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

2021

Journal articles

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, Nature Publishing Group, 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.
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Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars
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Felipe Pérez de los Cobos, Pedro Martínez-García, Agustí Romero, Xavier Miarnau, Iban Eduardo, Werner Howad, Mourad Mnejja, Federico Dicenta, Rafel Socias I Company, Maria Rubio-Cabetas, Thomas Gradziel, Michelle Wirthensohn, Henri Duval, Doron Holland, Pere Arús, Francisco Vargas, Ignasi Batlle
article
Horticulture research, Nature Publishing Group, 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.
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Tactics of host manipulation by intracellular effectors from plant pathogenic fungi
auteur
Melania Figueroa, Diana Ortiz, Eva Henningsen
article
Current Opinion in Plant Biology, Elsevier, In press, 62, ⟨10.1016/j.pbi.2021.102054⟩
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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.
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https://hal.inrae.fr/hal-03227294/file/Figueroa%2C%20Ortiz%20and%20Henningsen%202021.%20Host%20manipulation%20by%20intracellular%20effectors%20in%20fungi.pdf 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 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 Abbott, Tatiana Giraud, Véronique Decroocq
article
Nature Communications, Nature Publishing Group, 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.
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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.
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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, Elsevier, 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).
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https://hal.inrae.fr/hal-03229073/file/DataBrief-03-2021.pdf BibTex
titre
Phenotyping Brown Rot Susceptibility in Stone Fruit: A Literature Review with Emphasis on Peach
auteur
Majid Mustafa, Daniele Bassi, Marie-Noëlle Corre, Leandro Lino, Véronique Signoret, Bénédicte Quilot-Turion, Marco Cirilli
article
Horticulturae, MDPI, 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.
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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, Nature Publishing Group, 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.
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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, Elsevier, 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.
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Botanic Origin of Propolis Extract Powder Drives Contrasted Impact on Diabesity in High-Fat-Fed Mice
auteur
Nicolas Cardinault, Franck Tourniaire, Julien Astier, Charlene Couturier, Lauriane Bonnet, Eva Seipelt, Esma Karkeni, Claire Letullier, Naima Dlalah, Stephane Georgé, Lourdes Mounien, Jean-Francois Landrier
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Antioxidants , MDPI, 2021, 10 (3), pp.411. ⟨10.3390/antiox10030411⟩
resume
Propolis extracts are considered as nutraceutical products with potentialities towards obesity and comorbidities management. Nevertheless, propolis extracts composition is highly variable and depends on the botanic origin of plants used by the bees to produce propolis. This study aims to evaluate the differential effect of poplar propolis extract powder (PPEP), Baccharis propolis extract powder (BPEP), and/ or Dalbergia propolis extract powder (DPEP) on obesity and glucose homeostasis in high-fat-fed mice. PPEP supplementation reduced high-fat (HF)-mediated body weight gain, adiposity index, and improved glucose homeostasis in male C57Bl/6J mice that were submitted to a high-fat diet for 12 weeks, whereas BPEP, DPEP, or a mix of the three PEPs did not modify those parameters. Adipose tissue (AT) gene expression profiling highlighted an induction of mRNA related to lipid catabolism and an inhibition of mRNA coding for inflammatory markers. Several Nrf2 target genes, coding for antioxidant enzymes, were induced in AT under PPEP effect, but not by other PEP. Interestingly, representative PPEP polyphenols mediated the induction of Nrf2 target genes cell-autonomously in adipocytes, suggesting that this induction may be related to the specific polyphenol content of PPEP. Whereas PPEP supplementation has demonstrated a clear potential to blunt the onset of obesity and associated comorbidities, other PEPs (from Baccharis and Dalbergia) were inefficient to support their role in preventive nutrition.
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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, Oxford University Press (OUP), 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.
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Genomic inference of complex domestication histories in three Solanaceae species
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Stéphanie Arnoux, Christelle Fraïsse, Christopher Sauvage
article
Journal of Evolutionary Biology, Wiley, 2021, 34 (2), pp.270-283. ⟨10.1111/jeb.13723⟩
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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.
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Evaluation of tomato, eggplant and pepper accessions for resistance to Ralstonia solanacearum species complex (RSSC) strains from Louisiana
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Melanie Lewis Ivey, Alejandra Jimenez Madrid, Marie-Christine Daunay, Denis Shah
article
European Journal of Plant Pathology, Springer Verlag, 2021, 159 (2), pp.279-293. ⟨10.1007/s10658-020-02160-0⟩
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Validated MAGIC and GWAS population mapping reveals the link between vitamin E content and natural variation in chorismate metabolism in tomato
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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
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Plant Journal, Wiley, 2021, 105 (4), pp.907-923. ⟨10.1111/tpj.15077⟩
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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.
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Self-(in)compatibility analysis of apricot germplasm in Tunisia: S-RNase allele identification, S-genotype determination and crop history evolution
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Ayda Boubakri, Lamia Krichen, Mohamed-Amine Batnini, Neila Trifi-Farah, Guillaume Roch, Jean-Marc Audergon, Hedia Bourguiba
article
Scientia Horticulturae, Elsevier, 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.
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Phenolic compounds identified in apricot branch tissues and their role in the control of Monilinia laxa growth
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Jorge del Cueto, Agnieszka Kosinska-Cagnazzo, Patrick Stefani, Julien Heritier, Guillaume Roch, Thomas Oberhänsli, Jean-Marc Audergon, Danilo Christen
article
Scientia Horticulturae, Elsevier, 2021, 275, pp.109707. ⟨10.1016/j.scienta.2020.109707⟩
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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.
