakh, Catherine Wipf-Scheibel, Frederic Fabre, Michel Pitrat, M. Marrakchi, Hervé Lecoq
article
Plant Pathology, 2008, 57 (6), pp.1146-1154. ⟨10.1111/j.1365-3059.2008.01934.x⟩
resume
A study was conducted to better understand the population structure of Zucchini yellow mosaic virus (ZYMV), a severe virus affecting cucurbit crops worldwide, in Tunisia and to estimate whether the use of resistant cultivars may provide durable control. Analysis of the polymerase and coat protein (NIb-CP) partial sequences of 83 isolates collected in the three main cucurbit-growing areas in Tunisia showed that ZYMV grouped into two distinct clusters within ZYMV molecular group A. An important variability was observed in the MREK motif of the P3 protein, a motif associated with tolerance breaking in ZYMV-tolerant zucchini squash cultivars. Interestingly, significant differences were found in the distribution of the MREK variants in the two clusters defined by the partial NIb-CP sequences, MREK and MKEK sequences being more common in cluster 1 and cluster 2, respectively. When combining NIb-CP and P3 sequence information, ZYMV molecular variability was shown to be significantly higher in the Cap Bon region than in the Bizerte area. An important biological variability was observed in a subset of 23 isolates regarding symptomatology in susceptible or resistant cucurbits. Some isolates overcame ZYMV tolerance or resistance in zucchini squash and melon, but not in cucumber. Three serotypes were differentiated using a set of 13 monoclonal antibodies (MAbs). Seven parameters characterizing the 23 isolates, including molecular, serological and biological properties, were used for a multiple component analysis (MCA). This analysis revealed that symptom intensity of a given isolate was similar in different susceptible cucurbit hosts, suggesting similar degrees of aggressiveness in different hosts.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Vector and graft inoculations of Potato yellow mosaic virus reveal recessive resistance in Solanum pimpinellifolium
auteur
Nathalie Boissot, Cica Urbino, Jacques Dintinger, Claude Pavis
article
Annals of Applied Biology, 2008, 152 (2), pp.263-269. ⟨10.1111/j.1744-7348.2007.00213.x⟩
resume
Transmission of Potato yellow mosaic virus (PYMV) (bipartite begomovirus) to tomato by 50 Bemisia tabaci biotype B individuals was observed when the acquisition access period (AAP) was at least 3 h and the inoculation access period (IAP) at least 30 min. The transmission efficiency increased with the access period to reach 92% transmission after a 48-h IAP and 48-h AAP. The transmission efficiency decreased when whiteflies were fed on PYMV non-host plant between AAP and IAP. According to these results, we inoculated nine Solanum accessions with 50 whiteflies (48-h APP and 48-h IAP) to assess their resistance level. Four of these accessions with various levels of resistance were graft inoculated with PYMV. Although none of the accessions were immune, we observed a high level of resistance to PYMV in Solanum pimpinellifolium LA2187-5 (no symptoms after vector or graft inoculation) and in Solanum chilense LA1969 (no symptoms after vector inoculation and one plant with symptoms after graft inoculation). Inheritance of LA2187-5 resistance, investigated in F1 and F2 populations, appeared to be recessive. Fewer plants were infected by PYMV in S. pimpinellifolium LA1478 after vector inoculation than after graft inoculation. We hypothesised that this was because of vector resistance, which could also be effective against other begomoviruses.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Tomato fruit ascorbic acid content is linked with monodehydroascorbate reductase activity and tolerance to chilling stress
auteur
Rebecca Stevens, David Page, Barbara Gouble, Cecile Garchery, Daniel Zamir, Mathilde M. Causse
article
Plant, Cell and Environment, 2008, 31 (8), pp.1086-1096. ⟨10.1111/j.1365-3040.2008.01824.x⟩
resume
Quantitative trait loci (QTL) mapping is a step towards the identification of factors regulating traits such as fruit ascorbic acid content.A previously identified QTL controlling variations in tomato fruit ascorbic acid has been fine mapped and reveals that the QTL has a polygenic and epistatic architecture. A monodehydroascorbate reductase (MDHAR) allele is a candidate for a proportion of the increase in fruit ascorbic acid content.TheMDHARenzyme is active in different stages of fruit ripening, shows increased activity in the introgression lines containing the wild-type (Solanum pennellii) allele, and responds to chilling injury in tomato along with the reduced/oxidized ascorbate ratio. Low temperature storage of different tomato introgression lines with all or part of the QTL for ascorbic acid and with or without the wild MDHAR allele shows that enzyme activity explains 84% of the variation in the reduced ascorbic acid levels of tomato fruit following storage at 4 °C, compared with 38% at harvest under non-stress conditions. A role is indicated for MDHAR in the maintenance of ascorbate levels in fruit under stress conditions. Furthermore, an increased fruitMDHARactivity and a lower oxidation level of the fruit ascorbate pool are correlated with decreased loss of firmness because of chilling injury
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Characterization of a new potyvirus infecting pepper crops in Ecuador
auteur
Bérenger Janzac, Marie-Françoise Fabre, Alain Palloix, Benoît Moury
article
Archives of Virology, 2008, 153 (8), pp.1543-1548. ⟨10.1007/s00705-008-0132-8⟩
resume
Sequencing 2,951 nucleotides of the 3′ proximal region of the genome of a potyvirus isolate collected from Capsicum pubescens (rocoto) pepper in Ecuador revealed that this was the first representative of a new species tentatively named Ecuadorian rocoto virus (ERV). Phylogeny reconstruction showed that this isolate clustered with potato virus V (PVV), Peru tomato virus and wild potato mosaic virus into a monophyletic group, and was closest to PVV. The isolate was shown to be infectious in tobacco, tomato and, contrary to PVV, in pepper. The pvr2 1 , pvr2 2 , and Pvr4 genes present in many pepper cultivars conferred resistance toward this isolate and could help control ERV
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Adult plant resistance-related gene expression in 'Camp Remy' wheat inoculated with Puccinia Striiformis.
auteur
Stephanie Mallard, Sylvie Negre, Shala Pouya, Françoise Dedryver, Denis Gaudet, Zhen-Xiang Lu
article
Molecular Plant Pathology, 2008, 9 (2), pp.213-225. ⟨10.1111/j.1364-3703.2007.00459.x⟩
resume
The French wheat variety 'Camp Remy' (CR) possesses a durable, adult plant resistance to yellow rust (YR), caused by the pathogen Puccinia striiformis. Using cDNA–AFLP on different sets of heterogeneous inbred families (HIFs) derived from the cross CR × Récital, we compared gene expression profiles during one seedling and two adult developmental stages following inoculation with P. striiformis. Transcripts differentially expressed in response to YR infection were isolated and cloned. Sequence analysis of the resultant clones revealed several classes of putative genes, including those related to resistance/defence responses, transcription and signal transduction, and primary metabolism. The expression profiles of seven selected genes were obtained using real-time PCR in CR leaves at the same three stages of development. The results confirmed the stage-specific expression of the genes at one or two specific stages in response to P. striiformis infection and demonstrated that CR modifies the expression of some resistance/defence-related genes during its transition from the seedling to adult growth stages. These results provided the first clue to understand the molecular basis of quantitative trait loci for adult plant resistance to YR and connect it with durability.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
How does tomato quality (sugar, acid, and nutritional quality) vary with ripening stage, temperature, and irradiance
auteur
Hélène Gautier, Vicky Diakou-Verdin, Camille Benard, Maryse Reich, Michel Buret, Frederic Bourgaud, Jean-Luc Poessel, Catherine Caris-Veyrat, Michel M. Génard
article
Journal of Agricultural and Food Chemistry, 2008, 56 (4), pp.1241-1250. ⟨10.1021/jf072196t⟩
resume
The objective of this study was to understand the respective impact of ripening stage, temperature, and irradiance on seasonal variations of tomato fruit quality. During ripening, concentrations in reducing sugars, carotenes, ascorbate, rutin, and caffeic acid derivates increased, whereas those in titratable acidity, chlorophylls, and chlorogenic acid content decreased. Fruit temperature and irradiance affected final fruit composition. Sugars and acids (linked to fruit gustative quality) were not considerably modified, but secondary metabolites with antioxidant properties were very sensitive to fruit environment. Increased fruit irradiance enhanced ascorbate, lycopene, β-carotene, rutin, and caffeic acid derivate concentrations and the disappearance of oxidized ascorbate and chlorophylls. Increasing the temperature from 21 to 26 °C reduced total carotene content without affecting lycopene content. A further temperature increase from 27 to 32 °C reduced ascorbate, lycopene, and its precursor’s content, but enhanced rutin, caffeic acid derivates, and glucoside contents. The regulation by light and temperature of the biosynthesis pathways of secondary metabolites is discussed
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Change in anthocyanin concentrations in red apricot fruits during ripening
auteur
Sylvie Bureau, Catherine M.G.C. Renard, Maryse Reich, Christian Ginies, Jean Marc Audergon
article
LWT - Food Science and Technology, 2008, 42 (1), pp.372-377. ⟨10.1016/j.lwt.2008.03.010⟩
resume
Here we report on accumulation patterns of anthocyanins and of β-carotene during fruit maturation, between 82 and 125 days after flowering, of two apricot (Prunus armeniaca L.) cultivars, A3576 and A3751. Both cultivars displayed an intense red colour of the skin but differed in their genetic background. The pigments were extracted from skin and flesh, separately, and analysed using HPLC–DAD–MS. Out of three anthocyanins detected here, the major compound, cyanidin-3-O-rutinoside was present at 75%. The two minor compounds were cyanidin-3-O-glucoside and peonidin-3-O-rutinoside. This is the first time that peonidin-3-O-rutinoside has been detected in apricot fruit. During maturation, A3751 accumulated anthocyanins in both skin and flesh, whereas anthocyanins were present only in the skin of A3576. The skin anthocyanin content was higher in A3751 (296 mg kg−1) than in A3576 (41 mg kg−1). Maximum anthocyanin levels were attained after 108 and 118 days of flowering in A3751 and A3576, respectively, in conjunction with loss of firmness and red colour acquisition on the un-blushed side of the fruit. At the end of ripening, the β-carotene flesh concentration reached 5 mg kg−1 in A3576 and 15 mg kg−1 in A3751. A significant effect of environment was observed on the anthocyanin content in the two cultivars
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Application of reflectance colorimeter measurements and infrared spectroscopy methods to rapid and nondestructive evaluation of carotenoids content in apricot (Prunus armeniaca L.)
auteur
David Ruiz, Maryse Reich, Sylvie Bureau, Catherine M.G.C. Renard, Jean Marc Audergon
article
Journal of Agricultural and Food Chemistry, 2008, 56 (13), pp.4916-4922. ⟨10.1021/jf7036032⟩
resume
The importance of carotenoid content in apricot (Prunus armeniaca L.) is recognized not only because of the color that they impart but also because of their protective activity against human diseases. Current methods to assess carotenoid content are time-consuming, expensive, and destructive. In this work, the application of rapid and nondestructive methods such as colorimeter measurements and infrared spectroscopy has been evaluated for carotenoid determination in apricot. Forty apricot genotypes covering a wide range of peel and flesh colors have been analyzed. Color measurements on the skin and flesh (L*, a*, b*, hue, chroma, and a*/b* ratio) as well as Fourier transform near-infrared spectroscopy (FT-NIR) on intact fruits and Fourier transform mid-infrared spectroscopy (FT-MIR) on ground flesh were correlated with the carotenoid content measured by high-performance liquid chromatography. A high variability in color values and carotenoid content was observed. Partial least squares regression analyses between β-carotene content and provitamin A activity and color measurements showed a high fit in peel, flesh, and edible apricot portion (R2 ranged from 0.81 to 0.91) and low prediction error. Regression equations were developed for predicting carotenoid content by using color values, which appeared as a simple, rapid, reliable, and nondestructive method. However, FT-NIR and FT-MIR models showed very low R2 values and very high prediction errors for carotenoid content
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Insect-screened cultivation to reduce the invasion of tomato crops by Bemisia tabaci: modelling the impact on virus disease and vector
auteur
J. Holt, Claude Pavis, M. Marquier, T.C.B. Chancellor, Cica Urbino, Nathalie Boissot
article
Agricultural and Forest Entomology, 2008, 10 (1), pp.61-67. ⟨10.1111/j.1461-9563.2007.00356.x⟩
resume
In two experiments carried out in Guadeloupe, barriers were used to reduce the entry of the virus vector Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae)to tomato plots. The barriers erected around the crop were of insect-proof cloth fences (<50 mesh), 1.5 m in height, in the first experiment with a deltamethrintreated, insect-attracting strip facing inwards, and, in the second, with the barrier but no insecticide-treated strip. 2 A mathematical model of epidemic development was fitted to the symptom data from the treated and control (unprotected) tomato plots. There were two viruses present, tomato yellow leaf curl and potato yellow mosaic; specific detection confirmed that symptoms gave an accurate indication of infection and that the two virus diseases had similar progress curves. 3 Parameter estimates obtained by model-fitting suggested that the barriers reduced vector immigration by approximately 12-fold but that B. tabaci retention within the plots was also increased slightly despite the mortality caused by the insecticide-treated strips. Disease establishment was delayed by approximately 2 weeks. The results obtained in the second experiment involving barriers deployed without insecticide-treated strips could be explained by a large increase in B. tabaci retention within the barriers resulting in more rapid virus disease progress than in controls. The results of mathematical modelling indicate that partial insect barriers can be worse than none because sufficient whiteflies can enter to establish a population and, at the same time, large numbers are retained in the barrier plot, with the net effect being a more rapid population increase than in the absence of barriers.
typdoc
Journal articles
Accès au bibtex
BibTex