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Conservation of horticultural genetic resources in France
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Michel Roux-Cuvelier, Michel Grisoni, Arnaud Bellec, Emmanuel Bloquel, Charron, Carine, Magalie Delalande, Marine Delmas, Didier, Audrey, Charles-Eric Durel, Charles-Henry Duval, Florence Esnault, Laurence Feugey, Emmanuel Geoffriau, Khadari Bouchaïb, Sandra Lepers-Andrzejewski, Luro François, CÉcile Marchal, Alix Pernet, Jérémy Salinier, Marc Seguin, Rebecca Stevens, Bernice van Issum-Groyer, Remi Kahane
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Chronica Horticulturae, 2021
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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
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New Phytologist, Wiley, 2021, ⟨10.1111/nph.17171⟩
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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.
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Genetic diversity of tomato response to heat stress at the QTL and transcriptome levels
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Estelle Bineau, Isidore Diouf, Yolande Carretero, Renaud Duboscq, Frédérique Bitton, Anis Djari, Mohamed Zouine, Mathilde Causse
article
Plant Journal, Wiley, In press, ⟨10.1111/tpj.15379⟩
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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.
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2020

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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, Wiley, 2020, ⟨10.1111/mpp.13031⟩
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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.
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Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality
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Mariem Nsibi, Barbara Gouble, Sylvie Bureau, Timothée Flutre, Christopher Sauvage, Jean-Marc Audergon, Jean-Luc Regnard
article
G3, Genetics Society of America, 2020, 10 (12), pp.4513-4529. ⟨10.1534/g3.120.401452⟩
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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.
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‘Candidatus Liberibacter solanacearum’ distribution and diversity in Scotland and the characterisation of novel haplotypes from Craspedolepta spp. (Psyllidae: Aphalaridae)
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Jason Sumner-Kalkun, Fiona Highet, Yvonne Arnsdorf, Emma Back, Mairi Carnegie, Siobhán Madden, Silvia Carboni, William Billaud, Zoë Lawrence, David Kenyon
article
Scientific Reports, Nature Publishing Group, 2020, 10 (1), ⟨10.1038/s41598-020-73382-9⟩
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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).
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The apple REFPOP—a reference population for genomics-assisted breeding in apple
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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, Nature Publishing Group, 2020, 7 (1), ⟨10.1038/s41438-020-00408-8⟩
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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.
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Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif
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Kelsey Wood, Munir Nur, Juliana 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, Public Library of Science, 2020, 16 (10), pp.e1009012. ⟨10.1371/journal.ppat.1009012⟩
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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.
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Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population
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Isidore Diouf, Laurent Derivot, Shai Koussevitzky, Yolande Carretero, Frédérique Bitton, Laurence Moreau, Mathilde Causse
article
Journal of Experimental Botany, Oxford University Press (OUP), 2020, 71 (18), pp.5365-5376. ⟨10.1093/jxb/eraa265⟩
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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.
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Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple
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Morgane Roth, Helene Muranty, Mario Di Guardo, Walter Guerra, Andrea Patocchi, Fabrizio Costa
article
Horticulture research, Nature Publishing Group, 2020, 7, pp.148-161. ⟨10.1038/s41438-020-00370-5⟩
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Texture is a complex trait and a major component of fruit quality in apple. While the major effect of MdPG1, a gene controlling firmness, has already been exploited in elite cultivars, the genetic basis of crispness remains poorly understood. To further improve fruit texture, harnessing loci with minor effects via genomic selection is therefore necessary. 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.
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Selections issued from CEP INNOVATION, CENTREX and INRA: apricot breeding program in France
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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, pp.31-34. ⟨10.17660/ActaHortic.2020.1290.6⟩
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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.
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Evaluation of apricot fruit quality diversity in two countries, France and New Zealand
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B. Gouble, C. Scofield, A. Mcglone, H. Boldingh, C. Clark, J.M. Audergon, S. Bureau, J. Stanley
article
Acta Horticulturae, 2020, pp.147-154. ⟨10.17660/ActaHortic.2020.1290.27⟩
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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.
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Precision breeding made real with CRISPR: illustration through genetic resistance to pathogens
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Florian Veillet, Mickaël Durand, Thomas Kroj, Stella Cesari, Jean-Luc Gallois
article
Plant Communications, Cell Press, 2020, 1 (5), pp.100102. ⟨10.1016/j.xplc.2020.100102⟩
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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.
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Integration of QTL, Transcriptome and Polymorphism Studies Reveals Candidate Genes for Water Stress Response in Tomato
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Isidore Diouf, Elise Albert, Renaud Duboscq, Sylvain Santoni, Frédérique Bitton, Justine Gricourt, Mathilde Causse
article
Genes, MDPI, 2020, 11 (8), pp.900. ⟨10.3390/genes11080900⟩
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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.
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Ecological Specialization and Rarity of Arable Weeds: Insights from a Comprehensible Survey in France
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François Munoz, Guillaume Fried, Laura Armengot, Bérenger Bourgeois, Vincent Bretagnolle, Joel Chadoeuf, Lucie Mahaut, Christine Plumejeaud, Jonathan Storkey, Cyrille Violle, Sabrina Gaba
article
Plants, MDPI, 2020, 9 (7), pp.824. ⟨10.3390/plants9070824⟩
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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.
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Cuticular waxes of nectarines during fruit development in relation to surface conductance and susceptibility to Monilinia laxa
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Leandro Oliveira Lino, Bénédicte Quilot-Turion, Claire Dufour, Marie-Noëlle Corre, René Lessire, Michel Génard, Jean-Luc Poessel
article
Journal of Experimental Botany, Oxford University Press (OUP), 2020, ⟨10.1093/jxb/eraa284⟩
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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.
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Special issue in honour of Prof. Reto J. Strasser - Phenotyping with fast fluorescence sensors approximates yield component measurements in pepper (Capsicum annuum L.)
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S. Lenk, J.A. Dieleman, Véronique Lefebvre, E. Heuvelink, J.J. Magan, A. Palloix, F.A. Eeuwijk, A. Barocsi
article
Photosynthetica, Springer Verlag, 2020, 58 (SPECIAL ISSUE), pp.622-637. ⟨10.32615/ps.2020.016⟩
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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.
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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
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Hedia Bourguiba, Ivan Scotti, Christopher Sauvage, Tetyana Zhebentyayeva, Craig Ledbetter, Boris Krška, Arnaud Remay, Claudio D’onofrio, Hiroyuki Iketani, Danilo Christen, Lamia Krichen, Neila Trifi-Farah, Weisheng Liu, Guillaume Roch, Jean-Marc Audergon
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Frontiers in Plant Science, Frontiers, 2020, 11, ⟨10.3389/fpls.2020.00638⟩
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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.
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Competitive interactions in plant-parasitic nematode communities affecting organic vegetable cropping systems
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Thierry 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, Elsevier, 2020, 135, pp.105206. ⟨10.1016/j.cropro.2020.105206⟩
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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.
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Reducing a model of sugar metabolism in peach to catch different patterns among genotypes
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Hussein Kanso, Bénédicte Quilot-Turion, Mohamed-Mahmoud Memah, Olivier Bernard, Jean-Luc Gouzé, Valentina Baldazzi
article
Mathematical Biosciences, Elsevier, 2020, 321, pp.108321. ⟨10.1016/j.mbs.2020.108321⟩
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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.
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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, MDPI, 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.
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titre
Gearing Up for Warmer Times: Transcriptomic Response of Spongia officinalis to Elevated Temperatures Reveals Recruited Mechanisms and Potential for Resilience
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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, Frontiers Media, 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.
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Future development of apricot blossom blight under climate change in Southern France
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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, Elsevier, 2020, 112, pp.125960. ⟨10.1016/j.eja.2019.125960⟩
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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.
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Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
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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
Plant Journal, Wiley, 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.
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Knock-out mutation of eukaryotic initiation factor 4E2 (eIF4E2) confers resistance to pepper veinal mottle virus in tomato
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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, Elsevier, 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.
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Analysis of tomato spotted wilt virus RNA-dependent RNA polymerase adaptative evolution and constrained domains using homology protein structure modelling.
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Zoé Terret-Welter, Grégori Bonnet, Benoît Moury, Jean-Luc Gallois
article
Journal of General Virology, Microbiology Society, 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.
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Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding.
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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, Wiley, 2020, 21 (1), pp.03-16. ⟨10.1111/mpp.12874⟩
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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.
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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, American Society of Plant Biologists, 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.
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Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach
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Jiali Yu, Anna Conrad, Véronique Decroocq, Tetyana Zhebentyayeva, Daniel Williams, Dennis Bennett, Guillaume Roch, Jean-Marc Audergon, Christopher Dardick, Zongrang Liu, Albert Abbott, Michael Considine, Hisayo Yamane, Gabino Ríos, Carmen Leida, Margaret Staton
article
Frontiers in Plant Science, Frontiers, 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
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2019

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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 Morin, Catherine Dogimont, Adnane Boualem, Abdelhafid Bendahmane
article
Scientific Reports, Nature Publishing Group, 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.
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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, Elsevier, 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.
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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, Nature Publishing Group, 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.
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The Solanum tuberosum GBSSI gene: a target for assessing gene and base editing in tetraploid potato
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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, Springer Verlag, 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.
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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, MDPI, 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.
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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, Springer Verlag, 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.
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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 Robaglia, Jean-Luc Gallois
article
Plant Biotechnology Journal, Wiley, 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.
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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, Springer Verlag, 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.
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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, MDPI, 2019, 20 (2), pp.402. ⟨10.3390/ijms20020402⟩
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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.
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Resistance against melon chlorotic mosaic virus and tomato leaf curl New Delhi virus in melon
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Gustavo Romay, Michel Pitrat, Hervé Lecoq, Catherine Wipf-Scheibel, Pauline Millot, Gregory Girardot, Cecile Desbiez
article
Plant Disease, American Phytopathological Society, 2019, 103 (11), pp.2913-2919. ⟨10.1094/PDIS-02-19-0298-RE⟩
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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).
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https://hal.inrae.fr/hal-02619468/file/2019_Romay_PlantDis_postprint_1.pdf BibTex
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Limitation de l’usage des pesticides sur des cultures de laitue d’abri : bilan du projet DEPHY EXPE LILLA.