2007

Journal articles

titre
Inoculum production and long-term conservation methods for cucurbits and tomato powdery mildews
auteur
Marc Bardin, Muna E. Suliman, Anne-Marie Sage-Palloix, Youssif F. Mohamed, Philippe C. Nicot
article
Mycological Research, 2007, 111, pp.740-747. ⟨10.1016/j.mycres.2007.03.015⟩
resume
The behaviour of cucurbit powdery mildews (Podosphaera xanthii and Golovinomyces cichoracearum) and tomato powdery mildew (Oidium neolycopersici) infesting detached cotyledons of Lagenaria leucantha cv. 'Minibottle' was studied in order to develop an easy culture method for pure inoculum production, High spore production was found with a combination of mannitol (0.1 m), sucrose (0.02 m) and agar (8 g l(-1)) in the cotyledon survival medium. Sporulation on cotyledons and viability of conidia were affected by the age of culture for the three species of powdery mildew tested. The age of cotyledons had also an impact of the spore production. This method was used to produce large amounts of inoculum for P. xanthii, G. cichoracearum and O. neolycopersici and enable the development of other species of powdery mildew like Leveillula taurica. Freezing conidia in liquid nitrogen enabled the long-term conservation of P. xanthii without any loss of virulence. The same method was unsuccessful with G. cichotacearum, and L. taurica and partly successful with O. neolycopersici.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Sources of resistance to Watermelon Chlorotic Stunt Virus in melon
auteur
M.T. Yousif, A. Kheyr-Pour, B. Gronenborn, M. Pitrat, Catherine Dogimont
article
Plant Breeding, 2007, 126 (4), pp.422-427. ⟨10.1111/j.1439-0523.2007.01366.x⟩
resume
Watermelon Chlorotic Stunt Virus (WmCSV) is a bipartite geminivirus residing in the genus Begomovirus (family Geminiviridae) and is whitefly transmitted (Bemisia tabaci). WmCSV infects members of the Cucurbitaceae, and represents a considerable threat to melon and watermelon crops in Sudan, Yemen, and Iran. One hundred twenty-eight melon accessions, mostly collected from Sudan, were screened in the open-field in Sudan under severe whitefly inoculation pressure in order to identify sources of resistance to WmCSV. One WmCSV resistant line HSD 2445-005 selected from this first screening along with 22 new melon accessions were agro-inoculated with an infectious Sudanese clone of WmCSV. Ten accessions exhibited resistance to WmCSV infection upon agro-inoculation. Six of them were confirmed to have complete resistance to WmCSV through graft-inoculation as well as multiple field trials in Sudan. These lines include the Sudanese accession HSD 2445-005, the South African accession PI 282448, and three Indian accessions: 90625, PI 124112, and PI 414723. Resistant plants exhibited no disease symptoms, and virus DNA could not be detected by hybridization with a WmCSV-specific probe.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Diversity among landraces of Indian snapmelon (Cucumis melo var. momordica)
auteur
N.P.S. Dhillon, R. Ranjana, Kuldeep Singh, I. Eduardo, A.J. Monforte, Michel Pitrat, N.K. Dhillon, P.P. Singh
article
Genetic Resources and Crop Evolution, 2007, 54 (6), pp.1267-1283. ⟨10.1007/s10722-006-9108-2⟩
resume
Diversity among 36 snapmelon landraces, collected from 2 agro-ecological regions of India (9 agro-climatic sub-regions), was assayed using RAPD primers, morphological traits of plant habit and fruit, 2 yield-associated traits, pest and disease resistance and biochemical composition (TSS, ascorbic acid, titrable acidity). Typical differences among accessions were observed in plant and fruit characteristics and snapmelon germplasm with high titrable acidity and possessing resistance to downy mildew, Cucumber mosaic virus, Zucchini yellow mosaic virus, Papaya ringspot virus, Aphis gossypii and Meloidogyne incognita was noticed in the collection. RAPD based grouping analysis revealed that Indian snapmelon was rich in genetic variation and region and sub-region approach should be followed across India for acquisition of additional melon landraces. Accessions of var. agrestis and var. momordica clustered together and there was a separate cluster of the accessions of var. reticulatus. Comparative analysis of the genetic variability among Indian snapmelons and an array of previously characterized reference accessions of melon from Spain, Israel, Korea, Japan, Maldives, Iraq, Pakistan and India using SSRs showed that Indian snapmelon germplasm contained a high degree of unique genetic variability which was needed to be preserved to broaden the genetic base of melon germplasm available with the scientific community
typdoc
Journal articles
Accès au bibtex
BibTex
titre
History and iconography of the Solanaceae: Mandrake, a plant at the intersection of reason and irrationality
auteur
Jules Janick, M-Christin Daunay
article
Lettre Sol et Civilisation, 2007, 14, pp.3-4
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Sources de résistance naturelle au virus des plantes : statuts et perspectives
auteur
Andrew Maule, Carole Caranta, Margaret Boulton
article
Molecular Plant Pathology, 2007, 8 (2), pp.223-231
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Eurytoma amygdali menace l'amande en France
auteur
Muriel Millan, Jean François Mandrin, Henri Duval
article
Réussir Fruits et Légumes, 2007, 268, pp.48-49
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Are the polygenic architectures of resistance to Phytophthora capsici and P. parasitica independent in pepper
auteur
Julien Bonnet, Sarah Danan, Christine Boudet, Lorenzo Barchi, Anne-Marie Sage-Palloix, Bernard Caromel, Alain Palloix, Véronique Lefebvre
article
TAG Theoretical and Applied Genetics, 2007, 115 (2), pp.253-264. ⟨10.1007/s00122-007-0561-x⟩
resume
The pepper accession Criollo de Morelos 334 is the most efficient source of resistance currently known to Phytophthora capsici and P. parasitica. To investigate whether genetic controls of resistance to two Phytophthora species are independent, we compared the genetic architecture of resistance of CM334 to both Phytophthora species. The RIL population F5YC used to construct the high-resolution genetic linkage map of pepper was assessed for resistance to one isolate of each Phytophthora species. Inheritance of the P. capsici and P. parasitica resistance was polygenic. Twelve additive QTLs involved in the P. capsici resistance and 14 additive QTLs involved in the P. parasitica resistance were detected. The QTLs identified in this progeny were specific to these Phytophthora species. Comparative mapping analysis with literature data identified three colocations between resistance QTLs to P. parasitica and P. capsici in pepper. Whereas this result suggests presence of common resistance factors to the two Phytophthora species in pepper, which possibly derive from common ancestral genes, calculation of the colocation probability indicates that these colocations could occur by chance.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Evaluation de l'efficacité et de la durabilité des résistances à Globodera pallida PA2/3, provenant de Solanum vernei, S. Spegazzinii et S. sparsipilum.
auteur
Didier Mugniery, Olivier Plantard, Sylvain Fournet, Eric Grenier, Bernard Caromel, Marie-Claire Kerlan, Damien Picard, Daniel Ellisseche
article
Nematologia Mediterranea, 2007, 35 (2), pp.143-153
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Both additivity and epistasis control the genetic variation for fruit quality traits in tomato
auteur
Mathilde M. Causse, Jamila Chaïb, Laurent Lecomte, Michel Buret, Frederic F. Hospital
article
TAG Theoretical and Applied Genetics, 2007, 115 (3), pp.429-442. ⟨10.1007/s00122-007-0578-1⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Un marqueur de l'initiation de la maturité
auteur
Marie Grotte, Barbara Gouble, Patrice Reling, Jean Marc Audergon
article
Arboriculture Fruitière, 2007, 615-616, pp.21-25
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Sélection assistée par marqueurs pour une résistance polygénique : performance de différents schémas de sélection pour la résistance à Phytophthora capsici chez le piment
auteur
Alain Palloix, Arnaud Thabuis, Anne-Marie Sage-Palloix, Patrick Signoret, Frédéric Hospital, Véronique Lefebvre
article
Sélectionneur Français, 2007, 56, pp.15-18
resume
absent
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.science/hal-01193601/file/39369_20100128084711067_1.pdf BibTex
titre
Towards a virtual fruit focusing on quality: modelling features and potential uses
auteur
Michel M. Génard, Nadia Bertin, Charlotte Borel, Philippe Bussieres, Hélène Gautier, Robert Habib, M. Léchaudel, Alain Lecomte, Francoise F. Lescourret, Philippe Lobit, Bénédicte Quilot-Turion
article
Journal of Experimental Botany, 2007, 58 (5), pp.917-928. ⟨10.1093/jxb/erl287⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Inheritance and relationships of important agronomic traits in almond
auteur
Raquel Sánchez-Pérez, Encarnacion Ortega, Henri Duval, Pedro Martínez-Gómez, Federico Dicenta
article
Euphytica, 2007, 155 (3), pp.381-391. ⟨10.1007/s10681-006-9339-5⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Testing genetic control hypotheses for Plum pox virus (sharka) resistance in apricot
auteur
M. Rubio, Jean Marc Audergon, P. Martínez-Gómez, F. Dicenta
article
Scientia Horticulturae, 2007, 112 (4), pp.361-365. ⟨10.1016/j.scienta.2006.12.049⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
History and iconography of eggplant
auteur
M-Christin Daunay, Jules Janick
article
Chronica Horticulturae, 2007, 47 (3), pp.16-22
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced recombinant inbred line subsets for fast mapping
auteur
Lorenzo Barchi, Julien Bonnet, Christine Boudet, Patrick Signoret, Istvan Nagy, Sergio Lanteri, Alain Palloix, Véronique Lefebvre
article
Genome, 2007, 50 (1), pp.51-60. ⟨10.1139/G06-140⟩
resume
A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) was constructed from a population of 297 recombinant inbred lines. The parents were the large-fruited inbred cultivar ‘Yolo Wonder’ and the hot pepper line ‘Criollo de Morelos 334’, which is heavily used as a source of resistance to a number of diseases. A set of 587 markers (507 amplified fragment length polymorphisms, 40 simple sequence repeats, 19 restriction fragment length polymorphisms, 17 sequence-specific amplified polymorphisms, and 4 sequence tagged sites) were used to generate the map; of these, 489 were assembled into 49 linkage groups (LGs), including 14 LGs with 10 to 60 markers per LG and 35 with 2 to 9 markers per LG. The framework map covered 1857 cM with an average intermarker distance of 5.71 cM. Twenty-three LGs, composed of 69% of the markers and covering 1553 cM, were assigned to 1 of the 12 haploid pepper chromosomes, leaving 26 LGs (304 cM) unassigned. The chromosome framework map built with 250 markers led to a high level of mapping confidence and an average intermarker distance of 6.54 cM. By applying MapPop software, it was possible to select smaller subsets of 141 or 93 most informative individuals with a view to reducing the time and cost of further mapping and phenotyping. To define the smallest number of individuals sufficient for assigning any new marker to a chromosome, subsets from 12 to 45 individuals and a set of 13 markers distributed over all 12 chromosomes were screened. In most cases, the markers were correctly assigned to their expected chromosome, but the accuracy of the map position decreased as the number of individuals was reduced.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Coordinated and selective recruitment of eIF4E and eIF4G factors for potyvirus infection in Arabidopsis thaliana
auteur
Valerie Nicaise, Jean-Luc J.-L. Gallois, Faccila Chafiai, Leah M. Allen, Valerie Schurdi-Levraud, Karen Browning, Thierry Candresse, Carole Caranta, Olivier Le Gall, Sylvie S. German-Retana
article
FEBS Letters, 2007, 581 (5), pp.1041-1046. ⟨10.1016/j.febslet.2007.02.007⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Root-knot nematode (Meloidogyne spp.) Me resistance genes in pepper (Capsicum annuum L.) are clustered on the P9 chromosome
auteur
Caroline Djian-Caporalino, Ariane Fazari, Marie-Jeanne Arguel, Tatiana Vernié, Céline van de Casteele, Ingrid Faure, Geraldine Brunoud, Lucette Pijarowski, Alain Palloix, Véronique Lefebvre, Pierre Abad
article
TAG Theoretical and Applied Genetics, 2007, 114 (3), pp.473-486. ⟨10.1007/s00122-006-0447-3⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Molecular dissection of the potato virus Y VPg virulence factor reveals complex adaptations to the pvr2 resistance allelic series in pepper
auteur
Valérie Ayme, Julien Petit-Pierre, Sylvie Souche, Alain Palloix, Benoît Moury
article
Journal of General Virology, 2007, 88 (5), pp.1594-1601. ⟨10.1099/vir.0.82702-0⟩
resume
The virulence properties of potato virus Y (PVY) towards an allelic series at the pvr2 locus in pepper genotypes are related to variations in the genome-linked viral protein (VPg). Eleven amino acid substitutions in the central part of the VPg were identified in strains differing by their virulence properties and were introduced, either singly or in combination, in an infectious PVY clone to get an in-depth genetic analysis of the virulence determinant. The virulence spectrum of these mutants was evaluated by inoculation of four pepper genotypes carrying different alleles at the pvr2 locus. The mutations introduced had complex effects on virulence, including antagonistic epistasis and trade-offs for virulence towards different pvr2 alleles. In addition, several mutants showed new virulence properties that were unknown in the natural environment. Such complex effects of mutations on plant virus virulence are unprecedented. They provide a better understanding of the variable levels of durability of the resistance conferred by the different pvr2 alleles, and have important consequences for a durable management of the resistances.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
AtPRD1 is required for meiotic double strand break formation in Arabidopsis thaliana
auteur
Arnaud de Muyt, Daniel Vezon, Ghislaine G. Gendrot, Jean-Luc J.-L. Gallois, Rebecca Stevens, Mathilde Grelon
article
EMBO Journal, 2007, 26 (18), pp.4126-4137. ⟨10.1038/sj.emboj.7601815⟩
resume
The initiation of meiotic recombination by the formation of DNA double-strand breaks (DSBs) catalysed by the Spo11 protein is strongly evolutionary conserved. In Saccharomyces cerevisiae, Spo11 requires nine other proteins for meiotic DSB formation, but, unlike Spo11, few of these proteins seem to be conserved across kingdoms. In order to investigate this recombination step in higher eukaryotes, we have isolated a new gene, AtPRD1, whose mutation affects meiosis in Arabidopsis thaliana. In Atprd1 mutants, meiotic recombination rates fall dramatically, early recombination markers (e.g., DMC1 foci) are absent, but meiosis progresses until achiasmatic univalents are formed. Besides, Atprd1 mutants suppress DSB repair defects of a large range of meiotic mutants, showing that AtPRD1 is involved in meiotic recombination and is required for meiotic DSB formation. Furthermore, we showed that AtPRD1 and AtSPO11-1 interact in a yeast two-hybrid assay, suggesting that AtPRD1 could be a partner of AtSPO11-1. Moreover, our study reveals similarity between AtPRD1 and the mammalian protein Mei1, suggesting that AtPRD1 could be a Mei1 functional homologue.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Evaluation of watermelon and related species for resistance to race 1W powdery mildew
auteur
Angela Davis, Amnon Levi, Antonia Tetteh, Todd Wehner, Vincent Russo, Michel Pitrat
article
Journal of the American Society for Horticultural Science, 2007, 132 (6), pp.790-795
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Major proteome variations associated with cherry tomato pericarp development and ripening
auteur
Mireille Faurobert, Christina Mihr, Nadia Bertin, Tomasz Pawlowski, Luc Négroni, Nicolas Sommerer, Mathilde M. Causse
article
Plant Physiology, 2007, 143 (3), pp.1327-1346. ⟨10.1104/pp.106.092817⟩
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02667189/file/11011_20091103033129866_1.pdf BibTex
titre
Successful gene tagging in lettuce using the Tnt1 retrotransposon from tobacco
auteur
Marianne Mazier, Emmanuel Botton, Fabrice Flamain, Jean-Paul Bouchet, Béatrice Courtial, M-Christine M.-C. Chupeau, Yves Y. Chupeau, Brigitte B. Maisonneuve, Helene Lucas
article
Plant Physiology, 2007, 144 (1), pp.18-31. ⟨10.1104/pp.106.090365⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Biotechnology and horticulture
auteur
M-Christin Daunay, Jacques Boccon-Gibod, Alain Cadic, Marianne Mazier
article
Chronica Horticulturae, 2007, 47 (1), pp.6-16
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The distribution of copia-type retrotransposons and the evolutionary history of tomato and related wild species
auteur
S.M. Tam, Mathilde M. Causse, Cecile Garchery, Helene Burck, Corinne C. Mhiri, Marie Angele M. A. Grandbastien
article
Journal of Evolutionary Biology, 2007, 20 (3), pp.1056-1072. ⟨10.1111/j.1420-9101.2007.01293.x⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Physiological relationships among physical, sensory, and morphological attributes of texture in tomato fruits
auteur
Jamila Chaïb, Marie Francoise M. F. Devaux, Marie Grotte, Karine Robini, Mathilde M. Causse, Marc Lahaye, Isabelle Marty
article
Journal of Experimental Botany, 2007, 58 (8), pp.1915-1925. ⟨10.1093/jxb/erm046⟩
resume
Tomato texture is one of the critical components for the consumer's perception of fruit quality. Texture is a complex character composed of several attributes that are difficult to evaluate and which change during fruit ripening. This study investigated the texture of tomato fruits at the rheological, sensory, morphological, and genetic levels, and attempted to correlate several parameters. Analyses were performed on tomato fruits from introgressed lines carrying quantitative trait loci (QTLs) associated with texture traits localized on different chromosomes, in two genetic backgrounds. Rheological measurements were used to determine resistance to deformation and fruit elasticity. Sensory analysis was used to assess flesh firmness, juiciness, mealiness, and skin toughness. Image analysis was used to study fruit morphology and to define the cellular structure and heterogeneity of the pericarp. A highly significant correlation was observed between instrumental and sensory firmness. Moreover, correlations were also established between some texture traits and parameters of the pericarp cellular structure. Compared with QTLs detected in a previous study, the phenotypic effects expected for mealiness were confirmed in all lines, whereas, for firmness, they were not confirmed. Significant interactions between QTL and genetic background were observed for several traits. In addition, kinetic analysis showed that differences in firmness occurred from the early stages of fruit development. These results provide both a broad description of texture components and preliminary information to understand their genetic control.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Identification of plant genes regulated in resistant potato Solanum sparsipilum during the early stages of infection by Globodera pallida
auteur
Katell Jolivet, Eric Grenier, Jean-Paul Bouchet, Magali Esquibet, Marie-Claire Kerlan, Bernard Caromel, Didier Mugniery, Véronique Lefebvre
article
Genome, 2007, 50, pp.422-427. ⟨10.1139/G07-015⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Candidate Genes and Quantitative Trait Loci Affecting Fruit Ascorbic Acid Content in Three Tomato Populations
auteur
Rebecca Stevens, Michel Buret, Philippe Duffé, Cécile Garchery, Pierre Baldet, Christophe Rothan, Mathilde Causse
article
Plant Physiology, 2007, 143 (4), pp.1943-1953. ⟨10.1104/pp.106.091413⟩
resume
Fresh fruit and vegetables are a major source of ascorbic acid ( vitamin C), an important antioxidant for the human diet and also for plants. Ascorbic acid content in fruit exhibits a quantitative inheritance. Quantitative trait loci (QTL) for ascorbic acid content have been mapped in three tomato populations derived from crosses between cultivated tomato varieties (Solanum lycopersicum accessions) and three related wild species or subspecies. The first population consists of a set of introgression lines derived from Solanum pennellii, each containing a unique fragment of the wild species genome. The second population is an advanced backcross population derived from a cross between a cultivated tomato and a Solanum habrochaites (formerly Lycopersicum hirsutum) accession. The third population is a recombinant inbred line population derived from the cross between a cherry tomato line and a large fruited line. Common regions controlling ascorbic acid content have been identified on chromosomes 2, 8, 9, 10, and 12. In general, the wild alleles increased ascorbic acid content, but some improvement could also be provided by S. lycopersicum. Most QTLs appeared relatively stable over years and in different environments. Mapping of candidate genes involved in the metabolism of ascorbic acid has revealed a few colocations between genes and QTLs, notably in the case of a monodehydroascorbate reductase gene and a QTL present in two of the populations on chromosome 9 (bin 9-D), and a previously mapped GDP-mannose epimerase and a QTL on chromosome 9 (bin 9- J).
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTL analysis of resistance to sharka disease in the apricot (Prunus armeniaca L.) 'Polonais' x 'Stark Early Orange
auteur
Patrick Lambert, F. Dicenta, M. Rubio, Jean Marc Audergon
article
Tree Genetics and Genomes, 2007, 3 (4), pp.299-309. ⟨10.1007/S11295-006-0069-6⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Fast data preprocessing for chromatographic fingerprints of tomato cell wall polysaccharides using chemometric methods
auteur
Bernard Quemener, Dominique D. Bertrand, Isabelle Marty, Mathilde M. Causse, Marc Lahaye
article
Journal of Chromatography A, 2007, 1141 (1), pp.41-49. ⟨10.1016/j.chroma.2006.11.069⟩
resume
The variability in the chemistry of cell wall polysaccharides in pericarp tissue of red-ripe tomato fruit (Solanum lycopersicon Mill.) was characterized by chemical methods and enzymatic degradations coupled to high performance anion exchange chromatography (HPAEC) and mass spectrometry analysis. Large fruited line, Levovil (LEV) carrying introgressed chromosome fragments from a cherry tomato line Cervil (CER) on chromosomes 4 (LC4), 9 (LC9), or on chromosomes 1, 2, 4 and 9 (LCX) and containing quantitative trait loci (QTLs) for texture traits, was studied. In order to differentiate cell wall polysaccharide modifications in the tomato fruit collection by multivariate analysis, chromatograms were corrected for baseline drift and shift of the component elution time using an approach derived from image analysis and mathematical morphology. The baseline was first corrected by using a "moving window" approach while the peak-matching method developed was based upon location of peaks as local maxima within a window of a definite size. The fast chromatographic data preprocessing proposed was a prerequisite for the different chemometric treatments, such as variance and principal component analysis applied herein to the analysis. Applied to the tomato collection, the combined enzymatic degradations and HPAEC analyses revealed that the firm LCX and CER genotypes showed a higher proportion of glucuronoxylans and pectic arabinan side chains while the mealy LC9 genotype demonstrated the highest content of pectic galactan side chains. QTLs on tomato chromosomes 1, 2, 4 and 9 contain important genes controlling glucuronoxylan and pectic neutral side chains biosynthesis and/or metabolism.
typdoc
Journal articles
Accès au bibtex
BibTex