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François Lecompte, Claire Goillon, B. Gard, Christiane Raynal, Elise Vaud, Virginie Barrière, Brigitte Maisonneuve, Damien Rousselière, J. Garnodier, Philippe C. Nicot
article
Innovations Agronomiques, INRAE, 2019, 76, pp.35-50. ⟨10.15454/c1v2ph⟩
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La lutte chimique préventive est encore aujourd’hui le principal moyen de lutte contre les bioagresseurs en culture de laitue d’hiver sous abri. Des stratégies alternatives ont été explorées dans le projet LILLA, visant soit à fournir des références expérimentales manquantes sur des techniques non chimiques de protection des plantes, soit à tester des conduites de cultures basées sur des stratégies intégrées de protection, limitant le recours aux pesticides. Des leviers innovants, comme une résistance génétique accrue aux agents de la pourriture du collet, ou la conduite de l’irrigation en goutte à goutte au lieu de l’aspersion, ont pu être identifiés. En considérant un ensemble de 23 essais comparatifs de conduite des cultures, une diminution de moitié du nombre de traitements fongicides en association avec des techniques alternatives ne montre pas une augmentation statistique du risque de perte de récolte. Contre les pucerons, les stratégies de contrôle biologique testées restent à améliorer. Le coût de mise en oeuvre des techniques alternatives est significatif mais, pour la plupart d’entre elles, reste modéré. Les plus efficaces de ces techniques pourraient plus facilement être mises en oeuvre dans les exploitations si les incertitudes sur les revenus de la récolte étaient moins grandes.
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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, BioMed Central, 2019, 19:31, 18 p. ⟨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.
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https://hal.inrae.fr/hal-02621426/file/2019_Omrani_BMC%20Plant%20Biol_1.pdf BibTex
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Inheritance of Resistance to Cucurbit Powdery Mildew in Bitter Gourd
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Narinder P.S. Dhillon, Supannika Sanguansil, Supornpun Srimat, Suwannee Laenoi, Roland Schafleitner, Michel Pitrat, James D. Mccreight
article
HortScience, American Society for Horticultural Science, 2019, 54 (6), pp.1013-1016. ⟨10.21273/HORTSCI13906-19⟩
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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.
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La laitue : Une large diversité enrichie par des espèces sauvages européennes
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Brigitte Maisonneuve
article
Jardins de France, 2019, pp.54-59
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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 ?
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Model-based QTL detection is sensitive to slight modifications in model formulation
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Caterina Barrasso, Mohamed-Mahmoud Memah, Michel Génard, Bénédicte Quilot-Turion
article
PLoS ONE, Public Library of Science, 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.
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New data completing the spectrum of the Ma, RMia and RMja genes for resistance to root-knot nematodes Meloidogyne spp. in Prunus.
auteur
Daniel Esmenjaud, Cyril van Ghelder, Ulysse Portier, Carole Confolent, Pablo Meza, Henri Duval
article
Phytopathology, American Phytopathological Society, 2019, 109 (4), pp.615 - 622. ⟨10.1094/PHYTO-05-18-0173-R⟩
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Root-knot nematodes (RKN) Meloidogyne spp. are worldwide pests that affect a considerable number of plants among which stone fruits Prunus spp. are severely attacked. Prevalent RKN species are M. arenaria, M. incognita and M. javanica in stone fruits but the emergent M. ethiopica and M. enterolobii are also reported to challenge perennial crops. In Prunus, 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 towards 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 of the phenotype of the individuals indicates that the gene of interest is active against and thus controls the corresponding isolate of this RKN species. Segregating materials used were a Ma F1 plum progeny, a RMia F2 peach progeny, and a RMja F2 almond progeny. In addition to previous data, our results establish a clear spectrum for each of the three genes towards isolates from both the three prevalent RKN 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, nor M. enterolobii. Our data should have wide implications in RKN resistance management and breeding and in deciphering the molecular mechanisms of the spectrum of RKN R genes.
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Genetic analysis of cadmium accumulation in lettuce (Lactuca sativa)
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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, Elsevier, 2019, 136, pp.67-75. ⟨10.1016/j.plaphy.2019.01.011⟩
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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.
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A complex eIF4E locus impacts the durability of va resistance to Potato virus Y in tobacco
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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, Wiley, 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.
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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, MDPI, 2019, 9 (2), pp.51. ⟨10.3390/agronomy9020051⟩
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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.
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https://hal.inrae.fr/hal-02620117/file/abdelgawad-agronomy-2019_1.pdf BibTex
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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, Frontiers, 2019, 9, ⟨10.3389/fgene.2018.00749⟩
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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.
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https://hal.inrae.fr/hal-02620563/file/2019_Tsakogiannis_Front%20Gene_1.pdf BibTex
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Unravelling paralogous gene expression dynamics during three-spined stickleback embryogenesis
auteur
Elisavet Kaitetzidou, Ioanna Katsiadaki, Jacques Lagnel, Efthimia Antonopoulou, Elena Sarropoulou
article
Scientific Reports, Nature Publishing Group, 2019, 9, ⟨10.1038/s41598-019-40127-2⟩
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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.
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https://hal.inrae.fr/hal-02627533/file/Kaitetzidou-scientific-reports2019_1.pdf BibTex
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Conception et évaluation de systèmes de culture maraîchers méditerranéens innovants pour gérer les nématodes à galles
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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, Presses Agronomiques de Gembloux, 2019, 23 (1), pp.7-21. ⟨10.25518/1780-4507.17725⟩
resume
Description du sujet. Une approche système basée sur la co-conception et l’évaluation expérimentale in situ de prototypes de systèmes de culture (SDC) a été mise en œuvre dans le projet INRA « GeDuNem » pour une gestion durable des nématodes à galles (NG) dans les systèmes maraîchers sous abris.Objectifs. Il s’agissait (i) d’évaluer pendant quatre ans diverses stratégies de culture combinant résistances génétiques et pratiques culturales (rotations culturales incluant des plantes sensibles, résistantes et non-hôtes, gestion de l’interculture avec couvert végétal nématicide ou solarisation) pour réduire les populations de NG dans le sol et augmenter la durabilité des résistances variétales à ces bioagresseurs, (ii) d’étudier leur impact sur les communautés de nématodes rencontrées et (iii) d’évaluer l’acceptabilité des nouveaux SDC par les agriculteurs.Méthode. Trois prototypes de SDC, co-conçus entre acteurs de la recherche et ceux du développement, ont été comparés à des SDC appliqués classiquement en région méditerranéenne et évalués grâce à des dispositifs complémentaires : (i) expérimentations-système sur trois sites de producteurs du Sud de la France ; (ii) expérimentations analytiques pour approfondir les mécanismes d’action des leviers mobilisés ; (iii) enquêtes pour évaluer l’acceptabilité des prototypes par les agriculteurs. Résultats. Les trois SDC se sont révélés efficaces (90 % de réduction des NG, protection des Solanaceae à résistance partielle, pas d’effet négatif sur les nématodes non phytoparasites) et durables lorsque les conditions d’application et les équilibres biologiques du sol étaient favorables (nématofaune totale diversifiée et abondante). Leur degré d’acceptabilité dépendait du type d’exploitation et de la sensibilité des agriculteurs face à l’innovation.Conclusions. Ces nouveaux SDC doivent encore être améliorés, en interaction avec les producteurs, tant en termes d’efficacité, par l’introduction de nouveaux leviers agroécologiques, que de cout. Les recherches futures devront aussi s’ouvrir à la gestion plus globale de la santé des sols.
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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, Springer Verlag, 2019, 38 (4), pp.459-462. ⟨10.1007/s00299-019-02373-6⟩
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Root Architectural Trait Diversity in Aubergine (Solanum melongena L.) and Related Species and Correlations with Plant Biomass
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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⟩
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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.
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Gone with the wind: Aerial dispersal of Parthenolecanium corni crawlers in a newly planted grapevine plot
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Gerard Hommay, Louis Wiss, Joel Chadoeuf, Jean Le Maguet, Monique Beuve, Etienne Herrbach
article
Annals of Applied Biology, Wiley, 2019, 174 (3), pp.372-387. ⟨10.1111/aab.12505⟩
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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.
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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, Oxford University Press (OUP): Policy B - Oxford Open Option B, 2019, 39, pp.1136-1148. ⟨10.1093/treephys/tpz053⟩
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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.
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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, Nature Publishing Group, 2019, 10 (1), pp.1534. ⟨10.1038/s41467-019-09462-w⟩
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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.
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Trait discovery and editing in tomato.
auteur
Christophe Rothan, Isidore Diouf, Mathilde Causse
article
Plant Journal, Wiley, 2019, 97 (1), pp.73-90. ⟨10.1111/tpj.14152⟩
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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.
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Get the Balance Right: ROS Homeostasis and Redox Signalling in Fruit
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Guillaume Decros, Pierre Baldet, Bertrand Beauvoit, Rebecca Stevens, Amélie Flandin, Sophie Colombie, Yves Gibon, Pierre Pétriacq
article
Frontiers in Plant Science, Frontiers, 2019, 10, pp.1-16. ⟨10.3389/fpls.2019.01091⟩
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2018

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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, Wiley, 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.
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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, Springer Verlag, 2018, 12 (5), pp.725 - 731. ⟨10.1007/s11829-018-9619-8⟩
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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
Plant Journal, Wiley, 2018, 94 (4), pp.685-698. ⟨10.1111/tpj.13890⟩
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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.
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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 Ourry
article
Agriculture, MDPI, 2018, 8 (1), pp.14. ⟨10.3390/agriculture8010014⟩
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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.
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https://hal-normandie-univ.archives-ouvertes.fr/hal-02183699/file/ETIENNE%202018-33_1.pdf 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, MDPI, 2018, 19 (10), pp.2856. ⟨10.3390/ijms19102856⟩
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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.
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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, Wiley, 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.
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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, Wiley, 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.
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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 Chardot, Jean-Luc Gallois, Sabine d'Andrea
article
The Plant cell, American Society of Plant Biologists (ASPB), 2018, 30 (9), pp.2116-2136. ⟨10.1105/tpc.18.00275⟩
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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.
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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, American Society for Horticultural Science, 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.
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A Model for Temporal Dynamics of Brown Rot Spreading in Fruit Orchards
auteur
Danièle Bevacqua, Bénédicte Quilot-Turion, Luca Bolzoni
article
Phytopathology, American Phytopathological Society, 2018, 108 (5), pp.595-601. ⟨10.1094/PHYTO-07-17-0250-R⟩
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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.
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Seeking stable traits to characterize the root system architecture. Study on 60 species located at two sites in natura
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Loïc Pagès, Jocelyne Kervella
article
Annals of Botany, Oxford University Press (OUP), 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’.
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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, Frontiers Media S.A, 2018, 5, ⟨10.3389/fevo.2017.00170⟩
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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.
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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
Plant Journal, Wiley, 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.