2006

Journal articles

titre
An eIF4E allele confers resistance to an uncapped and non-polyadenylated RNA virus in melon
auteur
Christine Nieto, Monica Morales, Gisella Orjeda, Christian Clepet, Amparo Monfort, Bénédicte Sturbois, Pere Puigdomenech, Michel Pitrat, Michel M. Caboche, Catherine Dogimont, Jordi Garcia-Mas, Miguel. A. Aranda, Abdelhafid Bendhamane
article
The Plant Journal, 2006, 48 (3), pp.452-462. ⟨10.1111/j.1365-313X.2006.02885.x⟩
resume
The characterization of natural recessive resistance genes and virus-resistant mutants of Arabidopsis have implicated translation initiation factors of the 4E family [eIF4E and eIF(iso)4E] as susceptibility factors required for virus multiplication and resistance expression. To date, viruses controlled by these genes mainly belong to the family Potyviridae. Melon necrotic spot virus (MNSV) belongs to the family Tombusviridae (genus Carmovirus) and is an uncapped and non-polyadenylated RNA virus. In melon, nsv-mediated resistance is a natural source of recessive resistance against all strains of MNSV except MNSV-264. Analyses of chimeras between non-resistance-breaking and resistance-breaking strains have shown that the avirulence determinant maps to the 3'-untranslated region (3'-UTR) of the viral genome. Using a combination of positional cloning and microsynteny analysis between Arabidopsis thaliana and melon, we genetically and physically delimited the nsv locus to a single bacterial artificial chromosome clone and identified the melon eukaryotic translation initiation factor 4E (Cm-eIF4E) as a candidate gene. Complementation analysis using a biolistic transient expression assay, confirmed Cm-eIF4E as the product of nsv. A single amino acid change at position 228 of the protein led to the resistance to MNSV. Protein expression and cap-binding analysis showed that Cm-eIF4E encoded by a resistant plant was not affected in it's cap-binding activity. The Agrobacterium-mediated transient expression of the susceptibility allele of Cm-eIF4E in Nicotiana benthamiana enhanced MNSV-264 accumulation. Based on these results, a model to explain melon resistance to MNSV is proposed. These data, and data from other authors, suggest that translation initiation factors of the eIF4E family are universal determinants of plant susceptibility to RNA viruses.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Large-scale analysis of mRNA translation states during sucrose starvation in Arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control
auteur
Maryse Nicolaï, M.A. Roncato, A.S. Canoy, D. Rouquié, X. Sarda, Georges Freyssinet, Christophe Robaglia
article
Plant Physiology, 2006, 141 (2), pp.663-673. ⟨10.1104/pp.106.079418⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Identification of QTLs for Ralstonia solanacearum race 3-phylotype II resistance in tomato
auteur
Amandine Carmeille, Carole Caranta, Jacques Dintinger, Philippe Prior, P. Luisetti, Pascale Besse
article
TAG Theoretical and Applied Genetics, 2006, 113 (1), pp.110-121. ⟨10.1007/s00122-006-0277-3⟩
resume
Resistance against a Ralstonia solanacearum race 3-phylotype II strain JT516 was assessed in a F-2:3 and a population of inbred lines (RIL), both derived from a cross between L. esculentum cv. Hawaii 7996 (partially resistant) and L. pimpinellifolium WVa700 (susceptible). Resistance criteria used were the percentage of wilted plants to calculate the AUDPC value, and bacterial colonization scores in roots and stem (hypocotyl and epicotyl) assessed in two independent greenhouse experiments conducted during the cool and hot seasons in Reunion Island, France. Symptoms were more severe during the cool season trials. Heritability estimates in individual seasons ranged from 0.82 to 0.88, depending on resistance criterion. A set of 76 molecular markers was used for quantitative trait loci (QTL) mapping using the single- and composite- interval mapping methods, as well as ANOVA. Four QTLs, named Bwr- followed by a number indicating their map location, were identified. They explained from 3.2 to 29.8% of the phenotypic variation, depending on the resistance criterion and the season. A major QTL, Bwr-6, and a minor one, Bwr-3, were detected in each season for all resistance criteria. Both QTLs showed stronger effects in the hot season than in the cool one. Their role in resistance to R. solanacearum race 3-phylotype II was subsequently confirmed in the RIL population derived from the same cross. Two other QTLs, Bwr-4 and Bwr-8, with intermediate and minor effects, respectively, were only detected in the hot season, demonstrating that environmental factors may strongly influence the expression of resistance against the race 3-phylotype II strain JT516. These QTLs were compared with those detected in the RIL population against race 1-phylotype I strain JT519 as well as those detected in other previous studies in the same genetic background against other race 1-phylotype I and II strains. This comparison revealed the possible occurrence of some phylotype-specific resistance QTLs in Hawaii 7996.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
In memory of Richard Neville Lester 1937-2006
auteur
M-Christin Daunay
article
Lettre Sol et Civilisation, 2006, 10, pp.2
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetics of fertility restoration in cytoplasmic male sterile pepper
auteur
Li-Hao Wang, Bao-Xi Zhang, Anne-Marie Daubèze, San-Wen Huang, Jia-Zhen Guo, Sheng-Li Mao, Alain Palloix, Yong-Chen Du
article
Agricultural Sciences in China, 2006, 5 (3), pp.188-195. ⟨10.1016/S1671-2927(06)60037-0⟩
resume
Pepper hybrid seeds production using male sterility could lower cost by reducing time and labour, and increase the genetic purity of the F, seeds. To investigate the genetics of fertility restoration of the Peterson cytoplasmic sterility in pepper, a doubled haploid population of 115 pepper lines obtained from anther culture of the F, hybrid between Yo10 Wonder (sterility maintainer line) and Perennial (fertility restorer line) and the parental lines were test-crossed by 770 13A (a strict cytoplasmic-genic male sterile line). The fertility of the test-crossed lines was assessed in greenhouse and open field with the following three criteria: pollen index (PI, visual estimation of pollen amount per flower), pollen number (PN, pollen counting under microscope), and seed number (SN, the number of seeds per fruit in open pollination). Correlations between the each couple of criteria within, as well as between the cultivation methods ranged from 0.55 to 0.84. Analysis of variance showed that the genotype (DH line) and environment were the significant sources of variation of the fertility. Narrow sense of heritance of fertility restoration ranged from 0.38 to 0.92, depending on the criteria and environment. The distribution of the progeny was continuous between the parental genotypes indicating the quantitative inheritance of fertility restoration. Inferred from segregation according to Snape et al.( 1984), the number of segregating genes was estimated to be that three to four genetic factors were involved in pollen traits (PI and PN) and five to eight genetic factors in seed production (SN). The heredity analysis of the CMS will be helpful for understanding of the genetic mechanism of the fertility restoration and the exploitation of the CMS in hybrid seed production.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map
auteur
Hans van Os, Sandra Andrzejewski, Erin Bakker, Imanol Barrena, Glenn J. Bryan, Bernard Caromel, Bilal Ghareeb, Edwige Isidore, Walter de Jong, Paul van Koert, Véronique Lefebvre, Dan Milbourne, Enrique Ritter, Jeroen N.A.M. Rouppe van Der Voort, Françoise Rousselle-Bourgeois, Joke van Vliet, Robbie Waugh, Richard G.F. Visser, Jaap Bakker, Herman J. van Eck
article
Genetics, 2006, 173 (2), pp.1075-1087. ⟨10.1534/genetics.106.055871⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
First known image of Cucurbita in Europe, 1503-1508
auteur
Harry Paris, M-Christin Daunay, Michel Pitrat, Jules Janick
article
Annals of Botany, 2006, 98 (1), pp.41-47. ⟨10.1093/aob/mcl082⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Different mutations in the genome-linked protein VPg of potato virus Y confer virulence on the pvr2 3 resistance in pepper
auteur
Valérie Ayme, Sylvie Souche, Carole Caranta, Mireille Jacquemond, Joël Chadoeuf, Alain Palloix, Benoît Moury
article
Molecular Plant-Microbe Interactions, 2006, 19 (5), pp.557-563. ⟨10.1094/MPMI-19-0557⟩
resume
Five different amino acid substitutions in the VPg of Potato virus Y were shown to be independently responsible for virulence toward pvr23 resistance gene of pepper. A consequence of these multiple mutations toward virulence involving single nucleotide substitutions is a particularly high frequency of resistance breaking (37% of inoculated plants from the first inoculation) and suggests a potentially low durability of pvr23 resistance. These five mutants were observed with significantly different frequencies, one of them being overrepresented. Genetic drift alone could not explain the observed distribution of virulent mutants. More plausible scenarios were obtained by taking into account either the relative substitution rates, the relative fitness of the mutants in pvr23 pepper plants, or both.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic structure in Tunisian apricot, Prunus armeniaca L., populations propagated by grafting: a signature of bottleneck effects and ancient propagation by seedlings
auteur
Bouchaib Khadari, L Krichen, Patrick Lambert, M. Marrakchi, Jean Marc Audergon
article
Genetic Resources and Crop Evolution, 2006, 53 (4), pp.811-819. ⟨10.1007/s10722-004-5721-0⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Test de résistance du melon au mildiou
auteur
Didier Besombes, Nathalie Giovinazzo
article
Cahier des Techniques de l'INRA, 2006, 57, pp.5-9
resume
Le Mildiou du melon est une maladie fongique causée par Pseudoperonospora cubensis, un oomycète qui se développe essentiellement sur la partie foliaire. Très largement répandu dans le monde, il est apparu en France en 1984. Il occasionne bien souvent des dégâts très importants. Les produits chimiques existants ne semblent efficaces qu’en traitements préventifs, en particulier à cause du développement très rapide de la maladie en conditions favorables ; d’où l’importance de la recherche de résistances génétiques.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02660647/file/CT57_art1_Besombes.pdf BibTex
titre
PI 525088-PMR, a melon race 1 powdery mildew-resistant watermelon line
auteur
Angela R. Davis, Amnon Levi, Todd Wehner, Michel Pitrat
article
HortScience, 2006, 41 (7), pp.1527-1528
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Vers une lutte durable contre les virus de plantes
auteur
Valérie Ayme, Benoît Moury, Ghislaine Nemouchi, Vincent Simon, Pascale Mistral, Sylvie Souche, Alain Palloix
article
PHM Revue Horticole, 2006, 484, pp.31-35
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Méthodes d'échantillonnage de fruits appliquées à l'évaluation de la qualité de l'abricot
auteur
Marie Grotte, Barbara Gouble, Patrice Reling, Marielle Boge, Jean Marc Audergon
article
Fruits, 2006, 61 (2), pp.135-147. ⟨10.1051/fruits:2006012⟩
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02661376/file/11103_20091222024611113_1.pdf BibTex
titre
Identification and characterization of nuclear microsatellites in mediterranean cedars (Cedrus sp.)
auteur
Jamila Chaïb, Sarah Danan, Bruno Jouaud, Linda S. Hagen, Francois Lefèvre, Bruno Fady
article
Molecular Ecology Notes, 2006, 6 (3), pp.840-842. ⟨10.1111/j.1471-8286.2006.01364.x⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A major gene mapped on chromosome XII is the main factor of a quantitatively inherited resistance to Meloidogyne fallax in Solanum sparsipilum
auteur
Abou Kouassi, Marie-Claire Kerlan, Bernard Caromel, Jean-Paul Dantec, Didier Fouville, Maria M. Manzanares-Dauleux, Daniel Ellisseche, Didier Mugniery
article
TAG Theoretical and Applied Genetics, 2006, 112 (4), pp.699-707. ⟨10.1007/s00122-005-0173-2⟩
resume
Meloidogyne fallax is an emerging pest in Europe and represents a threat for potato production. We report the mapping of genetic factors controlling a quantitative resistance against M. fallax identified in the Solanum sparsipilum genotype 88S.329.15. When infected, this genotype develops a necrotic reaction at the feeding site of the juveniles and totally prevents their development to the female stage. A "F1" diploid progeny consisting of 128 individuals was obtained using the potato (S. tuberosum) dihaploid genotype BF15 H1 as female progenitor. Sixty-eight hybrid genotypes displayed necrosis at the feeding site of the juveniles and 60 other genotypes showed no defence reaction. This suggested a monogenic control of the resistance. However, when considering the number of nematode females developed in their roots, a continuous distribution was observed for both "necrotic" and "non-necrotic" hybrid genotypes, indicating a polygenic control of the resistance. A linkage map of! each parental genotype was constructed using AFLP markers. The necrotic reaction (NR) was mapped as a qualitative trait on chromosome XII of the resistant genotype 88S.329.15. Quantitative trait locus (QTL) analysis for the number of nematode females developed per "F1" plant genotype was performed using the QTL cartographer software. No QTL was detected on the linkage map of the susceptible parent. A QTL explaining 94.5% of the phenotypic variation was mapped on chromosome XII of the resistant progenitor. This QTL, named MfaXIIspl, was mapped in a genomic region collinear to the map position of the Mi-3 gene conferring resistance to Meloidogyne incognita in tomato. It corresponds to the NR locus.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genotypic variation in induced resistance and induced susceptibility in the peach-Myzus persicae aphid system
auteur
Marie-Hélène Sauge, Florence Mus, Jean Philippe Lacroze, Thierry Pascal, Jocelyne Kervella, Jean-Luc Poessel
article
Oikos, 2006, 113 (2), pp.305-313. ⟨10.1111/j.2006.0030-1299.14250.x⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Solanaceae genetic resources in Europe
auteur
M-Christin Daunay, Willem van Dooijeweert, Lorenzo Maggioni
article
Lettre Sol et Civilisation, 2006, 12, pp.1-2
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Simultaneous mutations in translation initiation factors elF4E and elF(iso)4E are required to prevent pepper veinal mottle virus infection of pepper
auteur
Sandrine Ruffel, Jean-Luc J.-L. Gallois, Benoît Moury, Christophe Robaglia, Alain Palloix, Carole Caranta
article
Journal of General Virology, 2006, 87 (7), pp.2089-2098. ⟨10.1099/vir.0.81817-0⟩
resume
Capsicum resistance to Pepper veinal mottle virus (PVMV) results from complementation between the pvr2 and pvr6 resistance genes: recessive alleles at these two loci are necessary for resistance, whereas any dominant allele confers susceptibility. In line with previous results showing that pvr2 resistance alleles encode mutated versions of the eukaryotic translation initiation factor 4E (eIF4E), the involvement of other members of the eIF4E multigenic family in PVMV resistance was investigated. It was demonstrated that pvr6 corresponds to an eIF(iso)4E gene, predicted to encode the second cap-binding isoform identified in plants, Comparative genetic mapping in pepper and tomato indicated that eIF(iso)4E maps in the same genomic region as pvr6. Sequence analysis revealed an 82 nt deletion in eIF(iso)4E cDNAs from genotypes with the pvr6 resistance allele, leading to a truncated protein. This deletion was shown to co-segregate with pvr6 in doubled haploid and F-2 progeny. Transient expression in a PVMV-resistant genotype of eIF(iso)4E derived from a genotype with the pvr6(+) susceptibility allele resulted in loss of resistance to subsequent PVMV inoculation, confirming that pvr6 encodes the translation factor eIF(iso)4E. Similarly, transient expression of eIF4E from a genotype with the pvr2(+)-eIF4E susceptibility allele also resulted in loss of resistance, demonstrating that wild-type eIF4E and eIF(iso)4E are susceptibility factors for PVMV and that resistance results from the combined effect of mutations in the two cap-binding isoforms. Thus, whilst most potyviruses specifically require one eIF4E isoform to perform their replication cycle, PVMV uses either eIF4E or eIF(iso)4E for infection of pepper.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Gene list for melon
auteur
Michel Pitrat
article
Report - Cucurbit Genetics Cooperative, 2006, 28-29, pp.142-163
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Ravageur de l'amandier. Mieux connaître Eurytoma amygdali Enderlein
auteur
Henri Duval
article
Arboriculture Fruitière, 2006, 602, pp.28-31
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Translation initiation factors: a weak link in plant RNA virus infection
auteur
Christophe Robaglia, Carole Caranta
article
Trends in Plant Science, 2006, 11 (1), pp.40-45. ⟨10.1016/j.tplants.2005.11.004⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Volatile compounds in the skin and pulp of Queen Anne's pocket melon
auteur
Christophe Aubert, Michel Pitrat
article
Journal of Agricultural and Food Chemistry, 2006, 54 (21), pp.8177-8182. ⟨10.1021/jf061415s⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Host factors recruited by plant viruses during the infection process
auteur
Valerie Nicaise, Sylvie S. German-Retana, Bénédicte Doublet, Thierry Michon, Genevieve Roudet, Jocelyne J. Walter, Carole Caranta, Olivier Le Gall
article
Phytopathology, 2006, 96 (6S), pp.S84. ⟨10.1094/PHYTO.2006.96.6.S1⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Stability over genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato
auteur
Jamila Chaïb, Laurent Lecomte, Michel Buret, Mathilde M. Causse
article
TAG Theoretical and Applied Genetics, 2006, 112 (5), pp.934-944. ⟨10.1007/s00122-005-0197-7⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Proteomic analysis of tomato fruits from two ecotypes during ripening
auteur
Mariapina Rocco, Chiara d'Ambrosio, Simona Arena, Mireille Faurobert, Andrea Scaloni, Mauro Marra
article
Proteomics, 2006, 6 (13), pp.3781-3791
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Histoire et recherches: Mémoires d'aubergine
auteur
M-Christin Daunay
article
INRA Mensuel, 2006, 128, pp.30-46
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Technique for rapid, small-scale analysis of vitamin C levels in fruit and application to a tomato mutant collection
auteur
Rebecca Stevens, Michel Buret, Cecile Garchery, Yolande Carretero, Mathilde M. Causse
article
Journal of Agricultural and Food Chemistry, 2006, 54 (17), pp.6159-6165. ⟨10.1021/jf061241e⟩
typdoc
Journal articles
Accès au bibtex
BibTex