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Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees
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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 , National Academy of Sciences, 2018, 115 (20), pp.E4690 - E4699. ⟨10.1073/pnas.1704515115⟩
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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.
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Arthropods life cycle and temperature: beyond isomorphy hypothesis
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Olivier Bonato, Joel Chadoeuf
article
Journal of Thermal Biology, Elsevier, 2018, 75, pp.1-6. ⟨10.1016/j.jtherbio.2018.05.004⟩
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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.
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Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance in plants
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Anna Bastet, Baptiste Lederer, Nathalie Giovinazzo, Xavier Arnoux, Sylvie German-Retana, Catherine Reinbold, Veronique Brault, Damien Garcia, Samia Djennane, Sophie Gersch, Olivier Lemaire, Christophe Robaglia, Jean-Luc Gallois
article
Plant Biotechnology Journal, Wiley, In press, 16 (9), pp.1569-1581. ⟨10.1111/pbi.12896⟩
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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.
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The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish
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A. Tsakogiannis, T. Manousaki, Jacques Lagnel, A. Sterioti, M. Pavlidis, N. Papandroulakis, C. C. Mylonas, C. S. Tsigenopoulos
article
Scientific Reports, Nature Publishing Group, 2018, 8 (1), pp.1-17. ⟨10.1038/s41598-018-21992-9⟩
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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.
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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, Elsevier, 2018, 39, pp.39-44. ⟨10.1016/j.margen.2018.01.002⟩
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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.
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Irrigation with salt water affects growth, yield, fruit quality, storability and marker-gene expression in cherry tomato
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Mohamed Zaki Elmogy, Cecile Garchery, Rebecca Stevens
article
Acta Agriculturae Scandinavica, Section B - Soil and Plant Science, Taylor & Francis, 2018, 68 (8), pp.727 - 737. ⟨10.1080/09064710.2018.1473482⟩
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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.
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Atmosphere–soil carbon transfer as a function of soil depth
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Jérôme Balesdent, Isabelle Basile-Doelsch, Joel Chadoeuf, Sophie Cornu, Delphine Derrien, Zuzana Fekiacova, Christine Hatté
article
Nature, Nature Publishing Group, 2018, 559 (7715), pp.599-602. ⟨10.1038/s41586-018-0328-3⟩
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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.
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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 - CB, Elsevier, 2018, 28 (20), pp.1-7. ⟨10.1016/j.cub.2018.08.023⟩
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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.
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Comparison of the responses to NaCl stress of three tomato introgression lines
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Fedia Rebah, Chayma Ouhibi, K. H. Alamer, Najoua Msilini, Mouhiba Ben Nasri, Rebecca Stevens, Houneida Attia
article
Acta Biologica Hungarica, Akadémiai Kiadó, 2018, 69 (4), pp.464-480. ⟨10.1556/018.69.2018.4.8⟩
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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.
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The DFR locus: A smart landing pad for targeted transgene insertion in tomato.
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Benoît Danilo, Laura Perrot, Emmanuel Botton, Fabien Nogué, Marianne Mazier
article
PLoS ONE, Public Library of Science, 2018, 13 (12), pp.e0208395. ⟨10.1371/journal.pone.0208395⟩
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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.
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Des résistances aux nématodes à galles du genre Meloidogyne dans le genre Lactuca : espoir pour la sélection de la laitue.
auteur
Brigitte Maisonneuve, Claire Jouan, B. Gard, Stéphanie Gimenez, Claire Goillon, Loic Jean, Yannie Trottin, Hélène Védie, Michel Pitrat
article
Innovations Agronomiques, INRAE, 2018, a paraitre
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Une collection de Lactuca a été évaluée pour son comportement vis-à-vis de Meloidogyne incognita, par des tests en laboratoire, sur jeunes plantes en pots inoculées avec 400 larves au stade J2. La sélection des accessions résistantes a été effectuée d’après le nombre de pontes par plante après un cycle de développement des nématodes. Parmi les 569 accessions étudiées aucune n’a été immune. Cependant, parmi 409 variétés de laitue, 3% se sont révélées peu sensibles avec de nombreuses galles mais très peu de pontes ; parmi les 160 accessions de Lactuca sauvages, 54% étaient résistantes car, bien que portant des galles, l’ensemble du système racinaire avait moins de 10 pontes par plante. Le criblage réalisé sur deux plantes par accession a permis de retenir 102 accessions. Des contrôles plurilaboratoires de 52 de ces accessions avec deux souches ont confirmé la grande majorité des résultats avec 14 variétés de laitue et 36 L. serriola résistantes. Parmi ces accessions, quelques-unes étaient également résistantes (huit L. serriola) ou peu sensibles (PI 419140) à M. arenaria en laboratoire. De plus, un test avec une forte pression d’inoculation (2000 J2/plante) a confirmé le haut niveau de résistance des quatre L. serriola évaluées. Par ailleurs, 10 accessions ont été testées en pots vis-à-vis de populations de Meloidogyne de deux sols agricoles de Provence naturellement contaminés, en particulier par M. arenaria ; sur six L. serriola résistantes en laboratoires à M. incognita et M. arenaria, le nombre de pontes ainsi que le nombre de pontes par galle étaient réduits, par rapport aux témoins L. serriola sensibles à M. arenaria en laboratoire. Mais, l’accession avec le moins de galles et de pontes a été une accession de L. virosa sensible à M. arenaria en laboratoire. Ainsi, des géniteurs intéressants pour la sélection de variétés de laitue résistantes aux nématodes ont été identifiés.