2005

Journal articles

titre
The tomato sequencing project, the first cornerstone of the International Solanaceae Project (SOL)
auteur
L.A. Mueller, S.D. Tanksley, J.J. Giovannoni, J. van Eck, S. Stack, - Doil Choi, - Byung Dong Kim, - Mingsheng Chen, - Zhukuan Cheng, - Chuanyou Li, - Hongqing Ling, - Yongbiao Xue, Graham Seymour, G. Bishop, Glenn Bryan, Ramesh Kumar Sharma, J. Khurana, A. Tyagi, D. Chattopadhyay, Nikki Singh, W. Stiekema, Pim Lindhout, T. Jesse, R. Klein Lankhorst, M. Bouzayen, D. Shibata, S. Tabata, A. Granell, M.A. Botella, G. Giuliano, L. Frusciante, Mathilde M. Causse, Daniel Zamir
article
Comparative and Functional Genomics, 2005, 6 (3), pp.153-158. ⟨10.1002/cfg.468⟩
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02680359/file/2005_Mueller_Comparative%20and%20Functional%20Genomics_1.pdf BibTex
titre
Effect of photoselective filters on the physical and chemical traits of vine-ripened tomato fruits
auteur
Hélène Gautier, H. Rocci, Michel Buret, Dominique Grasselly, Y. Dumas, Mathilde M. Causse
article
Canadian Journal of Plant Science, 2005, 85, pp.439-446
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Transcriptomic study of apricot fruit (Prunus armeniaca) ripening among 13 006 expressed sequence tags
auteur
Jérôme Grimplet, Charles Romieu, J.M. Audergon, Isabelle Marty, Guy Albagnac, P. Lambert, J.P. Bouchet, Nancy Terrier
article
Physiologia Plantarum, 2005, 125, pp.281-292. ⟨10.1111/j.1399-3054.2005.00563.x⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Sugar and acid concentrations associated with several qualitative traits in unselected Prunus persica x P. davidiana progenies
auteur
B.H. Wu, S.H. Li, Bénédicte Quilot, Michel M. Génard, Jocelyne Kervella, Laurent Gomez
article
Journal of Horticultural Science and Biotechnology, 2005, 80 (3), pp.335-339
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene
auteur
Sandrine Ruffel, Jean-Luc J.-L. Gallois, M.L. Lesage, Carole Caranta
article
Molecular Genetics and Genomics, 2005, 274 (4), pp.346-353
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Strain-specific and recessive QTLs involved in the control of partial resistance to Fusarium oxysporum f. sp. melonis race 1.2 in a recombinant inbred line population of melon
auteur
Laure Perchepied, Catherine Dogimont, Michel Pitrat
article
TAG Theoretical and Applied Genetics, 2005, 111, pp.65-74
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Inoculation contrôlée du melon par le CABYV
auteur
Nathalie Giovinazzo, Didier Besombes
article
Cahier des Techniques de l'INRA, 2005, Cahier des Techniques de l'INRA, N° Spécial : Bioagresseurs, pp.213-214
resume
Le CABYV (Cucurbit Aphid-Borne Yellows Virus) est un polérovirus dont l’intensité des symptômes (jaunissement) varie énormément suivant la saison et les variétés. Il n’affecte pas la qualité des fruits mais il engendre une baisse conséquente du rendement (avortement des fleurs femelles). Ce virus est transmis par pucerons selon le mode persistant. L’inoculation mécanique du CABYV est impossible.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02831478/file/CT2005_Bioagresseurs_art45.pdf BibTex
titre
Partial resistance of pepper to bacterial wilt is oligogenic and stable under tropical conditions
auteur
Denis Lafortune, M. Beramis, A.M. Daubèze, Nathalie Boissot, Alain Palloix
article
Plant Disease, 2005, 89 (5), pp.502-506
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Simulating genotypic variation of fruit quality in an advanced peach x Prunus davidiana cross
auteur
Bénédicte Quilot-Turion, Michel M. Génard, Francoise F. Lescourret, J. Kervella
article
Journal of Experimental Botany, 2005, 56 (422), pp.3071-3081. ⟨10.1093/jxb/eri304⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Ressources génétiques, diversité et amélioration du melon
auteur
Michel Pitrat
article
Sélectionneur Français, 2005, 55, pp.3-12
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Inheritance of resistance to Colletotrichum acutatum in Fragaria x ananassa
auteur
Beatrice Denoyes-Rothan, G. Guérin, E. Lerceteau-Köhler, G. Risser
article
Phytopathology, 2005, 95 (4), pp.405-412
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Tests de résistance du melon à l'oïdium sur disques de feuilles
auteur
Didier Besombes, Nathalie Giovinazzo
article
Cahier des Techniques de l'INRA, 2005, N° Spécial : Bioagresseurs, pp.153-156
resume
L’oïdium du melon se rencontre dans le monde entier en plein champ comme sous abri. Cette maladie qui atteint principalement les tiges et les feuilles (aspect blanc poudreux) provoque une baisse de rendement et une baisse de qualité des fruits. Les deux principaux agents responsables de l’oïdium sur melon sont Sphaerotheca fuliginea et Erysiphe cichoracearum (récemment rebaptisés respectivement Podosphaera xanthii et Golovinomyces cichoracearum). Au sein de ces deux espèces des races sont définies en fonction de réactions d’hôtes différentiels (à ce jour 2 races pour E. cichoracearum et 6 races pour S. fuliginea). Il s’agit de parasites obligatoires qui ne peuvent être multipliés que sur une plante sensible.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02832291/file/CT2005_Bioagresseurs_art33.pdf BibTex
titre
Analogues of virus resistance genes map to QTLs for resistance to sharka disease in Prunus davidiana
auteur
Véronique Decroocq, Marie Foulongne, Patrick Lambert, Olivier Le Gall, C. Mantin, Thierry Pascal, Valerie Schurdi-Levraud, J. Kervella
article
Molecular Genetics and Genomics, 2005, 272 (6), pp.680-689. ⟨10.1007/s00438-004-1099-0⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Replant diseases: bacterial community structure and diversity in peach rhizosphere as determined by metabolic and genetic fingerprinting
auteur
S. Piutti, S. Verger, Loic L. Pagès, Gilles Vercambre, Jean-Luc Poessel, P. Michelot
article
Soil Biology and Biochemistry, 2005, 37, pp.1738-1746
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Analysing the genetic control of peach fruit quality through an ecophysiological model combined with a QTL approach
auteur
Bénédicte Quilot-Turion, J. Kervella, Michel M. Génard, Francoise F. Lescourret
article
Journal of Experimental Botany, 2005, 56 (422), pp.3083-3092. ⟨10.1093/jxb/eri305⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Ethylene regulation of carotenoid accumulation and carotenogenic gene expression in colour-contrasted apricot varieties (Prunus armeniaca)
auteur
Isabelle Marty, S. Bureau, G. Sarkissian, Barbara Gouble, J.M. Audergon, Guy Albagnac
article
Journal of Experimental Botany, 2005, 56 (417), pp.1877-1886
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Molecular markers linked to papaya ring spot virus resistance and Fusarium race 2 resistance in melon
auteur
Y. Brotman, I. Kovalski, Catherine Dogimont, Michel Pitrat, V. Portnoy, N. Katzir, R. Perl-Treves
article
TAG Theoretical and Applied Genetics, 2005, 110 (2), pp.337-345
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Relationship between loci conferring downy mildew and powdery mildew resistance in melon assessed by quantitative trait loci mapping
auteur
Laure Perchepied, Marc Bardin, Catherine Dogimont, Michel Pitrat
article
Phytopathology, 2005, 95 (5), pp.556-565. ⟨10.1094/PHYTO-95-0556⟩
resume
Partial resistance to downy mildew (Pseudoperonospora cubensis) and complete resistance to powdery mildew (Podosphaera xanthii races 1, 2, 3, and 5 and Golovinomyces cichoracearum race 1) were studied using a recombinant inbred line population between ‘PI 124112’ (resistant to both diseases) and ‘Védrantais’ (susceptible line). A genetic map of melon was constructed to tag these resistances with DNA markers. Natural and artificial inoculations of Pseudoperonospora cubensis were performed and replicated in several locations. One major quantitative trait loci (QTL), pcXII.1, was consistently detected among the locations and explained between 12 to 38% of the phenotypic variation for Pseudoperonospora cubensis resistance. Eight other Pseudoperonospora cubensis resistance QTL were identified. Artificial inoculations were performed with several strains of four races of Podosphaera xanthii and one race of G. cichoracearum. Two independent major genes, PmV.1 and PmXII.1, were identified and shown to be involved in the simple resistance to powdery mildew. Three digenic epistatic interactions involving four loci were detected for two races of Podosphaera xanthii and one race of G. cichoracearum. Co-localization between PmV.1, resistance genes, and resistance genes homologues was observed. Linkage between the major resistance QTL to Pseudoperonospora cubensis, pcXII.1, and one of the two resistance genes to powdery mildew, PmXII.1, was demonstrated.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02682583/file/2005-Perchepied-Phytopath_1.pdf BibTex
titre
Cell expansion and endoreduplication show a large genetic variability in pericarp and contribute strongly to tomato fruit growth
auteur
Catherine Cheniclet, - Wen Ying Rong, Mathilde M. Causse, Nathalie Frangne, Laurence Bolling, Jean-Pierre Carde, Jean-Pierre Renaudin
article
Plant Physiology, 2005, 139, pp.1984-1994
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Systematic silencing of a tobacco nitrate reductase transgene in lettuce (Lactuca sativa L.)
auteur
V. Dubois, Emmanuel Botton, Christian C. Meyer, Aurélie Rieu, Magali M. Bedu, Brigitte B. Maisonneuve, Marianne Mazier
article
Journal of Experimental Botany, 2005, 56 (419), pp.2379-2388. ⟨10.1093/jxb/eri230⟩
resume
A population of 50 independent transgenic lettuces transformed with a nitrate reductase coding sequence under the control of the 35S promoter was studied. None of them showed significantly lower nitrate levels when compared with the untransformed plants, despite the presence of nitrate reductase (NR) activity that derives from the transgene in at least four of the transformants. No repercussion on total NR activity (endogenous1transgenic) was detected in these plants. Nevertheless, 28% of the transformants showed phenotypes characteristic of a general silencing of the NR genes as already described in tobacco and potato, i.e. bleaching of the leaves leading to the death of the plant. By northern blots, it was shown that the transgene was silenced in these chlorotic plants and also in the plants that did not show symptoms of chlorosis. Thus a silencing process specifically directed against the NR mRNA derived from the transgene occurred very early in the development of all the plants studied, whatever homologous endogenous NR mRNA is present in the plant. In some cases this transgene-specific silencing was shown subsequently to extend to the homologous endogenous NR mRNA. These results suggest that, in lettuce, the level of nitrate reductase mRNA is under tight expression control and this is able specifically to target transgenic transcripts by a post-transcriptional gene silencing (PTGS) mechanism during the first stage of development of the plantlet.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Fruit load or fruit position alters response to temperature and subsequently cherry tomato quality
auteur
Hélène Gautier, A. Rocci, Michel Buret, Dominique Grasselly, Mathilde M. Causse
article
Journal of the Science of Food and Agriculture, 2005, 85, pp.1009-1016. ⟨10.1002/jsfa.2060⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Evaluation of maize inbreds for maize stripe virus and maize mosaic virus resistance: disease progress in relation to time and the cumulative number of planthoppers
auteur
Jacques Dintinger, Nathalie Boissot, Frédéric Chiroleu, P. Hamon, Bernard Reynaud
article
Phytopathology, 2005, 95 (6), pp.600-607. ⟨10.1094/PHYTO-95-0600⟩
resume
Five tropical maize lines were tested and compared with the susceptible control line B73 for resistance to Maize stripe virus (MStV) and Maize mosaic virus (MMV), both propagatively transmitted by the planthopper Peregrinus maidis (Homoptera: Delphacidae). Resistance to each virus was evaluated separately by artificial inoculations with planthoppers viruliferous for either one virus or the other. Disease incidence and symptom severity progression were quantified in relation to time and the cumulative number of planthoppers. Line Hi40 was found to be susceptible to MStV and highly resistant to MMV. Generally, no MMV symptoms developed on Hi40, even under intense inoculation pressure by a large number of viruliferous planthoppers. Line Rev81 showed a partial but strong resistance to MStV, which mainly reduced disease incidence. Nevertheless, this resistance to MStV was the highest ever reported and held up, even when challenged by large numbers of planthoppers. The percentage of infected plants in line Rev81 never exceeded 30 to 40% in our experiments. Moderate levels of resistance to MStV, and to a lesser extent MMV, were found in lines 37-2, A211, and Mp705. However, resistance in these lines was completely overcome using a large number of insects transmitting either of the two viruses. These results suggest that different types of resistance to MMV and MStV are available in maize lines from Caribbean and Mascarene germ plasm. The expression of virus-specific resistance identified in Hi40 and Rev81 lines was not affected by intense inoculation pressure. In contrast, the moderate resistance in 37-2, A211, and Mp705 was partially effective against both viruses but not at high inoculation pressure. These different types of resistance, when present in the same genotype, could provide protection against both viruses.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02675954/file/EVALUATION_1.pdf BibTex
titre
Evaluacion de nuevas selecciones de patrones de melocotonero resistentes a nematodos agalladores
auteur
R. Rubio-Cabetas, J. Gomez-Aparisi, Pere Arus, C. Xiloyannis, B. Dichio, M. Di Vito, Marc M. Kleinhentz, Elisabeth Dirlewanger, Jean-Luc Poessel, Daniel Esmenjaud
article
Fruticultura Profesional, 2005, 152, pp.53-58
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Une méthode simple et efficace pour tester la résistance au virus de la mosaïque de la laitue sur des plantes de laitue cultivées in vitro
auteur
K. Bollore, Verane Sarnette, Sylvie S. German-Retana, Fabrice Flamain, V. Dubois, Emmanuel Botton, Hervé Lot, Sylvie Souche, Olivier Le Gall, Thierry Candresse, Yves Chupeau, M.C. Chupeau, Brigitte Maisonneuve, Marianne Mazier
article
Cahier des Techniques de l'INRA, 2005, N° Spécial : Bioagresseurs, pp.209-212
resume
Le virus de la mosaïque de la laitue (LMV) est un potyvirus potentiellement très grave pour la production de laitues. Les programmes d’étude des interactions potyvirus/plantes ont de plus en plus recours à la manipulation de matériel génétiquement modifié (virus ou plantes) ou de quarantaine. Le facteur limitant reste le nombre d’individus à cribler pour leur comportement vis-à-vis du virus dans les conditions de confinement appropriées. C’est pourquoi nous avons développé une méthode de criblage sur plantules cultivées in vitro.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02682892/file/2005_Bollore_TechINRA_Phenotyp_1.pdf BibTex
titre
Tests de résistance du melon à la fusariose vasculaire
auteur
Didier Besombes, Nathalie Giovinazzo
article
Cahier des Techniques de l'INRA, 2005, N° Spécial: Bioagresseurs, pp.119-122
resume
Fusarium oxysporum f. sp. melonis est présent dans de nombreux pays. Il est bien souvent dommageable et peut provoquer la mortalité de l’ensemble des plantes d’une parcelle. De ce fait c’est une des maladies les plus graves sur Melon. Quatre races ont été décrites pour lesquelles des gènes de résistance ont été trouvés : Fom-1 (résistance à la race 0 et à la race 2), Fom-2 (résistance à la race 0 et à la race 1) et une résistance partielle polygénique pour la race 1-2.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02832289/file/CT2005_Bioagresseurs_art25.pdf BibTex
titre
Impact of melon accessions resistant to aphids on the demographic potential of silverleaf whitefly
auteur
Nicolas Sauvion, V. Mauriello, Benjamin Renard, Nathalie Boissot
article
Journal of Economic Entomology, 2005, 98 (2), pp.557-567
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Resistance quantitative trait loci originating from Solanum sparsipilum act independently on the sex ratio of Globodera pallida and together for developing a necrotic reaction
auteur
Bernard Caromel, Didier Mugniery, Marie-Claire Kerlan, S. Andrzejewski, Alain Palloix, Daniel Ellissèche, F. Rousselle-Bourgeois, Véronique Lefebvre
article
Molecular Plant-Microbe Interactions, 2005, 18 (11), pp.1186-1194
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Modification of photosynthetic regulation in tomato overexpressing glutathione peroxidase
auteur
Stéphane Herbette, Aline Le Menn, Patrick Rousselle, Thierry Ameglio, Zehava Faltin, Gerard Branlard, Yuval Eshdat, Jean-Louis J.-L. Julien, Joël Drevet, Patricia Roeckel-Drevet
article
BBA - Biochimica et Biophysica Acta, 2005, 1724 (1-2), pp.108-118. ⟨10.1016/j.bbagen.2005.04.018⟩
resume
To investigate the function of glutathione peroxidase (GPX) in plants, we produced transgenic tomato plants overexpressing an eukaryotic selenium-independent GPX (GPX5). We show here that total GPX activity was increased by 50% in transgenic plants, when compared to control plants transformed with the binary vector without the insert (PZP111). A preliminary two-dimensional electrophoretic protein analysis of the GPX overexpressing plants showed notably a decrease in the accumulation of proteins identified as rubisco small subunit I and fructose-1,6-bisphosphate aldolase, two proteins involved in photosynthesis. These observations, together with the fact that in standard culture conditions, GPX-overexpressing plants were not phenotypically distinct from control plants prompted us to challenge the plants with a chilling treatment that is known to affect photosynthesis activity. We found that upon chilling treatment with low light level, photosynthesis was not affected in GPX-overexpressing plants while it was in control plants, as revealed by chlorophyll fluorescence parameters and fructose-1,6-biphosphatase activity. These results suggest that overexpression of a selenium-independent GPX in tomato plants modifies specifically gene expression and leads to modifications of photosynthetic regulation processes.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Serological, molecular, and pathotype diversity of pepper veinal mottle virus and chili veinal mottle virus
auteur
Benoît Moury, Alain Palloix, Carole Caranta, Patrick Gognalons, Sylvie Souche, Kahsay Gebre Selassie, Georges Marchoux
article
Phytopathology, 2005, 95 (3), pp.227-232. ⟨10.1094/PHYTO-95-0227⟩
resume
Variability within the pepper-infecting potyviruses Pepper veinal mottle virus (PVMV) and Chili veinal mottle virus (ChiVMV) in Africa and Asia was investigated. Coat protein (CP) gene sequence diversity revealed three clades that corresponded to three geographic locations and there was no evidence of presence of the ChiVMV/Asian group in western or central Africa. These clades included closely related isolates that potentially belong to two viral species, which is consistent with current nomenclature. These clades could not be unambiguously identified with polyclonal antisera; however, reverse transcription-polymerase chain reactions allowed differentiation of the isolates into two species based on a large indel in the CP gene. PVMV and ChiVMV isolates were classified into three and two pathotypes, respectively, in relation to pepper genotypes carrying different resistance factors. Specificity of resistance only partially corresponded to molecular diversity of the isolates. Only one isolate of PVMV could infect pepper genotypes carrying the two recessive genes pvr6 and pvr2 2; however, these genotypes were not infected by PVMV in field trials in Senegal, despite a high prevalence of PVMV in the surrounding pepper plants.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02683216/file/2005-Moury-Phytopath_1.pdf BibTex
titre
Changes in sugar and organic acid concentrations during fruit maturation in peaches, P. davidiana and hybrids as analyzed by principal component analysis
auteur
B.H. Wu, Bénédicte Quilot-Turion, Michel M. Génard, J. Kervella, S.H. Li
article
Scientia Horticulturae, 2005, 103, pp.429-439
typdoc
Journal articles
Accès au bibtex
BibTex

2004

Journal articles

titre
Molecular characterization of a WEE1 gene homologue in tomato (Lycopersicon esculentum Mill.)
auteur
Nathalie Gonzalez, Michel Hernould, F. Delmas, Frederic Gévaudant, Philippe Duffe, Mathilde M. Causse, Armand Mouras, C. Chevalier
article
Plant Molecular Biology, 2004, 56, pp.849-861
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Shape, mass and dry matter content of peaches of varieties with different domestication levels
auteur
Bénédicte Quilot-Turion, J. Kervella, Michel M. Génard
article
Scientia Horticulturae, 2004, 99, pp.387-393
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTL analysis of quality traits in an advanced backcross between Prunus persica cultivars and the wild relative species P. davidiana
auteur
Bénédicte Quilot-Turion, B.H. Wu, J. Kervella, Michel M. Génard, Marie Foulongne, K. Moreau
article
TAG Theoretical and Applied Genetics, 2004, 109, pp.884-897. ⟨10.1007/s00122-004-1703-z⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Marker-assisted selection for the wide-spectrum resistance to root-knot nematodes conferred by the Ma gene from Myrobolan plum (Prunus cerasifera) in interspecific Prunus material
auteur
A.C. Lecouls, Véronique Bergougnoux, M.J. Rubio-Cabetas, Nathalie Bosselut, R. Voisin, Jean-Luc Poessel, Mireille Faurobert, A. Bonnet, G. Salesses, Elisabeth Dirlewanger, Daniel Esmenjaud
article
Molecular Breeding, 2004, 13, pp.113-124
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Marker-assisted introgression of 4 Phytophthora capsici resistance QTL alleles into a bell pepper line: validation of additive and epistatic effects
auteur
A. Thabuis, Alain Palloix, Bertrand Servin, A.M. Daubèze, Patrick Signoret, Frederic F. Hospital, Véronique Lefebvre
article
Molecular Breeding, 2004, 14, pp.9-20
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Salade. Interpréter le code sextet d'une race
auteur
Brigitte B. Maisonneuve
article
Réussir Fruits et Légumes, 2004, 234, pp.48
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A genetic map of candidate genes and QTLs involved in tomato fruit size and composition
auteur
Mathilde M. Causse, Philippe Duffe, M.C. Gomez, Michel Buret, Rene Damidaux, Daniel Zamir, A. Gur, Christian Chevalier, M. Lemaire-Chamley, Christophe Rothan
article
Journal of Experimental Botany, 2004, 55 (403), pp.1671-1685. ⟨10.1093/jxb/erh207⟩
resume
In order to screen for putative candidate genes linked to tomato fruit weight and to sugar or acid content, genes and QTLs involved in fruit size and composition were mapped. Genes were selected among EST clones in the TIGR tomato EST database (http://www.tigr.org/tdb/tgi/Igi/) or corresponded to genes preferentially expressed in the early stages of fruit development. These clones were located on the tomato map using a population of introgression lines (ILs) having one segment of Lycopersicon pennellii (LA716) in a L. esculentum (M82) background. The 75 ILs allowed the genome to be segmented into 107 bins. Sixty-three genes involved in carbon metabolism revealed 79 loci. They represented enzymes involved in the Calvin cycle, glycolysis, the TCA cycle, sugar and starch metabolism, transport, and a few other functions. In addition, seven cell-cycle-specific genes mapped into nine loci. Fourteen genes, primarily expressed during the cell division stage, and 23 genes primarily expressed during the cell expansion stage, revealed 24 and 26 loci, respectively. The fruit weight, sugars, and organic acids content of each IL was measured and several QTLs controlling these traits were mapped. Comparison between map location of QTLs and candidate gene loci indicated a few candidate genes that may influence the variation of sugar or acid contents. Furthermore, the gene/QTL locations could be compared with the loci mapped in other tomato populations.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Mutations in potato virus Y genome-linked protein determine virulence toward recessive resistances in Capsicum annuum and Lycopersicon hirsutum
auteur
Benoît Moury, Caroline Morel, Elisabeth Ida Johansen, Laurent Guilbaud, Sylvie Souche, Valérie Ayme, Carole Caranta, Alain Palloix, Mireille Jacquemond
article
Molecular Plant-Microbe Interactions, 2004, 17 (3), pp.322-329. ⟨10.1094/MPMI.2004.17.3.322⟩
resume
The recessive resistance genes pot-1 and pvr2 in Lycopersicon hirsutum and Capsicum annuum, respectively, control Potato virus Y (PVY) accumulation in the inoculated leaves. Infectious cDNA molecules from two PVY isolates differing in their virulence toward these resistances were obtained using two different strategies. Chimeras constructed with these cDNA clones showed that a single nucleotide change corresponding to an amino acid substitution (Arg119His) in the central part of the viral protein genome-linked (VPg) was involved in virulence toward the pot-1 resistance. On the other hand, 15 nucleotide changes corresponding to five putative amino acid differences in the same region of the VPg affected virulence toward the pvr21 and pvr22 resistances. Substitution models identified six and five codons within the central and C terminal parts of the VPg for PVY and for the related potyvirus Potato virus A, respectively, which undergo positive selection. This suggests that the role of the VPg-encoding region is determined by the protein and not by the viral RNA apart from its protein-encoding capacity.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02682733/file/2004-Moury-MPMI_1.pdf BibTex
titre
Durable virus resistance in plants through conventional approaches: a challenge
auteur
Hervé Lecoq, Benoît Moury, Cecile Desbiez, Alain Palloix, Michel Pitrat
article
Virus Research, 2004, 100, pp.31-39. ⟨10.1016/j.virusres.2003.12.012⟩
resume
Breeding for virus resistance is often considered the most efficient and simplest way to avoid the losses due to plant virus diseases. Resistance mechanisms are very diverse and interact with various stages of the virus cycle in the host plant. Resistances may also differ in their specificity, stability and durability. Breeding for resistance is a long and costly process, therefore to be cost effective it should provide durable protection. Three pathosystems are discussed to illustrate some of the field and laboratory approaches that can be used to assess resistance durability: Cucumber mosaic virus-specific resistance in melon, Zucchini yellow mosaic virus tolerance in zucchini squash, and extreme resistance to Potato virus X in potato. The possibility of predicting resistance durability is discussed in relation to the nature of the resistance, the genetic changes required for a virus to overcome the resistance and the effects of such changes on virus fitness.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Analysis of genotypic variation in fruit flesh total sugar content via an ecophysiological model applied to peach
auteur
Bénédicte Quilot-Turion, Michel M. Génard, J. Kervella, Francoise F. Lescourret
article
TAG Theoretical and Applied Genetics, 2004, 109 (2), pp.440-449. ⟨10.1007/s00122-004-1651-7⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Polygenic inheritance of partial resistance to Fusarium oxysporum f.sp. melonis race 1.2 in melon
auteur
Laure Perchepied, Michel Pitrat
article
Phytopathology, 2004, 94 (12), pp.1331-1336
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTL analysis of fertility restoration in cytoplasmic male sterile pepper
auteur
L.H. Wang, B.X. Zhang, Véronique Lefebvre, S.W. Huang, A.M. Daubèze, Alain Palloix
article
TAG Theoretical and Applied Genetics, 2004, 109, pp.1058-1063
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Leaf light-saturated photosynthesis for wild and cultivated peach genotypes and their hybrids: a simple mathematical modelling analysis
auteur
Bénédicte Quilot-Turion, Michel M. Génard, J. Kervella
article
Journal of Horticultural Science and Biotechnology, 2004, 79 (4), pp.546-553
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A putative CA2+ and calmodulin dependent protein kinase required for bacterial and fungal symbioses
auteur
Julien Lévy, Cécile Bres, René Geurts, Boulos Chalhoub, Olga Kulikova, Gérard Duc, Etienne-Pascal Journet, Jean-Michel Ané, Emmanuelle Lauber, Ton Bisseling, Jean Dénarié, Charles Rosenberg, Frédéric Debellé
article
Science, 2004, 303 (5662), pp.1361-1364. ⟨10.1126/science.1093038⟩
resume
Legumes can enter into symbiotic relationships with both nitrogen-fixing bacteria (rhizobia) and mycorrhizal fungi. Nodulation by rhizobia results from a signal transduction pathway induced in legume roots by rhizobial Nod factors. DMI3 , a Medicago truncatula gene that acts immediately downstream of calcium spiking in this signaling pathway and is required for both nodulation and mycorrhizal infection, has high sequence similarity to genes encoding calcium and calmodulin-dependent protein kinases (CCaMKs). This indicates that calcium spiking is likely an essential component of the signaling cascade leading to nodule development and mycorrhizal infection, and sheds light on the biological role of plant CCaMKs.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Are neopolyploids a likely route for a transgene walk to the wild ? The Aegilops ovata x Triticum tirgidum durum case
auteur
J.L. David, E. Benavente, C. Brès-Patry, J.C. Dusautoir, M. Echaide
article
Biological Journal of the Linnean Society, 2004, 82, pp.503-510
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Intérêt nutritionnel de la tomate: impact des variétés et des itinéraires post-récolte
auteur
B. Navez, M. Jost, Michel Buret, Mathilde M. Causse
article
Infos CTIFL, 2004, 204, pp.27-33
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A simple and efficient method for testing lettuce mosaic virus resistance in in vitro cultivated lettuce
auteur
Marianne Mazier, Sylvie S. German-Retana, Fabrice Flamain, V. Dubois, Emmanuel Botton, Verane Sarnette, Olivier Le Gall, Thierry Candresse, Brigitte B. Maisonneuve
article
Journal of Virological Methods, 2004, 116 (2), pp.123-131
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Quelles tomates pour quel goût
auteur
Mathilde M. Causse
article
Campagnes Solidaires , 2004, 187, 1 p
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Structural analysis of the eucaryotic initiation factor 4E gene controlling potyvirus resistance in pepper: exploitation of a BAC library
auteur
Sandrine Ruffel, Carole Caranta, Alain Palloix, Véronique Lefebvre, Michel M. Caboche, Abdelhafid Bendahmane
article
Gene, 2004, 338, pp.209-216. ⟨10.1016/j.gene.2004.05.010⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Bactériose du melon: acquis et perspectives
auteur
P. Mention, Daniel Lavigne, F. Leix-Henry, S. Bochu, Cindy E. Morris, Philippe Prior, Michel Pitrat, Louis Mercy, O. Dours
article
PHM Revue Horticole, 2004, 459, pp.22-26
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genomic and cDNA microsatellites from apricot (Prunus armeniaca L.)
auteur
L.S. Hagen, Jamila Chaïb, Bruno Fady, Véronique Decroocq, J.P. Bouchet, P. Lambert, J.M. Audergon
article
Molecular Ecology Notes, 2004, 4, pp.742-745
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Microsatellite markers in the hexaploid Prunus domestica species and parentage lineage of three European plum cultivars using nuclear and chloroplast simple-sequence repeats
auteur
Véronique Decroocq, L.S. Hagen, M.G. Favé, Jean-Philippe Eyquard, Andre Pierronnet
article
Molecular Breeding, 2004, 13 (2), pp.135-142. ⟨10.1023/B:MOLB.0000018761.04559.b3⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
An integrated genetic linkage map of pepper (Capsicum spp.)
auteur
I. Paran, J. Rouppe van Der Voort, Véronique Lefebvre, M. Jahn, Laurane Landry, M. van Schriek, B. Tanyolac, Carole Caranta, A. Ben Chaim, K. Livingstone, Alain Palloix, J. Peleman
article
Molecular Breeding, 2004, 13, pp.251-261
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Breeding for resistance to begomovirus in tropic-adapted tomato genotypes
auteur
Océane Gomez, M. Pinion, Yolande Martinez, M. Quinones, D. Fonseca, H. Laterrot
article
Plant Breeding, 2004, 123, pp.275-279
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Marker-assisted introgression of five QTLs controlling fruit quality traits into three tomato lines revealed interactions between QTLs and genetic backgrounds
auteur
L. Lecomte, Philippe Duffe, Michel Buret, Bertrand Servin, Frederic F. Hospital, Mathilde M. Causse
article
TAG Theoretical and Applied Genetics, 2004, 109, pp.658-668. ⟨10.1007/s00122-004-1674-0⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic linkage maps of two apricot cultivars (Prunus armeniaca L.) compared with the almond Texas x peach Earlygold reference map for Prunus
auteur
Patrick Lambert, L.S. Hagen, Pere Arus, Jean Marc Audergon
article
TAG Theoretical and Applied Genetics, 2004, 108 (6), pp.1120-1130. ⟨10.1007/s00122-003-1526-3⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The Am gene controlling resistance to Alfalfa mosaic virus in tomato is located in the cluster of dominant resistance genes on chromosome 6
auteur
Giuseppe Parrella, André Moretti, Patrick Gognalons, Marie-Laure Lesage, Georges Marchoux, Kahsay Gebre Selassie, Carole Caranta
article
Phytopathology, 2004, 94 (4), pp.345-350. ⟨10.1094/PHYTO.2004.94.4.345⟩
resume
The dominant gene Am from Lycopersicon hirsutum f. sp. glabratum PI134417 confers resistance to most strains of Alfalfa mosaic virus, including the recently identified necrotic strains. The phenotypic response includes a lack of symptom development following mechanical inoculation of leaves. To study the resistance mechanism controlled by Am, biological (back-inoculation to susceptible hosts), serological (double-antibody sandwich, enzyme-linked immunosorbent assay), and molecular (reverse transcription-polymerase chain reaction and hybridization with specific riboprobes) methods of virus detection have been conducted on mechanically inoculated PI134417 leaves. The virus was never recovered, indicating that Am acts by an inhibition of viral accumulation during the early events of the virus life cycle. Am has been mapped genetically to the short arm of tomato chromosome 6 in the resistance hotspot, which includes the R-genes Mi and Cf-2/Cf-5 and the quantitative resistance factors Ty-1, Ol-1, and Bw-5.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02683338/file/2004-Parella-Phytopath_1.pdf BibTex
titre
The arabidopsis root transcriptome by serial analysis of gene expression. Gene identification using the genome sequence
auteur
Cécile Fizames, Stephane Munos, C. Cazettes, Philippe Nacry, Jossia Boucherez, Frédéric Gaymard, D. Piquemal, Valérie Delorme, T. Commes, Patrick Doumas, R. Cooke, Julien Marti, Herve Sentenac, Alain Gojon
article
Plant Physiology, 2004, 134, pp.67-80. ⟨10.1104/pp.103.030536⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Sugar and acid content and their genotypic correlations of unselected P. persica x P. davidiana progenies as affected by hairness and flesh color
auteur
- Wu Ben-Hong, - Li Shao-Hua, Bénédicte Quilot-Turion, Michel M. Génard, J. Kervella
article
Agricultural Sciences in China, 2004, 3 (2), pp.136-142
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato
auteur
L. Lecomte, V. Saliba-Colombani, A. Gautier, M.C. Gomez-Jimenez, Philippe Duffe, Michel Buret, Mathilde M. Causse
article
Molecular Breeding, 2004, 13, pp.1-14
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Phenotypic and molecular evaluation of a recurrent selection program for a polygenic resistance to Phytophthora capsici in pepper
auteur
A. Thabuis, Véronique Lefebvre, G. Bernard, A.M. Daubèze, Therese Phaly, E. Pochard, Alain Palloix
article
TAG Theoretical and Applied Genetics, 2004, 109, pp.342-351. ⟨10.1007/s00122-004-1633-9⟩
typdoc
Journal articles
Accès au bibtex
BibTex

2003

Journal articles

titre
Somatic hybrids between Solanum melongena and S. sisymbrifolium, as a useful source of resistance against bacterial and fungal wilts
auteur
Cécile Collonnier, Isabelle Fock-Bastide, Marie-Christine Daunay, Aline Servaes, Fernand Vedel, Sonja Siljak-Yakovlev, Vongthip Souvannavong, Darasinh Sihachakr
article
Plant Science, 2003, 164 (5), pp.849 - 861. ⟨10.1016/S0168-9452(03)00075-X⟩
resume
By using electrofusion of mesophyll protoplasts, 4 clones of somatic hybrids were produced between Solanum melongena cv. Pusa purple cluster and Solanum sisymbrifolium, a sexually incompatible wild relative resistant to bacterial (Ralstonia solanacearum) and fungal (Verticillium dahliae ) wilts. All hybrids were morphologically homogeneous, normal and intermediate between the parents. They set flowers and produced fruits with empty seeds. Their hybrid status was confirmed by examining isoenzymes and random amplified polymorphism DNA analysis. Chloroplast-specific-cleaved amplified polymorphism sequence markers provided evidence that the 4 somatic hybrids possessed chloroplast genome from S. sisymbrifolium . Flow cytometry and chromosome countings revealed that all selected hybrids were tetraploids (2n /4x /48 chromosomes). The parental origin of the hybrid chromosomes was determined by using the techniques of genomic in situ hybridisation. Each hybrid contained one complete set of chromosomes from both parents. Neither spatial separation and recombinant chromosomes nor translocation could be demonstrated during mitotic metaphase. In vitro tests for resistance, using suspensions of two strains of R. solanacearum (race 1 and race 3) and the filtrate of culture medium of one strain of V. dahliae revealed that S. melongena was highly susceptible, whereas S. sisymbrifolium had variable levels of resistance. All somatic hybrids tested showed good levels of resistance, intermediate between those of the parents.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Do genetic make-up and growth manipulation affect tomato fruit size by cell number, or cell size and DNA endoreduplication
auteur
Nadia Bertin, C. Borel, B. Brunel, Catherine Cheniclet, Mathilde M. Causse
article
Annals of Botany, 2003, 92 (3), pp.415-424
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Influence of hairless of fruit epidermis and flesh color on contents of sugars and acids and their relationship in peach
auteur
- Wu Ben-Hong, - Li Shao-Hua, Bénédicte Quilot-Turion, Michel M. Génard, J. Kervella
article
Scientia Agricultura Sinica, 2003, 36 (12), pp.1540-1544
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Stylar ribonucleases in almond: correlation with and prediction of incompatibility genotypes
auteur
R. Boskovic, K.R. Tobutt, I. Batlle, Henri Duval, P. Martínez-Gómez, T.M. Gradziel
article
Plant Breeding, 2003, 122, pp.70-76
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Comparative mapping of Phytophthora resistance loci in pepper germplasm: evidence for conserved resistance loci across Solanaceae and for a large genetic diversity
auteur
A. Thabuis, Alain Palloix, Stéphanie Pflieger, A.M. Daubèze, Carole Caranta, Véronique Lefebvre
article
TAG Theoretical and Applied Genetics, 2003, 106, pp.1473-1485
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Quel est votre diagnostic ?
auteur
Dominique Blancard, Sophie Chamont, Marie-Christine Daunay
article
PHM Revue Horticole, 2003, 445, pp.53-54
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Relationship between skin speckle, soluble solids content and transpiration rate in nectarines
auteur
B.H. Wu, Michel M. Génard, J. Kervella, S.H. Li, Remi Laurent
article
European Journal of Horticultural Science, 2003, 68 (2), pp.83-85
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Analysis of genotypic variation of sugar and acid contents in peaches and nectarines through the principle component analysis
auteur
- Benhong Wu, Bénédicte Quilot-Turion, J. Kervella, Michel M. Génard, - Shaohua Li
article
Euphytica, 2003, 132, pp.375-384
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The potential of Prunus davidiana for introgression into peach (Prunus persica (L.) Batsch) assessed by comparative mapping
auteur
Marie Foulongne, Thierry Pascal, Pere Arus, J. Kervella
article
TAG Theoretical and Applied Genetics, 2003, 107 (2), pp.227-238
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTLs for powdery mildew resistance in peach x Prunus davidiana crosses: consistency across generations and environments
auteur
Marie Foulongne, Thierry Pascal, F. Pfeiffer, J. Kervella
article
Molecular Breeding, 2003, 12, pp.33-50
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Regolazione genica e composizione dei carotenoidi in varieta di albicocco a diversa colorazione
auteur
Isabelle Marty, G. Sarkissian, S. Bureau, M. Reich, Barbara Gouble, Marie Josèphe Amiot, J.M. Audergon, Guy Albagnac
article
Rivista di Frutticoltura e di Ortofloricoltura, 2003, 5, pp.73-76
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Gènes naturels de résistance aux virus chez les plantes: relations entre structure et fonction
auteur
Carole Caranta, Sandrine Ruffel, M.H. Dussault
article
Virologie, 2003, 7 (3), pp.165-175
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Localisation and movement of plum pox virus in apricot stem tissues
auteur
F. Dicenta, P. Martínez-Gómez, M. Rubio, J.M. Audergon
article
Annals of Applied Biology, 2003, 142, pp.99-105
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Mapping QTLs for resistance against Globodera pallida (Stone) Pa2/3 in a diploid potato progeny originating from Solanum spegazzinii
auteur
Bernard Caromel, Didier Mugniery, Véronique Lefebvre, S. Andrzejewski, D. Ellisèche, Marie-Claire Kerlan, Patrick Rousselle, F. Rousselle-Bourgeois
article
TAG Theoretical and Applied Genetics, 2003, 106, pp.1517-1523
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The eukaryotic translation initiation factor 4E controls lettuce susceptibility to the potyvirus Lettuce mosaic virus
auteur
Valerie Nicaise, Sylvie German Retana, R. Sanjuan, Marie-Pierre Dubrana, Marianne Mazier, Brigitte B. Maisonneuve, Thierry Candresse, Carole Caranta, Olivier Le Gall
article
Plant Physiology, 2003, 132, pp.1272-1282
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02679237/file/2003_Nicaise_PlantPhysiol_eIF4E_1.pdf BibTex
titre
Chromosome location of tomato ESTs related to carbon metabolism
auteur
Philippe Duffe, M.C. Gomez, D. Just, M. Lemaire-Chamley, Christophe Rothan, Mathilde M. Causse
article
Report of the Tomato Genetics Cooperative, 2003, 53, pp.16-18
typdoc
Journal articles
Accès au bibtex
BibTex
titre
SNP-based codominant markers for a recessive gene conferring resistance to corky root rot (Rhizomonas suberifaciens) in lettuce (Lactuca sativa)
auteur
S. Moreno-Vazquez, O.E. Ochoa, N. Faber, S. Chao, J.M.E. Jacobs, Brigitte B. Maisonneuve, R.V. Kesseli, R.W. Michelmore
article
Genome, 2003, 46, pp.1059-1069
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTLs for resistance to powdery mildew in pepper under natural and artificial infections
auteur
Véronique Lefebvre, A.-M. Daubèze, J. Rouppe van Der Voort, J. Peleman, Marc Bardin, Alain Palloix
article
TAG Theoretical and Applied Genetics, 2003, 107 (4), pp.661-666. ⟨10.1007/s00122-003-1307-z⟩
resume
Epidemics of powdery mildew due to Leveillula taurica is an increasing problem in pepper production areas, particularly in coastal regions or greenhouse cultivation. The highly resistant genitor 'H3' was submitted to genetic analysis and QTL mapping in order to promote the introgression of its oligogenic resistance into large and sweet-fruited cultivars. The doubled-haploid progeny from the cross 'H3' (resistant) by 'Vania' (susceptible) was tested for resistance under both natural field infection and artificial inoculation tests, and QTL detection was compared for those two methods. Seven genomic regions including additive QTLs and epistatic interactions were detected, explaining altogether the major part of genotypic variance. Two genomic regions were common to both the evaluation methods, whereas other QTLs were method-specific, reflecting the environment dependence of powdery mildew epidemics. Orthologies with tomato genomic regions carrying resistance genes to L. taurica and Oidium lycopersicum were revealed by comparative mapping with pepper. Tight linkages between the detected QTLs and virus resistance or fruit color traits in pepper were also shown, which adds to the agronomic importance of these regions in pepper breeding programs.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Amélioration de la qualité gustative des tomates: les avancées des recherches
auteur
Mathilde M. Causse, Michel Buret
article
Presse Info INRA, 2003, 6, 3 p
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Inheritance of nutritional and sensory quality traits in fresh market tomato and relation to consumer preferences
auteur
Mathilde M. Causse, Michel Buret, K. Robini, P. Verschave
article
Journal of Food Science, 2003, 68 (7), pp.2342-2350
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Biochemical basis of low fruit quality of Prunus davidiana, a pest and disease resistance donor for peach breeding
auteur
Annick Moing, Jean-Luc Poessel, Laurence Svanella-Dumas, Michèle Loonis, J. Kervella
article
Journal of the American Society for Horticultural Science, 2003, 128 (1), pp.55-62
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Toward a marker-dense meiotic map of the potato genome: lessons from linkage group 1
auteur
E. Isidore, H. van Os, S. Andrzejewski, Julie Bakker, I. Barrena, G.J. Bryan, Bernard Caromel, H. van Eck, B. Ghareeb, W. de Jong, P. van Kroert, Véronique Lefebvre, D. Milbourne, E. Ritter, J. Rouppe van Der Voort, F. Rousselle-Bourgeois, J. van Vliet, Robbie Waugh
article
Genetics, 2003, 165, pp.2107-2116
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Development and transferability of apricot and grape EST microsatellite markers across taxa
auteur
Véronique Decroocq, M.G. Favé, Lynda Hagen, Louis Bordenave, Stephane Decroocq
article
TAG Theoretical and Applied Genetics, 2003, 106, pp.912-922
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Field resistance to Bemisia tabaci in Cucumis melo
auteur
Nathalie Boissot, Denis Lafortune, Claude Pavis, Nicolas Sauvion
article
HortScience, 2003, 38 (1), pp.77-80
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Linkage map of Cucumis melo including phenotypic traits and sequence-characterized genes
auteur
L. Silberstein, I. Kovalski, Y. Brotman, Christophe Périn, Catherine Dogimont, Michel Pitrat, J. Klingler, G. Thompson, V. Portnoy, N. Katzir, R. Perl-Treves
article
Genome, 2003, 46, pp.761-773
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Aubergine. Evolution des problèmes de viroses
auteur
Georges Marchoux, Patrick Gognalons, Marie-Christine Brand-Daunay
article
Réussir Fruits et Légumes, 2003, 217, pp.42-44
resume
Aubergine. Evolution des problèmes de viroses
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTL analysis of morphological traits in eggplant and implications for conservation of gene function during evolution od solanaceous species
auteur
A. Frary, S. Doganlar, M.C. Daunay, S.D. Tanksley
article
TAG Theoretical and Applied Genetics, 2003, 107 (2), pp.359-370
typdoc
Journal articles
Accès au bibtex
BibTex
titre
There is more to tomato fruit colour than candidate carotenoid genes
auteur
- Yong-Sheng Liu, A. Gur, G. Ronen, Mathilde M. Causse, Rene Damidaux, Michel Buret, J. Hirschberg, Daniel Zamir
article
Plant Biotechnology Journal, 2003, 1 (3), pp.195-207
typdoc
Journal articles
Accès au bibtex
BibTex