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Impact of canning and storage on apricot carotenoids and polyphenols
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Carine Le Bourvellec, Barbara Gouble, Sylvie Bureau, Patrice Reling, Romain Bott, Albert Ribas, Jean Marc Audergon, Catherine Renard
article
Food Chemistry, Elsevier, 2018, 240, pp.615-625. ⟨10.1016/j.foodchem.2017.07.147⟩
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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.
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Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato
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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
Plant Journal, Wiley, 2018, 96 (3), pp.635-650. ⟨10.1111/tpj.14057⟩
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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.
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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, Springer Verlag, 2018, 38 (4), ⟨10.1007/s11032-018-0793-2⟩
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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.
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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
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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, Frontiers, 2018, 9 (137), 16 p. ⟨10.3389/fpls.2018.00137⟩
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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.
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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, Frontiers, 2018, 9, pp.1-13. ⟨10.3389/fpls.2018.00279⟩
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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.
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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, Frontiers, 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.
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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, MDPI, 2018, 19 (2), pp.1-24. ⟨10.3390/ijms19020357⟩
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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.
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2017

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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 Piry, Mbacké Sembene, Jean-François Cosson, Nathalie Charbonnel, Carine Brouat, Mamadou Kane
article
Scientific Reports, Nature Publishing Group, 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.
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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, Public Library of Science, 2017, 13 (11), pp.1-25. ⟨10.1371/journal.ppat.1006702⟩
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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.
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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, Frontiers, 2017, 8, pp.1126 - 1126. ⟨10.3389/fpls.2017.01126⟩
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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.
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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, Microbiology Society, 2017, 98 (7), pp.1923 - 1931. ⟨10.1099/jgv.0.000835⟩
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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.
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The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo
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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, BioMed Central, 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
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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 Santoni, Laure Sauné, Morgane Ardisson, Nathalie 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, Wiley/Blackwell, 2017, 17 (3), pp.565-580. ⟨10.1111/1755-0998.12587⟩
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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.
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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, BioMed Central, 2017, 18 (1), ⟨10.1186/s12864-017-3783-6⟩
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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.
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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, BioMed Central, 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.
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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.
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Impact of Vat resistance in melon on viral epidemics and genetic structure of virus populations
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Alexandra Schoeny, Cecile Desbiez, Pauline Millot, Catherine Wipf-Scheibel, Karine Nozeran, Patrick Gognalons, Hervé Lecoq, Nathalie Boissot
article
Virus Research, Elsevier, 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.
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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, Wiley, 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.
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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, Cambridge University Press (CUP), 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
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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, Wiley, 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.
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A kinetic model of sugar metabolism allows the simulation of sugar concentrations and their genetic variability during peach fruit growth
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Elsa Desnoues, Michel Génard, Bénédicte Quilot-Turion, Valentina Baldazzi
article
Acta Horticulturae, International Society for Horticultural Science, 2017, pp.361-366. ⟨10.17660/ActaHortic.2017.1160.52⟩
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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.
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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, INRAE, 2017, 59, pp.103-118. ⟨10.15454/1.5138445077696033E12⟩
resume
Le projet « Prunus » a exploré la question de la (re)conception de vergers « durables » au travers d’une approche intégrée prenant en compte à la fois le choix variétal, les conduites de cultures et les évolutions plus larges du système « agri-alimentaire » (filières, politiques publiques, recherche, conseil). Il a associé des chercheurs en sciences sociales, en agronomie et en génétique, ainsi que plusieurs acteurs de la filière autour d’une analyse socio-historique, d’enquêtes auprès des arboriculteurs, et enfin de séminaires de co-construction autour de l'innovation variétale. Nos analyses montrent l’impact des contraintes imposées par l’aval, dans un contexte d’allongement des calendriers de production, sur le modèle d’innovation variétale, aux dépens des possibilités de réduction d’intrants et même de la pérennisation du verger et des exploitations. Les résultats des enquêtes indiquent une grande variabilité des pratiques même pour des niveaux de production comparables, et un réel potentiel de réduction de l’utilisation des pesticides en production d’abricot. Il apparait nécessaire de développer de nouveaux leviers techniques mais aussi davantage de références et d’espaces d’échanges sur ces leviers. Le levier variétal reste majeur (notamment sur les maladies), mais il faut privilégier une approche multicritères et non plus le ciblage de caractères ponctuels dans l’innovation variétale. Nous montrons enfin l’intérêt des démarches multi-acteurs pour mettre en discussion les contraintes et critères des différents maillons du système
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Nucleotide diversity in the two co-resident genomes of allopolyploid cotton
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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, Springer Verlag (Germany), 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.
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Ascorbate degradation in tomato leads to accumulation of oxalate, threonate and oxalyl threonate
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Vincent Truffault, Stephen C. Fry, Rebecca Stevens, Hélène Gautier
article
Plant Journal, Wiley, 2017, 89 (5), pp.996 - 1008. ⟨10.1111/tpj.13439⟩
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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.
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eIF4E Resistance: Natural Variation Should Guide Gene Editing
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Anna Bastet, Christophe Robaglia, Jean-Luc Gallois
article
Trends in Plant Science, Elsevier, 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.
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Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement
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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
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New Phytologist, Wiley, 2017, 215 (2), pp.624-641. ⟨10.1111/nph.14615⟩
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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.