2002

Journal articles

titre
Recessive resistance genes against potyviruses are localized in colinear genomic regions of the tomato (Lycopersicon spp.) and pepper (Capsicum spp.) genomes
auteur
G. Parrella, S. Ruffel, A. Moretti, C. Morel, A. Palloix, C. Caranta
article
TAG Theoretical and Applied Genetics, 2002, 105 (6), pp.855-861. ⟨10.1007/s00122-002-1005-2⟩
resume
Resistance against both Potato virus Y (PVY) and Tobacco etch virus (TEV) was identified in the wild tomato relative Lycopersicon hirsutum PI247087. Analysis of the segregation ratio in F2/F3 and BC1 interspecific progenies indicated that a single recessive gene, or two very tightly linked recessive loci, are involved in resistance to both potyviruses. This locus was named pot-1. Using amplified fragment length polymorphism markers and a set of L. hirsutum introgression lines, pot-1 was mapped to the short arm of tomato chromosome 3, in the vicinity of the recessive py-1 locus for resistance to corky root rot. Because of the occurrence of phenotypically similar genes in pepper (Capsicum spp.), the comparative genetics of resistance to potyviruses between tomato and pepper was investigated. Unlike most of the comparative genetic studies on resistance genes, pot-1 was tightly flanked by the same restriction fragment length polymorphism (RFLP) markers than the pvr2/pvr5 locus for resistance to PVY and TEV from pepper. These results may indicate that recessive resistance genes against potyviruses evolve less rapidly than the majority of the dominant genes cloned so far, and consequently may belong to a different family of resistance genes.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Two expansin cDNAs from Prunus armeniaca expressed during fruit ripening are differently regulated by ethylene
auteur
Didier Mbéguié-A-Mbéguié, Barbara Gouble, Rose-Marie Gomez, Jean-Marc Audergon, Guy Albagnac, Bernard Fils-Lycaon
article
Plant Physiology and Biochemistry, 2002, 40 (5), pp.445-452. ⟨10.1016/S0981-9428(02)01391-8⟩
resume
Little is known about gene expression during fruit ripening of apricot (Prunus armeniaca L. cv. Bergeron), especially for enzymes involved in cell wall modifications. A partial cDNA clone encoding a protein homologous to expansin was isolated from a ripe apricot fruit cDNA library. This clone was used to isolate two full-length expansin cDNAs, Pa-Exp1 (accession no. U93167) and Pa-Exp2 (accession no. AF038815) from the same cDNA library. The predicted polypeptides encoded by these two cDNAs are different and belong to the α-expansin family; Pa-Exp1 and Pa-Exp2 are two different members of a multigene family. These two clones are mostly expressed in fruit, during its ripening. Pa-Exp1 mRNA accumulated abundantly at the half-ripe stage of fruit development and decreased thereafter. Pa-Exp2 mRNA level increased from the immature-green stage to the half-ripe stage where it peaked before declining. During the ripening process, Pa-Exp1 and Pa-Exp2 gene expression appeared to be positively correlated with fruit size. Post-harvest treatments by air, ethylene, and 1-methyl cyclopropene led us to conclude that Pa-Exp1 appears to be developmentally down-regulated by ethylene while Pa-Exp2 is not affected. The relationship between Pa-Exp1, Pa-Exp2 and the softening process is also discussed.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits
auteur
Mathilde M. Causse, V. Saliba-Colombani, L. Lecomte, Philippe Duffe, Patrick Rousselle, Michel Buret
article
Journal of Experimental Botany, 2002, 53 (377), pp.2089-2098
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes
auteur
Véronique Lefebvre, Stéphanie Pflieger, A. Thabuis, Carole Caranta, Anne Blattes, J.C. Chauvet, A.M. Daubèze, Alain Palloix
article
Genome, 2002, 45 (5), pp.839-854
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The Arabidopsis eukaryotic initiation factor (iso)4E is dispensable for plant growth but required for susceptibility to potyviruses
auteur
A. Duprat, Carole Caranta, Frederic Revers, Benoît Menand, K.S. Browning, Christophe Robaglia
article
The Plant Journal, 2002, 32, pp.927-934
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Inheritance of green peach aphid resistance in the peach cultivar 'Rubira
auteur
Thierry Pascal, F. Pfeiffer, J. Kervella, J.P. Lacroze, M.H. Sauge
article
Plant Breeding, 2002, 121, pp.459-461
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Lutte génétique contre les pathogènes des légumes en cultures abritées. Où en est-on dans le bassin méditerranéen
auteur
H. Laterrot
article
Phytoma la Défense des Végétaux, 2002, 552, pp.29-31
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Stade de maturité à la récolte et température de conservation : quelle influence sur les qualités organoleptiques de la tomate ? Des choix décisifs en récolte et en post-récolte
auteur
B. Navez, M. Jost, Nicolas Lancelin, Dominique Grasselly, Michel Buret, Mathilde M. Causse
article
L'Echo - Centre d'affaires du MIN, 2002, 177, pp.36-41
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The use of green fluorescent protein-tagged recombinant viruses to test Lettuce mosaic virus resistance in lettuce
auteur
Thierry Candresse, Olivier Le Gall, Brigitte B. Maisonneuve, Sylvie S. German-Retana, E. Redondo
article
Phytopathology, 2002, 92 (2), pp.169-176
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant
auteur
S. Doganlar, A. Frary, M.C. Daunay, R.N. Lester, S.D. Tanksley
article
Genetics, 2002, 161, pp.1713-1726
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic control of fruit shape acts prior to anthesis in melon (Cucumis melo L.)
auteur
Christophe Périn, L.S. Hagen, Nathalie Giovinazzo, Didier Besombes, Catherine Dogimont, Michel Pitrat
article
Molecular Genetics and Genomics, 2002, 266, pp.942-950
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic diversity in apricot revealed by AFLP markers: species and cultivar comparisons
auteur
L.S. Hagen, Bouchaïb Khadari, P. Lambert, J.M. Audergon
article
TAG Theoretical and Applied Genetics, 2002, 105, pp.298-305
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Arbres à noyau. La technique de greffage herbacé. Nouvelle perspective en matière de multiplication végétative des arbres fruitiers
auteur
F. Gurrieri, M. Massé, M.C. Lemoine, Jean-Luc Poessel
article
Arboriculture Fruitière, 2002, 557, pp.56-58
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A fruit-specific phospho enol pyruvate carboxylase is related to rapid growth of tomato fruit
auteur
Carine Guillet, Daniel Just, Nathalie Bénard, Agnès Destrac-Irvine, Pierre Baldet, Michel Hernould, Mathilde Causse, Philippe Raymond, Christophe Rothan
article
Planta, 2002, 214 (5), pp.717-726. ⟨10.1007/s00425-001-0687-z⟩
resume
Malic and citric acids accumulate in cherry tomato (Lycopersicon esculentum Mill.) fruit during the period of rapid growth, from the end of cell division to the onset of ripening. The involvement of phosphoenolpyruvate carboxylase (PEPCase, EC 4.1.1.31) in organic acid accumulation and tomato fruit development was investigated. Two PEPCases, named LYCes;Ppc1 and LYCes;Ppc2 and mapped to chromosomes 12 and 7, respectively, were shown to be differentially expressed during tomato fruit development. LYCes;Ppc1 mRNA was present in all fruit tissues and in all other plant organs examined. In contrast, LYCes;Ppc2 was strongly and specifically expressed in fruit from the end of cell division to ripening. No LYCes;Ppc2 expression was detected by northern blot in other plant tissues. In fruit, the increase in LYCes;Ppc2 mRNA was closely followed by an increase in fruit PEPCase protein and activity, and was coincident with the increased accumulation of malate and citrate during the initial period of rapid growth rate, from 8 to 20 days post anthesis. Localization of LYCes;Ppc2 mRNA in young tomato fruit by in situ hybridization revealed that LYCes;Ppc2 is preferentially expressed in large cells of the pericarp and in enlarging cells of the gel surrounding the seeds. Examination of the kinetic and regulatory properties of the PEPCases of growing and ripening fruit further showed that PEPCase in growing fruit is less sensitive to low pH and malate inhibition, indicating a high phosphorylation state and/or the presence of a PEPCase isoform with these characteristics. Taken together, these results indicate that in developing tomato fruit PEPCase is probably important in permitting the synthesis of organic acids to provide the turgor pressure necessary for cell expansion.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Resistance gene homologues in melon are linked to genetic loci conferring disease and pest resistance
auteur
Y. Brotman, L. Silberstein, I. Kovalski, Christophe Périn, Catherine Dogimont, Michel Pitrat, J. Klinger, G.A. Thompson, R. Perl-Treves
article
TAG Theoretical and Applied Genetics, 2002, 104, pp.1055-1063
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Induced resistance by Myzus persicae in the peach cultivar 'Rubira
auteur
Marie-Hélène Sauge, Jean Philippe Lacroze, Jean-Luc Poessel, Thierry Pascal, Jocelyne Kervella
article
Entomologia Experimentalis et Applicata, 2002, 102 (1), pp.29-37. ⟨10.1046/j.1570-7458.2002.00922.x⟩
resume
The effect of a previous infestation by the green peach aphid Myzus persicae (Sulzer) on the settling behaviour and reproduction of the same aphid species was investigated in the resistant peach cultivar Rubira, and compared with that observed in the susceptible control cultivar GF305. A previous infestation of 48 h triggered induced resistance in Rubira. There were significantly fewer aphids settling on preinfested than on uninfested plants, indicating an increased rejection of Rubira as a host plant. The level of induced resistance in preinfested plants was positively related to the duration of the first infestation. In GF305, previous infestation had no detrimental effect on aphid settlement and even slightly enhanced larviposition by adult females. The aphid probing behaviour after a 48-h preinfestation was also monitored for 8 h with the electrical peneration graph (EPG) technique. On preinfested GF305, most EPG parameters indicated an enhanced host plant acceptance. On preinfested GF305, aphids produced less sieve element salivation and more continuous sap ingestion than on uninfested GF305, indicating that the previous aphids provoked changes in plant properties beneficial to the test aphids. In Rubira, a major induced factor of resistance was thought to be expressed in the sieve element as phloem sap ingestion was 4-fold shorter on preinfested than on uninfested plants. The time taken by the aphid stylets to reach a sieve element was also significantly increased on preinfested Rubira, suggesting the induction of resistance factors outside the phloem. The originality of the Rubira/M. persicae interaction is discussed in the perspective of a better understanding of plant induced responses to aphids.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A natural recessive resistance gene against potato virus Y in pepper corresponds to the eukariotic initiation factor 4E (elF4E)
auteur
Sandrine Ruffel, M.H. Dussault, Alain Palloix, Benoît Moury, Abdelhafid Bendahmane, Christophe Robaglia, Carole Caranta
article
The Plant Journal, 2002, 32 (6), pp.1067-1075. ⟨10.1046/j.1365-313X.2002.01499.x⟩
resume
We show here that the pvr2 locus in pepper, conferring recessive resistance against strains of potato virus Y (PVY), corresponds to a eukaryotic initiation factor 4E (eIF4E ) gene. RFLP analysis on the PVY-susceptible and resistant pepper cultivars, using an eIF4E cDNA from tobacco as probe, revealed perfect map co-segregation between a polymorphism in the eIF4E gene and the pvr2 alleles, pvr2(1) (resistant to PVY-0) and pvr2(2) (resistant to PVY-0 and 1). The cloned pepper eIF4E cDNA encoded a 228 amino acid polypeptide with 70-86% nucleotide sequence identity with other plant eIF4E s. The sequences of eIF4E protein from two PVY-susceptible cultivars were identical and differed from the eIF4E sequences of the two PVY-resistant cultivars Yolo Y (YY) (pvr2(1) ) and FloridaVR2 (F) (pvr2(2) ) at two amino acids, a mutation common to both resistant genotypes and a second mutation specific to each. Complementation experiments were used to show that the eIF4E gene corresponds to pvr2 . Thus, potato virus X-mediated transient expression of eIF4E from susceptible cultivar Yolo Wonder (YW) in the resistant genotype YY resulted in loss of resistance to subsequent PVY-0 inoculation and transient expression of eIF4E from YY (resistant to PVY-0; susceptible to PVY-1) rendered genotype F susceptible to PVY-1. Several lines of evidence indicate that interaction between the potyvirus genome-linked protein (VPg) and eIF4E are important for virus infectivity, suggesting that the recessive resistance could be due to incompatibility between the VPg and eIF4E in the resistant genotype.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A reference map of Cucumis melo based on two recombinant inbred line populations
auteur
Christophe Périn, L.S. Hagen, Véronique de Conto, N. Katzir, Y. Danin-Poleg, V. Portnoy, S. Baudracco-Arnas, Joel J. Chadoeuf, Catherine Dogimont, Michel Pitrat
article
TAG Theoretical and Applied Genetics, 2002, 104, pp.1017-1034
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Multiplication végétative des arbres fruitiers : le greffage herbacé
auteur
F. Gurrieri, M. Massé, M.C. Lemoine, Jean-Luc Poessel
article
PHM Revue Horticole, 2002, 433, pp.47-48
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Isolation and characterization of six peach cDNAs encoding key proteins in organic acid metabolism and solute accumulation: involvement in regulating peach fruit acidity
auteur
Christelle Etienne, Annick Moing, Elisabeth Dirlewanger, Philippe Raymond, René Monet, Christophe Rothan
article
Physiologia Plantarum, 2002, 114, pp.259-270. ⟨10.1034/j.1399-3054.2002.1140212.x⟩
resume
As in many other fleshy fruits, the predominant organic acids in ripe peach (Prunus persica (L.) Batsch) fruit are malic and citric acids. The accumulation of these metabolites in fruit flesh is regulated during fruit development. Six peach fruitrelated genes implicated in organic acid metabolism (mitochondrial citrate synthase; cytosolic NAD-dependent malate dehydrogenase, and cytosolic NADP-dependent isocitrate dehydrogenase) and storage (vacuolar proton translocating pumps: one vacuolar H¹-ATPase, and two vacuolar H¹-pyrophosphatases) were cloned. Five of these peach genes were homologous to genes isolated from fruit in other fleshy fruit species. Phylogenetic and expression analyses suggested the existence of a particular vacuolar pyrophosphatase highly expressed in fruit. The sixth gene was the first cytosolic NAD dependent malate dehydrogenase gene isolated from fruit. Gene expression was studied during the fruit development of two peach cultivars, a normal-acid (Fantasia) and a low-acid (Jalousia) cultivar. The overall expression patterns of the organic acid-related genes appeared strikingly similar for the two cultivars. The genes involved in organic acid metabolism showed a stronger expression in ripening fruit than during the earlier phases of development, but their expression patterns were not necessarily correlated with the changes in organic acid contents. The tonoplast proton pumps showed a biphasic expression pattern more consistent with the patterns of organic acid accumulation, and the tonoplast pyrophosphatases were more highly expressed in the fruit of the low-acid cultivar during the second rapid growth phase of the fruit.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02674641/file/Etienne2001.pdf BibTex
titre
Situacion practica de la lucha genetica contra los agentes patogenos de las hortalizas en cultivos protegidos, en la cuenca mediterranea
auteur
H. Laterrot
article
Phytoma España, 2002, 135, pp.61-64
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Characterization of the developmental stages of cypress zygotic embryos by two-dimensional electrophoresis and by cytochemistry
auteur
A. Sallandrouze, Mireille Faurobert, Mohamed El Maataoui
article
Physiologia Plantarum, 2002, 114, pp.608-618
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Isolation, mapping and characterization of allelic polymorphism of Chi3-P1, a class III chitinase of Capsicum annuum L
auteur
- Ching-Ming Cheng, Alain Palloix, Véronique Lefebvre
article
Plant Science, 2002, 163 (3), pp.481-489
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Molecular and genetic characterization of a non-climacteric phenotype in melon reveals two loci conferring altered ethylene response in fruit
auteur
Christophe Périn, M.C. Gomez-Jimenez, Lynda Hagen, Catherine Dogimont, J.C. Pech, Alain Latche, Michel Pitrat, Jean-Marc J.-M. Lelievre
article
Plant Physiology, 2002, 129, pp.300-309. ⟨10.1104/pp.010613⟩
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02675336/file/Perin_2002.pdf BibTex
titre
Recessive resistance genes against potyviruses are localized in colinear genomic regions of the tomato (Lycopersicon spp.) and pepper (Capsicum spp.) genomes
auteur
Giuseppe Parrella, Sandrine Ruffel, André Moretti, Caroline Morel, Alain Palloix, Carole Caranta
article
TAG Theoretical and Applied Genetics, 2002, 105, pp.855-861. ⟨10.1007/s00122-002-1005-2⟩
resume
Resistance against both Potato virus Y (PVY) and Tobacco etch virus (TEV) was identified in the wild tomato relative Lycopersicon hirsutum P1247087. Analysis of the segregation ratio in F-2/F-3 and BC, interspecific progenies indicated that a single recessive gene, or two very tightly linked recessive loci, are involved in resistance to both potyviruses. This locus was named pot-L Using amplified fragment length polymorphism markers and a set of L. hirsutum introgression lines, pot-1 was mapped to the short arm of tomato chromosome 3, in the vicinity of the recessive py-1 locus for resistance to corky root rot. Because of the occurrence of phenotypically similar genes in pepper (Capsicum spp.), the comparative genetics of resistance to potyviruses between tomato and pepper was investigated. Unlike most of the comparative genetic studies on resistance genes, pot-1 was tightly flanked by the same restriction fragment length polymorphism (RFLP) markers than the pvr2/pvr5 locus for resistance to PVY and TEV from pepper. These results may indicate that recessive resistance genes against potyviruses evolve less rapidly than the majority of the dominant genes cloned so far, and consequently may belong to a different family of resistance genes.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic analysis of organoleptic quality components in fresh market tomato
auteur
Mathilde M. Causse, V. Saliba-Colombani, L. Lecomte, Michel Buret
article
Comparative Biochemistry and Physiology - A: Comparative Physiology, 2002, 132, pp.S99
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Ecophysiological analysis of genotypic variation in peach fruit growth
auteur
Bénédicte Quilot-Turion, Michel M. Génard, J. Kervella, Francoise F. Lescourret
article
Journal of Experimental Botany, 2002, 53 (374), pp.1613-1625
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Introgression of resistance against Mi-1-virulent Meloidogyne spp. from Lycopersicon peruvianum into L. esculentum
auteur
A. Moretti, Michel Bongiovanni, P. Castagnone-Sereno, Carole Caranta
article
Report of the Tomato Genetics Cooperative, 2002, 52, pp.21-23
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the Solanaceae
auteur
S. Doganlar, A. Frary, M.C. Daunay, R.N. Lester, S.D. Tanksley
article
Genetics, 2002, 161, pp.1697-1711
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Des gènes pour protéger les salades
auteur
Brigitte B. Maisonneuve
article
Réussir Fruits et Légumes, 2002, 07, pp.30-34
typdoc
Journal articles
Accès au bibtex
BibTex
titre
2002 gene list for melon
auteur
Michel Pitrat
article
Report - Cucurbit Genetics Cooperative, 2002, 25, pp.76-93
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Oïdium du melon. Biologie et méthodes de lutte
auteur
Marc Bardin, Michel Pitrat, Philippe C. Nicot
article
Le Maraîcher, 2002, 436, pp.16-19
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines
auteur
Agnes Bouchez, Frederic F. Hospital, Mathilde M. Causse, A. Gallais, Alain A. Charcosset
article
Genetics, 2002, 162, pp.1945-1959
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTLs involved in the restriction of cucumber mosaic virus (CMV) long-distance movement in pepper
auteur
Carole Caranta, Stéphanie Pflieger, Véronique Lefebvre, A.M. Daubèze, A. Thabuis, Alain Palloix
article
TAG Theoretical and Applied Genetics, 2002, 104, pp.586-591
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Isolation and characterization of six peach cDNAs encoding key proteins in organic acid metabolism and solute accumulation: involvement in regulating peach fruit acidity
auteur
Christelle Etienne, Annick Moing, Elisabeth Dirlewanger, Philippe Raymond, René Monet, Christophe Rothan
article
Physiologia Plantarum, 2002, 114 (2), pp.259-270. ⟨10.1034/j.1399-3054.2002.1140212.x⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Un regard sur 40 ans d'amélioration des plantes maraîchères
auteur
Michel Pitrat
article
Sélectionneur Français, 2002, 53, pp.149-155
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Differences in susceptibility of pruning wounds and leaves to infection by Botrytis cinerea among wild tomato accessions
auteur
Philippe C. Nicot, André Moretti, Corinne Romiti, Marc Bardin, Carole Caranta
article
Report of the Tomato Genetics Cooperative, 2002, 52 (2002), pp.24-26
typdoc
Journal articles
Accès au bibtex
BibTex

2001

Journal articles

titre
High-resolution genetic mapping of the pepper (Capsicum annuum L.) resistance loci Me3 and Me4 conferring heat-stable resistance to root-knot nematodes (Meloidogyne spp.)
auteur
Caroline Djian‐caporalino, Pijarovsky Lucette, Ariane Fazari, Samson M, Gaveau L, Véronique Lefebvre, Carole Caranta, Alain Palloix, Pierre Abad
article
TAG Theoretical and Applied Genetics, 2001, 103 (4), pp.592-600. ⟨10.1007/PL00002914⟩
resume
The PM687 line of Capsicum annuum L. has a single dominant gene, Me-3, that confers heat-stable resistance to root-knot nematodes (RKN). Me-3 was mapped using doubled-haploid (DH) lines and F-2 progeny from a cross between the susceptible cultivar 'Yolo Wonder' ('YW') and the highly resistant line 'PM687'. Bulked-segregant analysis with DNA pools, from susceptible or resistant DH lines, was performed to identify RAPD and AFLP markers linked to Me-3. There was no polymorphism between bulks of ten DH lines using over 800 RADP primers (4,000 amplified fragments analysed). Using 512 AFLP primers (74,000 amplified fragments analysed), and bulked DNA templates from 20 resistant and 20 susceptible plants, we identified eight repulsion-phase and four coupling-phase markers linked to Me-3. Analysed in 103 DH progeny, they defined a 56.1-cM interval containing the target gene. The nearest were located 0.5, 1.0, 1.5 and 3.0 centimorgans (cM) on both sides of the gene. Analysis of the F-2 progeny (162 plants) with the nearest coupling-phase marker confirmed its close position. Another resistance gene to RKN, present in 'PM687' (Me-4), was shown to be linked to Me-3, 10 cM from it. In order to localize Me-3 and Me-4 on our reference intraspecific pepper linkage map, two AFLP markers were mapped. The Me-3 nearest marker was 10,1 cM from a RAPD marker named Q04_0.3 and 2.7 cM from a RFLP marker named CT135. We investigated map-position orthologies between Me-3 and two other nematode resistance genes, the tomato Mi-3 and the potato Gpa(2) genes, which mapped in the telomeric region of the short arm of the tomato and potato chromosome 12 (or XII for potato).
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Evaluation of genetic distances between pepper inbred lines for cultivar protection purposes : comparison of AFLP, RAPD and phenotypic data
auteur
Véronique Lefebvre, Bruno B. Goffinet, J.C. Chauvet, Bernard Caromel, Patrick Signoret, Richard Brand, Alain Palloix
article
TAG Theoretical and Applied Genetics, 2001, 102, pp.741-750
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Detection, stability and selection of loci involved in tomato organoleptic quality
auteur
L. Lecomte, V. Saliba-Colombani, N. Baffert, Philippe Duffe, A. Gautier, Frederic F. Hospital, Michel Buret, Mathilde M. Causse
article
Comptes Rendus de l'Académie d'Agriculture de France, 2001, 87 (5), pp.209-216
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La sharka: 30 anos de investigacion en Francia sobre una importante enfermedad de los arboles frutales de hueso. Cuales son las estrategias de lucha contra la sharka (III parte)?
auteur
Jean Dunez, Thierry Candresse, C. Jacquet, Michel Ravelonandro, Véronique Decroocq, F. Dosba, V. Schurdi Levraud-Escalettes, J.B. Quiot, Laurence Quiot, Gérard Labonne, J.M. Audergon, J. Kervella
article
Phytoma España, 2001, 131, pp.27-37
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La sharka: 30 anos de investigacion en Francia sobre una importante enfermedad de los arboles frutales de hueso. Caracteristicas de la enfermedad y del virus (I parte)
auteur
Jean Dunez, Thierry Candresse, C. Jacquet, Michel Ravelonandro, Véronique Decroocq, F. Dosba, V. Schurdi Levraud-Escalettes, J.B. Quiot, Laurence Quiot, Gérard Labonne, J.M. Audergon, J. Kervella
article
Phytoma España, 2001, 126, pp.22-28
typdoc
Journal articles
Accès au bibtex
BibTex
titre
QTLs for grain dry milling properties, composition and vitreousness in maize recombinant inbred lines
auteur
M. Sene, C. Thévenot, D. Hoffmann, F. Bénétrix, Mathilde M. Causse, J.L. Prioul
article
TAG Theoretical and Applied Genetics, 2001, 102, pp.591-599
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Applications of biotechnology in eggplant
auteur
C. Collonier, I. Fock, V. Kashyap, G.L. Rotino, M.C. Daunay, Y. Lian, I.K. Mariska, M.V. Rajam, A. Servaes, G. Ducreux, D. Sihachakr
article
Plant Cell, Tissue and Organ Culture, 2001, 65, pp.91-107
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Viroses du melon. Les aleurodes s'en mêlent
auteur
Catherine Dogimont
article
PHM Revue Horticole, 2001, 11, 2 p
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits
auteur
V. Saliba-Colombani, Mathilde M. Causse, D. Langlois, J. Philouze, Michel Buret
article
TAG Theoretical and Applied Genetics, 2001, 102, pp.259-272
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Soluble sugars and carboxylic acids in ripe apricot fruit as parameters for distinguishing different cultivars
auteur
F. Gurrieri, J.M. Audergon, Guy Albagnac, M. Reich
article
Euphytica, 2001, 117, pp.183-189
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic analysis of organoleptic quality in fresh market tomato. 2. Mapping QTLs for sensory attributes
auteur
Mathilde M. Causse, V. Saliba-Colombani, Isabelle Lesschaeve, Michel Buret
article
TAG Theoretical and Applied Genetics, 2001, 102, pp.273-283
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Porte-greffes pour l'abricotier (Prunus armeniaca L.). La diversification régionale et le matériel végétal employé en Italie
auteur
F. Gurrieri, Jean-Luc Poessel, P. Michelot
article
Arboriculture Fruitière, 2001, 552, pp.35-40
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Analysis of stylar ribonucleases (S-Rnases) in an almond progeny of 'Ferralise x Tuono
auteur
Henri Duval, A. Boutard, Mireille Faurobert
article
Cahiers Options Méditerranéennes, 2001, 26, pp.91-93
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Defense response genes co-localize with quantitative disease resistance loci in pepper
auteur
Stéphanie Pflieger, Alain Palloix, Carole Caranta, Anne Blattes, Véronique Lefebvre
article
TAG Theoretical and Applied Genetics, 2001, 103, pp.920-929
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Une coopération cubano-française réussie
auteur
H. Laterrot
article
Cuba Sί, 2001, 141, pp.13-14
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La Sharka: 30 anos de investigacion en Francia sobre una importante enfermedad de los arboles frutales de hueso. Caracteristicas de la enfermedad y del virus (II parte)
auteur
Jean Dunez, Thierry Candresse, C. Jacquet, Michel Ravelonandro, Véronique Decroocq, F. Dosba, V. Schurdi Levraud-Escalettes, J.B. Quiot, Laurence Quiot, Gérard Labonne, J.M. Audergon, J. Kervella
article
Phytoma España, 2001, 128, pp.18-25
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The candidate gene approach in plant genetics : a review
auteur
Stéphanie Pflieger, Véronique Lefebvre, Mathilde M. Causse
article
Molecular Breeding, 2001, 7, pp.275-291
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La résistance du melon au puceron Aphis gossypii
auteur
Michel Pitrat, Catherine Dogimont, Lynda Hagen, E. Burget, Hervé Lecoq, Abdelhafid Bendahmane
article
INRA Mensuel, 2001, 111, pp.17-19
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Résistance à Globodera pallida Pa2/3 chez Solanum sparsipilum
auteur
Didier Mugniery, Didier Fouville, J.P. Dantec, R. Pelle, F. Rousselle-Bourgeois, D. Ellisèche
article
Nematology, 2001, 3 (7), pp.619-626
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Les qualités organoleptiques de la tomate. Des essais concluants ! Influence des températures de conservation et du stade de maturité à la récolte
auteur
B. Navez, M. Jost, N. Lespinasse, Dominique Grasselly, Michel Buret, Mathilde M. Causse
article
Infos CTIFL, 2001, 173, pp.24-28
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Molecular mapping of the Am gene conferring resistance to alfalfa mosaic virus (AMV) in tomato
auteur
Giuseppe Parrella, André Moretti, Patrick Gognalons, Georges Marchoux, Kahsay Gebre Selassie, Carole Caranta
article
Report of the Tomato Genetics Cooperative, 2001, 51, pp.27-28
typdoc
Journal articles
Accès au bibtex
BibTex

2000

Journal articles

titre
Efficiency of RFLP, RAPD and and AFLP markers for the construction of an intraspecific map of the tomato genome
auteur
V. Saliba-Colombani, Mathilde M. Causse, L. Gervais, J. Philouze
article
Genome, 2000, 43, pp.29-40
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Cultivar pollinizer does not affect almond flavor
auteur
F. Dicenta, P. Matinez-Gomez, E. Ortega, Henri Duval
article
HortScience, 2000, 35 (6), pp.1153-1154
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Simple sequence repeats in Cucumis mapping and map merging
auteur
Y. Danin-Poleg, N. Reis, S. Baudracco-Arnas, Michel Pitrat, J.E. Staub, M. Oliver, Pere Arus, C.M. de Vicente, N. Katzir
article
Genome, 2000, 43, pp.963-974
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Amande : quatre nouvelles variétés
auteur
Henri Duval, Pascal Froment
article
Réussir Fruits et Légumes, 2000, 183, pp.65-67
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Valorisation des ressources génétiques de la tomate par l'utilisation de marqueurs moléculaires
auteur
Mathilde M. Causse, Carole Caranta, V. Saliba-Colombani, A. Moretti, Rene Damidaux, Patrick Rousselle
article
Cahiers Agricultures, 2000, 9, pp.197-210
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Behaviour of apricot (Prunus armeniaca L.) cultivars in the presence of sharka (plum pox potyvirus) : a review
auteur
P. Martínez-Gómez, F. Dicenta, J.M. Audergon
article
Agronomie, 2000, 20, pp.407-422
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A CAPS marker to assist selection of tomato spotted wilt virus (TSWV) resistance in pepper
auteur
Benoît Moury, Stéphanie Pflieger, Anne Blattes, Véronique Lefebvre, Alain Palloix
article
Genome, 2000, 43, pp.137-142
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A genetic linkage map of eggplant
auteur
S. Doganlar, A. Frary, M.C. Daunay, R.N. Lester, S.D. Tanksley
article
Report of the Tomato Genetics Cooperative, 2000, 50, pp.13
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Quantitative trait loci affecting amylose, amylopectin and starch content in maize recombinant inbred lines
auteur
M. Sene, Mathilde M. Causse, C. Damerval, C. Thévenot, J.L. Prioul
article
Plant Physiology and Biochemistry, 2000, 38 (6), pp.459-472
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Biological and molecular characterization of two tomato strains of potato virus Y (PVY)
auteur
Caroline Morel, Patrick Gognalons, Laurent Guilbaud, Carole Caranta, Kahsay Gebre Selassie, Georges Marchoux, Mireille Jacquemond
article
Acta Physiologiae Plantarum, 2000, 22 (3), pp.336-343. ⟨10.1007/s11738-000-0050-1⟩
resume
Two PVY tomato strains (LYE 84 and LYE 84.2), arising from the same natural isolate, and a strain originating from a wild Solanaceous host, Solanum nigrum (SON 41.2), were compared for host range and symptomatology. All strains induced mosaic without necrosis on tobacco as PVYO strains. The two tomato strains behaved similarly on pepper, infecting only susceptible pepper cultivars (pathotype 0), whereas SON 41.2 was able to overcome the two alleles of the recessive resistance gene pvr2 (pathotype 1.2). On the other hand, only LYE 84.2 was virulent on tomato and broke the resistance of the wild genitor Lycopersicon hirsutum PI 247087. Sequence determination of the capsid gene and the 3′ non-coding region of LYE 84 and LYE 84.2 showed a total homology at both nucleic acid and amino acid levels. This suggests that LYE 84.2 has probably derived from LYE 84, that both strains have very similar sequences and that the capsid protein does not play a direct role in the resistance-breaking capacity of LYE 84.2.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Integration of architectural types in french programmes of ligneous fruit species genetic improvement
auteur
F. Laurens, J.M. Audergon, J. Claverie, Henri Duval, E. Germain, J. Kervella, M. Le Lezec, P.E. Lauri, J.M. Lespinasse
article
Fruits, 2000, 55 (2), pp.141-152
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Identification and comparative mapping of a dominant potyvirus resistance gene cluster in Capsicum
auteur
R.C. Grube, J.R. Blauth, M.S. Arnedo Andres, Carole Caranta, M.K. Jahn
article
TAG Theoretical and Applied Genetics, 2000, 101, pp.852-859
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Resistance to Oidium lycopersicum : allelism test between Lycopersicon hirsutum G1.1560 and L. hirsutum PI247087
auteur
A. Moretti, Carole Caranta
article
Report of the Tomato Genetics Cooperative, 2000, 50, pp.28-29
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Identification of QTLs contributing to resistance to different strains of cucumber mosaic cucumovirus in melon
auteur
Catherine Dogimont, L. Leconte, Christophe Périn, A. Thabuis, Hervé Lecoq, Michel Pitrat
article
Acta Horticulturae, 2000, 510, pp.391-398. ⟨10.17660/ActaHortic.2000.510.62⟩
resume
A population of 122 recombinant inbred lines obtained by crossing a Charentais-type cultivar, Vedrantais, and the resistant Korean PI 161375 was evaluated for resistance to cucumber mosaic cucumovirus (CMV) in melon (Cucumis melo L.). Dates of appearance and intensity of symptoms were recorded upon infection with three CMV strains, two strains from Subgroup I (TL and P9), and one from Subgroup II (To 72). A saturated molecular map was constructed from the same population and was used for detecting quantitative trait loci (QTL). Seven genomic regions were found to carry factors for resistance to CMV. One of them, located in linkage group XII and accounting for a large amount of the phenotypic variation, is common to the three CMV strains. Other detected QTLs are strain-specific and are provided either by the resistant parental line or by the susceptible one.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Identification of differentially expressed genes during early development of tomato fruit. Characterization of a novel cDNA coding for a RAD23 protein
auteur
M. Lemaire-Chamley, J. Petit, Mathilde M. Causse, P. Raymond, C. Chevalier
article
Australian Journal of Plant Physiology, 2000, 27, pp.911-920
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Pollinisation de l'artichaut (Cynara scolymus L.) par l'abeille domestique (Apis mellifera L.) en production de semences hybrides sous abris grillagés
auteur
Nicolas Morison, Bernard Vaissière, F. Martin, P. Pécaut, G. Cambon
article
Apidologie, 2000, 31, pp.115-128
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02699214/file/54179_20091210090224642_1.pdf BibTex
titre
Molecular tagging of the Am gene from Lycopersicon hirsutum f. glabratum PI 134417 using AFLP markers
auteur
Giuseppe Parrella, Isabelle Hochu, Kahsay Gebre Selassie, Patrick Gognalons, André Moretti, Georges Marchoux, Carole Caranta
article
Acta Physiologiae Plantarum, 2000, 22 (3), pp.291-293. ⟨10.1007/s11738-000-0036-z⟩
resume
Recently important epidemics caused by Alfalfa Mosaic Virus (AMV) have been reported in field grown canning tomatoes in southern Italy. The Am resistance gene identified in Lycopersicon hirsutum PI 134417 confers a complete resistance to several isolates of AMV with different geographical and botanical origins. In order to identify linked molecular markers, a segregant back-cross population of 120 individuals was obtained from the intraspecific cross between the resistant L. hirsutum accession PI 134417 and the susceptible accession L. hirsutum PI 247087. Using bulked segregant analysis combined with AFLP technology, four AFLP markers were found to be linked to the Am resistance gene. This gene will be assigned to a tomato chromosome using L. pennellii introgression lines.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Tracking paternal genes with DALP markers in a pseudoarrhenotokous reproductive system: biparental transmission but haplodiploid-like inheritance in the mite Neoseiulus californicus.
auteur
Marie-Jeanne Perrot-Minnot, Jacques Lagnel, Alain Migeon, Maria Navajas
article
Heredity, 2000, 84 ( Pt 6) (6), pp.702-709. ⟨10.1046/j.1365-2540.2000.00708.x⟩
resume
The complexity of some sexual reproductive systems in arthropods still leaves both their genetic and epigenetic determinism and their evolutionary significance poorly understood. Pseudoarrhenotoky is characterized by obligate fertilization and differential inactivation and/or elimination of paternal chromosomes in embryos that develop into males. Here, we investigate how the paternal genome is transmitted in a pseudoarrhenotokous mite, Neoseiulus californicus, using codominant genetic markers detected by DALP (direct amplification of length polymorphism). Transmission patterns of parental alleles through one and two generations are reported at four or five loci corresponding to four linkage groups. Our data provide strong evidence for selective elimination of the paternal genome among male tissues. Sperm contained maternal genes exclusively, whereas some male somatic tissues retained most if not all paternal chromosomes. No recombination between parental genomes prior to paternal genome elimination from the embryonic germ line was observed. These data allow a reinterpretation of previous phenotypic and cytogenetic observations in these mites, from which we suggest some relevant mechanistic and evolutionary implications. In addition, this is the first published study using polymorphic codominant loci detected by the recently developed DALP method.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
L'approche gène candidat pour la caractérisation moléculaire et fonctionnelle de locus de résistance aux parasites chez les plantes
auteur
Véronique Lefebvre, Stéphanie Pflieger
article
Sélectionneur Français, 2000, 51, pp.31-45
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Eggplants : present and future
auteur
M.C. Daunay, R.N. Lester, J.W. Hennart, C. Duranton
article
Capsicum and Eggplant Newsletter, 2000, 19, pp.11-18
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Disease resistance in tomato : practical situation
auteur
H. Laterrot
article
Acta Physiologiae Plantarum, 2000, 22 (3), pp.328-331. ⟨10.1007/s11738-000-0048-8⟩
typdoc
Journal articles
Accès au bibtex
BibTex

1999

Journal articles

titre
Mandaline, a new french almond variety
auteur
Henri Duval
article
Nucis Newsletter, 1999, 8, pp.36
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Photoperiod and temperature effect on growth of strawberry plant (Fragaria X ananassa Duch.): development of a morphological test to assess the dormancy induction
auteur
F. Robert, G. Risser, Gilles Petel
article
Scientia Horticulturae, 1999, 82, pp.217-226
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Race identification in powdery mildew (Sphaerotheca fuliginea) on melon (Cucumis melo) in Japan
auteur
K. Hosoya, K. Narisawa, Michel Pitrat, Hiroshi Ezura
article
Plant Breeding, 1999, 118, pp.259-262
typdoc
Journal articles
Accès au bibtex
BibTex
titre
From QTLs for enzyme activity to candidate genes in maize
auteur
J.L. Prioul, S. Pelleschi, M. Sene, C. Thévenot, Mathilde M. Causse, D. de Vienne, Agnès Leonardi
article
Journal of Experimental Botany, 1999, 50 (337), pp.1281-1288
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Comparison of ploidy level screening methods in a watermelon : Citrullus lanatus (Thunb.) Matsum. and Nakai
auteur
Nebahat Sari, K. Abak, Michel Pitrat
article
Scientia Horticulturae, 1999, 82, pp.265-277
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Description and inheritance of an albino mutant in melon
auteur
Didier Besombes, Nathalie Giovinazzo, C. Olivier, Catherine Dogimont, Michel Pitrat
article
Report - Cucurbit Genetics Cooperative, 1999, 22, pp.14-15
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Disease resistance gene analogs as candidates for QTLs involved in pepper-pathogen interactions
auteur
Stéphanie Pflieger, Véronique Lefebvre, Carole Caranta, Anne Blattes, Bruno Goffinet, Alain Palloix
article
Genome, 1999, 42, pp.1100-1110
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic analysis of resistance of melon line PI 124112 to Sphaerotheca fuliginea and Erysiphe cichoracearum studied in recombinant inbred lines
auteur
Marc Bardin, Catherine Dogimont, Philippe C. Nicot, Michel Pitrat
article
Acta Horticulturae, 1999, 492, pp.163-168. ⟨10.17660/ActaHortic.1999.492.19⟩
resume
Inheritance of resistance of the Indian melon line PI 124112 to several races of Sphaerotheca fuliginea and Erysiphe cichoracearum was studied. A set of homozygous recombinant inbred lines has been produced by single seed descent after a cross with the susceptible line Védrantais. Nine strains of powdery mildew were tested for powdery mildew resistance using a leaf disk assay and a whole plant test. Among the six strains of S. fuliginea tested, four different races were distinguished based on the reaction of nine different melon cultivars. The three strains of E. cichoracearum belong to the same race (race 1). Genotype PI 124112 was resistant to all the strains tested. Genetic analysis revealed that PI 124112 possessed four genes for resistance. One gene was able to control the races 1 and 2 of S. fuliginea, one gene controls the races 1, 2 and 4 and one gene controls the four races of S. fuliginea and also E. cichoracearum. One gene controls only E. cichoracearum (and not S. fuliginea). All these genes are linked in a cluster spanning 22 cM.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic control and linkages of some fruit characters in melon
auteur
Christophe Périn, Catherine Dogimont, Nathalie Giovinazzo, Didier Besombes, L. Guitton, Lynda Hagen, Michel Pitrat
article
Report - Cucurbit Genetics Cooperative, 1999, 22, pp.16-18
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Development of a CAPS marker for the Pvr4 locus : a tool for pyramiding potyvirus resistance genes in pepper
auteur
Carole Caranta, A. Thabuis, Alain Palloix
article
Genome, 1999, 42, pp.1111-1116
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Aggressiveness of Leveillula taurica on pepper
auteur
Muna E. Suliman, Marc Bardin, A.M. Daubèze, Youssif F. Mohamed, Philippe C. Nicot
article
Capsicum and Eggplant Newsletter, 1999, 18, pp.83-86
resume
The aggressiveness of several isolates of L. taurica from different locations in France, Sudan and Italy, on pepper (Capsicum annuum) was investigated. A susceptible line (Vania) and a partially resistant line (PM687) were used in the study. Evaluations of disease severity were carried out 5 times a week, from 7 days after inoculation until 49 days after inoculation. All isolates of L. taurica were virulent to the susceptible line, wiith mild symptoms observed after 14 days. Only weak symptoms were observed on the partially resistant line for 4 of the 6 isolates, and no symptoms were observed for the other 2 isolates. The most aggressive and least aggressive isolates were both obtained from Sudan. It is suggested that levels of aggressiveness can be determined on the pepper line Vania, and that aggressiveness may not be related to the geographic origin of the isolate.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
One dominant gene conferring the resistance to the leafminer, Liriomyza trifolii (Burgess) diptera : Agromyzidae in melon (Cucumis melo L.)
auteur
Catherine Dogimont, D. Bordat, C. Pages, Nathalie Boissot, Michel Pitrat
article
Euphytica, 1999, 105, pp.63-67. ⟨10.1023/A:1003436428847⟩
resume
The line Nantais Oblong, a melon of Charentais type, was shown to be a source of resistance by antibiosis to the leafminer, Liriomyza trifolii (Burgess), Diptera, Agromyzidae. We studied the genetic control of this resistance in F2 and back-cross progenies from the cross between Nantais Oblong and Védrantais, a Charentais line susceptible to the leafminer. Tests were carried out on young plants in plastic cages with controlled infestation. Complete mortality of the L. trifolii larvae was used as indicator of plant resistance. Segregation ratios were consistent with monogenic dominant control of the resistance. The symbol Lt for Liriomyza trifolii resistance is proposed.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La tomate, origine, diversité et création variétale
auteur
H. Laterrot
article
La Garance Voyageuse, 1999, 46, pp.10-12
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Tibish, a melon type from Sudan
auteur
I.M. El Tahir, Michel Pitrat
article
Report - Cucurbit Genetics Cooperative, 1999, 22, pp.21-23
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Julior-Ferdor et variétés d'abricotier
auteur
M.H. Simard, G. Olivier
article
Arboriculture Fruitière, 1999, 523, pp.39-42
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Prunes japonaises : un défi à relever
auteur
Henri Duval
article
Arboriculture Fruitière, 1999, 524, pp.35-41
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Enroulement chlorotique de l'abricotier. Evaluation de la sensibilité des principales variétés de prunier japonais... et du nouveau sur un vecteur
auteur
Henri Duval, Jean-Pierre Jullian, Jean-Marc Lemaire
article
Phytoma la Défense des Végétaux, 1999, 516, pp.38-40
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Résistance to PepMoV and PVY-0 from Avelar are controlled by distinct recessive genes and evidence for independence between pvr3 and pvr5
auteur
Carole Caranta, Ghislaine Nemouchi, A.M. Daubèze, Therese Phaly, Alain Palloix
article
Capsicum and Eggplant Newsletter, 1999, 18, pp.63-65
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Molecular cloning and expression of a cDNA encoding 1-aminocyclopropane-1-carboxylate (ACC) oxidase from apricot fruit (Prunus armeniaca)
auteur
Didier Mbeguie-A-Mbeguie, H. Chahine, R.M. Gomez, Barbara Gouble, M. Reich, J.M. Audergon, M. Souty, Guy Albagnac, B. Fils-Lycaon
article
Physiologia Plantarum, 1999, 105, pp.294-303
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Development and utility of cleaved amplified polymorphic sequences (CAPS) and restriction fragment length polymorphisms (RFLPs) linked to the fom-2 fusarium wilt resistance gene in melon (Cucumis melo L.)
auteur
X.Y. Zheng, D.W. Wolf, S. Baudracco-Arnas, Michel Pitrat
article
TAG Theoretical and Applied Genetics, 1999, 99, pp.453-463
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Spectrum of resistance to root-knot nematodes and inheritance of heat-stable resistance in pepper (Capsicum annuum L.)
auteur
C. Djian-Caporalino, Lucette Pijarowski, Ariane Januel, Véronique Lefebvre, A. Daubèze, Alain Palloix, A. Dalmasso, Pierre Abad
article
TAG Theoretical and Applied Genetics, 1999, 99 (3-4), pp.496-502
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A stylar ribonuclease assay to detect self-compatible seedlings in almond progenies
auteur
R. Boskovic, K.R. Tobutt, Henri Duval, I. Batlle, F. Dicenta, F.J. Vargas
article
TAG Theoretical and Applied Genetics, 1999, 99, pp.800-810
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Two-dimensional electrophoretic analysis of proteins associated with somatic embryogenesis development in Cupressus sempervirens L.
auteur
A. Sallandrouze, Mireille Faurobert, M.E. Maataoui, H. Espagnac
article
Electrophoresis, 1999, 20, pp.1109-1119
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Influence of rootstock and the height of grafting on the susceptibility of apricot cultivars to bacterial canker
auteur
J.P. Prunier, Jean-Pierre Jullian, J.M. Audergon
article
Acta Horticulturae, 1999, 488, pp.643-648. ⟨10.17660/ActaHortic.1999.488.104⟩
resume
Bacterial canker due to Pseudomonas sp. infections is a major source of apricot tree diebacks during the winter in the northern part of the French apricot production area. Some of the factors involved are well known such as frost intensity, hydration of the tissues and the period of inoculation, even if they cannot be kept under control. The objective of our study was to highlight the influence of two technical practices, rootstock choice and height of the grafting point, on the induced susceptibility of the tree. The cumulative effect of the rootstock type and the height of the grafting point (modern method: at the soil level (0.3 meter), old method (1.4 meter) on the severity of bacterial canker damages were observed during four years in two different orchards, on the cultivar "Bergeron" grafted on six different rootstocks. An artificial inoculation was conducted twice during the spring (on one and two-year-old trees) by spraying with suspensions of Ps. syringae pv. syringae and Ps. viridiflava. A highly significant effect has been observed on both factors studied: rootstock effect: apricot seedlings showed their non-adaptation to the given soil conditions (lower growth, higher susceptibility to die-back) whereas peach rootstock and P. mariana induced a higher vigor of the plants and to a lesser extend P. myrobolan seemed to reduce the severity of the symptoms on the grafted variety. height of the grafting point: the grafted plants with a crown between 1.8 and 2.5 meter high were more resistant to the disease than the plant grafted at soil level. A positive interaction between both factors on the induced plant resistance has been observed.These results must be checked in other conditions of cultivation before they can be generalized.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Localized graft incompatibility in pear/quince (Pyrus communis / Cydonia oblonga) combinations : multivariate analysis of histological data from 5-month-old grafts
auteur
F.F. Ermel, J. Kervella, A.M. Catesson, Jean-Luc Poessel
article
Tree Physiology, 1999, 19, pp.645-654
typdoc
Journal articles
Accès au bibtex
BibTex

1998

Journal articles

titre
Abricot : le choix du porte-greffe
auteur
M.H. Simard, G. Olivier
article
Réussir Fruits et Légumes, 1998, 160, pp.38-39
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La progression d'Eurytoma amygdali en France et les méthodes de lutte possibles
auteur
Henri Duval, Pascal Froment
article
Cahiers Options Méditerranéennes, 1998, 33, pp.87-90
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La bactériose du melon : connaissances acquises et travaux en cours
auteur
Cindy E. Morris, Michel Pitrat
article
PHM Revue Horticole, 1998, 393, pp.44-47
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Confirmation of incompatibility alleles in almond cultivars prodicted by analysis of stylar ribonucleases
auteur
Henri Duval, I. Batlle, R. Boskovic, K.R. Tobutt
article
Cahiers Options Méditerranéennes, 1998, 33, pp.25-27
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Des fruits sur mesure
auteur
Michel Pitrat
article
Sciences et Avenir, 1998, 10, pp.21-27
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Evaluation agronomique. Variétés et porte-greffe de l'amandier
auteur
Henri Duval, Pascal Froment
article
Arboriculture Fruitière, 1998, 514, pp.57-62
typdoc
Journal articles
Accès au bibtex
BibTex
titre
L'émergence des tospovirus
auteur
Benoît Moury, Alain Palloix, Kahsay Gebre Selassie, Georges Marchoux
article
Virologie, 1998, 2 (5), pp.357-367
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Settling behaviour and reproductive potential of the green peach aphid Myzus persicae on peach varieties and a related wild Prunus
auteur
Marie-Hélène Sauge, Jocelyne Kervella, Thierry Pascal
article
Entomologia Experimentalis et Applicata, 1998, 89 (3), pp.233-242. ⟨10.1046/j.1570-7458.1998.00404.x⟩
resume
Discovery in the late seventies of resistance to the green peach aphid Myzus persicae (Sulzer) (Homoptera: Aphididae) in Prunus species was based on screening in the field or in greenhouses with natural aphid populations. Here, we assess the impact of these wild and domesticated peach trees on the behaviour, development, reproductive performance and demography of cloned aphids under controlled light and temperature. Four peach varieties, i.e., Rubira, Weeping Flower Peach, Summergrand and Malo konare and the clone P1908 of the related species Prunus davidiana were tested against the highly susceptible cultivar GF305. Besides a variability in the performance of aphids among experiments, our results showed that (i) distinct mechanisms were involved in the sources of resistance studied and (ii) the ranking of the genotypes on their resistance/susceptibility status remained roughly stable throughout the experiments. Observations on the settling behaviour of first instar nymphs demonstrated antixenosis components in the resistance conferred by Rubira and Weeping Flower Peach. Nymphs began to leave the plants after a short exposure (19–21 h) and no aphid was left after 4 days. Nymphal mortality remained rather low (16%) compared to the repellent effect on aphids of both genotypes. Nymphs disappeared from Weeping Flower Peach significantly earlier than from Rubira. Summergrand, Malo konare and P. davidiana clone P1908 were accepted as host plants by aphids. On P. davidiana, decreased fecundity and intrinsic rate of natural increase (rm= 0.20, averaged on all experiments) were clear expression of antibiosis. In addition, the mean length of the mature embryos within the gonads of the females on the day of adult moult was negatively correlated with the total number of embryos, providing evidence that aphids on this genotype lacked sufficient ressources to be directed both towards production and growth of embryos. Compared to the most susceptible cultivar GF305 (rm= 0.36), Summergrand (rm= 0.26) and Malo konare (rm= 0.28) had, to a lesser extent, a negative impact on nymph production and rate of increase.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Le TYLCV sur tomate : une méthode de détection en série contre une menace sérieuse
auteur
Anne Dalmon, H. Laterrot, D. Allex, Georges Marchoux
article
Culture légumière, 1998, 44, pp.31-34
typdoc
Journal articles
Accès au bibtex
BibTex
titre
The capsanthin-capsorubin synthase gene: a candidate gene for the y locus controlling the red fruit colour in pepper
auteur
Véronique Lefebvre, B. Camara, Alain Palloix
article
Plant Molecular Biology, 1998, 36, pp.785-789
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Genetic mapping of Ph-2, a single locus controlling partial resistance to Phytophthora infestans in tomato
auteur
P. Moreau, P. Thoquet, J. Olivier, H. Laterrot, N. Grimsley
article
Molecular Plant-Microbe Interactions, 1998, 11 (4), pp.259-269
typdoc
Journal articles
Accès au bibtex
BibTex
titre
High temperature effects on hypersensitive resistance to tomato spotted wilt tospovirus (TSWV) in pepper (Capsicum chinense Jacq.)
auteur
Benoît Moury, Kahsay Gebre Selassie, Georges Marchoux, A.-M. Daubèze, Alain Palloix
article
European Journal of Plant Pathology, 1998, 104 (5), pp.489-498. ⟨10.1023/A:1008618022144⟩
resume
The tomato spotted wilt virus resistance in pepper conferred by the Tsw gene is less stable at 32 degrees C continuous temperature. Continuous high temperatures for at least nine days lead to systemic spread and necrotic symptoms in plants that are totally resistant at a lower temperature (22 degrees C). We show that continuous high temperatures destabilize this resistance in young plants, but older inoculated plants rarely develop systemic symptoms. Populations segregating for the Tsw gene showed that heterozygosity at the Tsw locus increased the chance of inoculated seedlings to develop systemic necrotic symptoms. Genetic background was less significantly involved in the thermosensitivity of the resistant response. As a consequence, it would be preferable to grow cultivars homozygous at the Tsw locus in high temperature conditions.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Probing behaviour of the green peach aphid Myzus persicae on resistant Prunus genotypes
auteur
Marie-Hélène Sauge, Jocelyne Kervella, Yvan Rahbé
article
Entomologia Experimentalis et Applicata, 1998, 89 (3), pp.223-232. ⟨10.1046/j.1570-7458.1998.00403.x⟩
resume
Electrical penetration graphs of Myzus persicae (Sulzer) (Homoptera: Aphididae) feeding behaviour on four resistant and two susceptible genotypes of peach (Prunus persica L. Batsch) and related species showed that resistance was mainly linked to (i) reduced duration of phloem sap uptake, (ii) reduced percentage of pattern E1 (salivary secretion into sieve elements) followed by pattern E2 (sap ingestion) and (iii) increased number of shifts from E1 to E2 and back. These results suggest the unsuitability of phloem sap, and thus repetitive failures to initiate sustained ingestion. Extensive comparisons of the EPGs also revealed more specific trends. Aphids on the most susceptible cultivar GF305 produced significantly longer potential drops than on other peach genotypes. On the resistant Rubira, aphids generated more penetrations before the first E occurred, indicating the possible presence of a resistance factor before the phloem was reached. The clone P1908 of the wild species Prunus davidiana displayed traits of both susceptibility (less but longer probes) and resistance. In particular, aphids produced more E1, suggesting difficulties in preparing sieve elements before feeding. The aphid probing process could be correlated with aphid settling behaviour and bionomics, as previously reported, and gave evidence for the existence of different mechanisms underlying resistance in the tested genotypes against M. persicae.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
La tomate : origine, diversité, création variétale
auteur
H. Laterrot
article
Bulletin de Liaison de la Société Botanique du Vaucluse, 1998, 6, pp.4
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Deux nouvelles techniques utilisées pour l'amélioration du melon
auteur
Michel Pitrat
article
PHM Revue Horticole, 1998, 11, pp.6-7
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Melon biotechnology
auteur
M. Guis, J.P. Roustan, Catherine Dogimont, Michel Pitrat, J.C. Pech
article
Biotechnology and Genetic Engineering Reviews, 1998, 15, pp.289-311
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Enroulement chlorotique de l'abricotier. Symptomatologie et gamme d'hôtes
auteur
Jean-Marc Lemaire, Jean-Pierre Jullian, J.M. Audergon, Claude Castelain
article
Arboriculture Fruitière, 1998, 520, pp.21-24
typdoc
Journal articles
Accès au bibtex
BibTex
titre
1998 gene list for melon
auteur
Michel Pitrat
article
Report - Cucurbit Genetics Cooperative, 1998, 21, pp.69-81
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Evaluation of the interspecific progeny Prunus persica cv Summergrand x Prunus davidiana for disease resistance and some agronomic features
auteur
Thierry Pascal, F.G. Pfeiffer, M.H. Sauge, Daniel Esmenjaud
article
Acta Horticulturae, 1998, 465, pp.185-190
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Recherche de références sur les teneurs foliaires en éléments minéraux chez l'amandier
auteur
D. Courtial, Pascal Froment, Henri Duval
article
Cahiers Options Méditerranéennes, 1998, 33, pp.75-79
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Temporal analysis of western flower thrips (Thysanoptera: Thripidae) population dynamics on Réunion Island.
auteur
Nathalie Boissot, Bernard Reynaud, Philippe Letourmy
article
Environmental Entomology, 1998, 27 (6), pp.1437-1443
resume
The western flower thrips, Frankliniella occidentalis (Pergande), has been present on Reunion Island since 1987. The tomato spotted wilt virus, which is transmitted by F. occidentalis, was first observed on the island in 1991. Because of the strong threat to flower crops, we studied western flower thrips dynamics at a flower farm (900 m elevation) from 1993 to 1997. The population dynamics were monitored using sticky traps. The density of western flower thrips was studied through auto-correlograms and cross-correlograms with climatic data (temperature, relative humidity, rainfall). Thrips populations varied annually, typically due to temperature variation. Stepwise regression allowed us to fit a model of density increment including 2 climatic parameters: In (R) at lag = 0 and H at lag = ?3 (with R for rainfall, and H for relative humidity; 1 lag = 15 d) and auto-regressive moving average terms for residuals. It appeared the western flower thrips was present all year round on the site but density started to increase when temperatures reached 15°C. Nevertheless, the density decreased before the mean temperature reached its maximum. Heavy rainfall, involving submergence of pupae or high relative humidity, conditions which are favorable to an entomopathogen, could explain this early decrease.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Inheritance of resistance to alfalfa mosaic virus in Lycopersicon hirsutum f. glabratum PI 134417
auteur
Giuseppe Parrella, H. Laterrot, Kahsay Gebre Selassie, Georges Marchoux
article
Journal of Plant Pathology, 1998, 80 (3), pp.241-243. ⟨10.4454/jpp.v80i3.824⟩
resume
Alfalfa mosaic virus (AMV) is of sporadic occurrence in tomato crops. More recently, important epidemics caused by AMV have been reported in fieldgrown canning tomatoes in southern Italy. Since no lines or commercial varieties resistant to AMV are available, we have studied the inheritance of resistance to this virus, derived from the accession of Lycopersicon hirsutum f. glabratum PI 134417. A necrogenic tomato isolate of AMV was used as source of inoculum. Visual observations of symptoms and enzyme-linked immunosorbent assay (ELISA) were used to screen plants after mechanical inoculation. All the F1 tested were resistant while the segregation ratios of F2 and BC1 generations were consistent with a simple dominant inheritance. We propose tentatively to name this gene Am.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02694959/file/1998-Parella-JPP_1.pdf BibTex
titre
Qualité organoleptique de la tomate: Des progrès en contrôle génétique
auteur
Mathilde M. Causse, V. Saliba, J. Philouze, Michel Buret, Isabelle Lesschaeve, Sylvie Issanchou, D. Langlois, M.C. Bardet
article
Culture légumière, 1998, 4, pp.19-22
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Tomate d'industrie : nouvelles variétés adaptées aux exigences des professionnels
auteur
Rene Damidaux
article
PHM Revue Horticole, 1998, 389, pp.52-53
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A carbon balance model of peach tree growth and development for studying the pruning response
auteur
Michel M. Génard, Loic L. Pagès, J. Kervella
article
Tree Physiology, 1998, 18, pp.351-362
typdoc
Journal articles
Accès au bibtex
BibTex

1997

Journal articles

titre
Almond production in France
auteur
Henri Duval
article
Nucis Newsletter, 1997, 6, pp.5
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Tomate : des variétés fixées aux hybrides F1
auteur
J. Philouze
article
Réussir Fruits et Légumes, 1997, 151, pp.8
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Protection sanitaire. La diagonale du fou
auteur
Mireille Bru, Georges Marboutie, Michel Pitrat
article
Réussir Fruits et Légumes, 1997, 151, pp.14-22
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Abricot : élaboration de la qualité
auteur
M. Souty, J.M. Audergon
article
Réussir Fruits et Légumes, 1997, 151, pp.37
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Dissecting complex physiological functions through the use of molecular quantitative genetics
auteur
J.L. Prioul, S. Quarrie, Mathilde M. Causse, D. de Vienne
article
Journal of Experimental Botany, 1997, 48 (311), pp.1151-1163
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Melon: les résistances aux virus
auteur
Michel Pitrat
article
Réussir Fruits et Légumes, 1997, 151, pp.15
typdoc
Journal articles
Accès au bibtex
BibTex

1996

Journal articles

titre
Aubergine ? Aubergines
auteur
M.C. Daunay
article
PHM Revue Horticole, 1996, 374, pp.48-49
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Selection for Meloidogyne incognita virulence against resistance genes from tomato and pepper and specificity of the virulence/resistance determinants
auteur
P. Castagnone Sereno, Michel Bongiovanni, Alain Palloix, A. Dalmasso
article
European Journal of Plant Pathology, 1996, 102 (6), pp.585-590. ⟨10.1007/BF01877026⟩
typdoc
Journal articles
Accès au bibtex
BibTex
titre
L'aubergine en Turquie
auteur
M.C. Daunay, J.W. Hennart, K. Abak
article
PHM Revue Horticole, 1996, 374, pp.53-54
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Selection for Meloidogyne incognita virulence against resistance genes from tomato and pepper and specificity of the virulence/resistance determinants
auteur
Philippe Castagnone-Sereno, M. Bongiovanni, A. Palloix, A. Dalmasso
article
European Journal of Plant Pathology, 1996, 102 (6), pp.585-590. ⟨10.1007/BF01877026⟩
resume
Experiments were designed to analyze the relationships between the root-knot nematode Meloidogyne incognita and resistant tomato and pepper genotypes. From a natural avirulent isolate, near-isogenic nematode lineages were selected with virulence either against the tomato Mi resistance gene or the pepper Me3 resistance gene. Despite the drastic selection pressure used, nematodes appeared unable to overcome the pepper Mel gene, therefore suggesting some differences in the resistance conferred by Mel and Me3 in this species. Nematodes virulent on Mi-resistant tomatoes were not able to reproduce on Mel-resistant nor on Me3-resistant peppers, and nematodes virulent on Me3-resistant peppers were not able to reproduce on Mi-resistant tomatoes nor on Mel-resistant peppers. These results clearly demonstrate the specificity of M. incognita virulence against resistance genes from both tomato and pepper, and indirectly suggest that gene-for-gene relationships could occur between these two solanaceous crops and the nematode.
typdoc
Journal articles
Accès au bibtex
BibTex
titre
L'aubergine à travers les âges et les usages
auteur
M.C. Daunay
article
PHM Revue Horticole, 1996, 374, pp.35-36
typdoc
Journal articles
Accès au bibtex
BibTex

1995

Journal articles

titre
TE7, An Inefficient Symbiotic Mutant of Medicago truncatula Gaertn. cv Jemalong
auteur
Véronique Bénaben, Gérard Duc, Véronique Lefebvre, Thierry Huguet
article
Plant Physiology, 1995, 107 (1), pp.53-62. ⟨10.1104/pp.107.1.53⟩
resume
A mutagenesis program using ethylmethane sulfonate on Medicago fruncafula Caertn cv Jemalong, an annual, autogamous and diploid lucetne, permitted the isolation of a mutant (TE7) unable to establish an effective nitrogen-fixing symbiosis, [Nod+Fix-], with Rhizobium melilofi wild-type strains. The mutant phenotype is characterized by an altered infection process that leads to the formation of two kinds of inefficient nodules on the same root system. A certain proportion of the nodules are small, round, and uninfected, with infection threads limited to the outer root cortical cells. Others develop to a normal elongated shape and are infected; bacterial release occurs but the bacteria do not differentiate into bacteroids. l h e ratio of invaded to uninvaded nodules depends on the bacterial strain used. Throughout the infection process, certain events correlated with the plant defense response against pathogens can be observed: (a) the presence of polyphenolic compounds associated with the walls of infected cells and also with some parts of infection threads in the root cortex; (b) appositions on infection thread walls during the early stage of infection and also within the central tissue of infected nodules; and (c) autophagy of the plant cells that contain released bacteria. Cenetic data suggest that the phenotype of TE7 is under monogenic and recessive control; this gene has been designated Mtsyml.
typdoc
Journal articles
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03737690/file/Benaben-Duc-Lefebvre-Huguet_1995_PlantPhys_Te7SymbioticMutantMedicagoTruncatula.pdf BibTex

1994

Journal articles

titre
Investigation of the effect of genetic background on QTL expression using three connected RIL populations
auteur
Alain A. Charcosset, Mathilde M. Causse, A. Gallais
article
Maize Genetics Cooperation Newsletter, 1994, 68, pp.44
typdoc
Journal articles
Accès au bibtex
BibTex
titre
A composite map of expressed sequences, based on four individual maps
auteur
Mathilde M. Causse, C. Damerval, Aurélie Maurice, Alain A. Charcosset, Sylvain Santoni, D. de Vienne
article
Maize Genetics Cooperation Newsletter, 1994, 68, pp.42-44
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Locating QTLs for carbon metabolism and early growth, using candidate gene approach
auteur
Mathilde M. Causse, J.P. Rocher
article
Maize Genetics Cooperation Newsletter, 1994, 68, pp.44-45
typdoc
Journal articles
Accès au bibtex
BibTex
titre
Les ressources génétiques des espèces légumières à l'INRA
auteur
Marie-Christine Daunay
article
Sauve qui Peut! Sauve qui Veut, 1994, 6-7, pp.6-15
typdoc
Journal articles
Accès au bibtex
BibTex

1992

Journal articles

titre
Reoccurence of gene ai in an albanian tomato line
auteur
P. Pasko, André Moretti, Henri Laterrot
article
Report of the Tomato Genetics Cooperative, 1992, 42, pp.29
typdoc
Journal articles
Accès au bibtex
BibTex

1978

Journal articles

titre
la résistance à Corynebacterium michiganense chez la tomate
auteur
Henri Laterrot, Richard Brand, M-Christin Daunay
article
Annales de l'Amélioration des Plantes, 1978, 28 (5), pp.579-591
typdoc
Journal articles
Accès au bibtex
BibTex

1963

Journal articles

titre
Description de quelques variétés de fraisiers
auteur
G. Risser
article
Annales de l'Amélioration des Plantes, 1963, 13 (2), 38 p
typdoc
Journal articles
Accès au bibtex
BibTex