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Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study
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Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Julien Bonnet, Laurent Grivet, Mathilde Causse
article
TAG Theoretical and Applied Genetics, Springer Verlag, 2017, 130 (5), pp.875-889. ⟨10.1007/s00122-017-2857-9⟩
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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
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Mapping of new resistance (Vr2, Rm1) and ornamental (Di2, pl) Mendelian trait loci in peach
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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⟩
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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.
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Eggplant Resistance to the Ralstonia solanacearum Species Complex Involves Both Broad-Spectrum and Strain-Specific Quantitative Trait Loci
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Sylvia Salgon, Cyril Jourda, Christopher Sauvage, Marie-Christine Brand-Daunay, Bernard Reynaud, Emmanuel Wicker, Jacques Dintinger
article
Frontiers in Plant Science, Frontiers, 2017, 8, ⟨10.3389/fpls.2017.00828⟩
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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.
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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 Renard
article
LWT - Food Science and Technology, Elsevier, 2017, 85 (Part B), pp.385-389. ⟨10.1016/j.lwt.2016.10.040⟩
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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
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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 Renard
article
Food and Bioprocess Technology, Springer, 2017, 10 (4), pp.1-12. ⟨10.1007/s11947-016-1850-7⟩
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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.
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Is monodehydroascorbate reductase activity in leaf tissue critical for the maintenance of yield in tomato?
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Vincent Truffault, Gisele Riqueau, Cecile Garchery, Hélène Gautier, Rebecca Stevens
article
Journal of Plant Physiology, Elsevier, 2017, 222, pp.1-28. ⟨10.1016/j.jplph.2017.12.012⟩
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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.
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Domestication rewired gene expression and nucleotide diversity patterns in tomato
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Christopher Sauvage, Andrea Rau, Charlotte Aichholz, Joel Chadoeuf, Gautier Sarah, Manuel Ruiz, Sylvain Santoni, Mathilde Causse, Jacques David, Sylvain Glémin
article
Plant Journal, Wiley, 2017, 91 (4), pp.631-645. ⟨10.1111/tpj.13592⟩
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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.
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The timeline of corona formation around silica nanocarriers highlights the role of the protein interactome
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Cedric Pisani, Jean-Charles Gaillard, Michaël Odorico, Jeff Nyalosaso, Clarence Charnay, Yannick Guari, Joël Chopineau, Jean-Marie Devoisselle, J. Armengaud, Odette Prat
article
Nanoscale, Royal Society of Chemistry, 2017, 9 (5), pp.1840-1851. ⟨10.1039/C6NR04765C⟩
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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.
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A kinetic model of sugar metabolism in peach fruit allows the exploration of genetic variability
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Elsa Desnoues, Michel Génard, Bénédicte Quilot-Turion, Valentina Baldazzi
article
Acta Horticulturae, International Society for Horticultural Science, 2017, pp.169-176. ⟨10.17660/ActaHortic.2017.1182.20⟩
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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.
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Evolutionary forces affecting synonymous variations in plant genomes
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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, Public Library of Science, 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.
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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, American Phytopathological Society, 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.
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2016

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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, B. Nabholtz, 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, 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
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titre
The battle for survival between viruses and their host plants
auteur
Adnane Boualem, Catherine Dogimont, Abdelhafid Bendahmane
article
Current Opinion in Virology, Elsevier, 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.
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https://hal.archives-ouvertes.fr/hal-02889521/file/Revue.Virus.pdf BibTex
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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, Wiley, 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.
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Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression
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Elise Albert, Justine Gricourt, Nadia Bertin, Julien Bonnefoi, Stephanie Pateyron, Jean-Philippe Tamby, Frederique Bitton, Mathilde Causse
article
TAG Theoretical and Applied Genetics, Springer Verlag, 2016, 129 (2), pp.395-418. ⟨10.1007/s00122-015-2635-5⟩
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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
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A TILLING approach to generate broad-spectrum resistance to potyviruses in tomato is hampered by eIF4E gene redundancy
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Camille Gauffier, Caroline Lebaron, André Moretti, Carole Constant, Frédéric Moquet, Grégori Bonnet, Carole Caranta, Jean-Luc Gallois
article
Plant Journal, Wiley, 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.
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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 German-Retana, Benoît Moury, Jean-Luc Gallois
article
Journal of General Virology, Microbiology Society, 2016, 97 (11), pp.3063-3072. ⟨10.1099/jgv.0.000609⟩
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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
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https://hal.inrae.fr/hal-02639858/file/2016_Lebaron_J%20Gen%20Virol_postprint_1.pdf BibTex
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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
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Julie Quenouille, Ludovic Saint-Félix, Benoît Moury, Alain Palloix
article
Molecular Plant Pathology, Wiley, 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.
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https://hal.inrae.fr/hal-02640439/file/2016_Quenouille_MPP_postprint_2.pdf BibTex
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Quelles associations de QTL chez la pomme de terre pour une résistance efficace et durable au nématode à kyste globodera pallida ?
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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, INRAE, 2016, 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.
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https://hal.inrae.fr/hal-02637067/file/2016_Caromel_Innovations%20Agronomiques_1.pdf BibTex
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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, Botanical Society of America, 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.
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https://hal.archives-ouvertes.fr/hal-01315233/file/ajb.1500539.full-1_%7BA9854ED1-F285-4212-97BD-E220AF4C735C%7D.pdf BibTex
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Sensibilité des variétés de laitue aux pourritures du collet
auteur
François Lecompte, Brigitte Maisonneuve, Philippe C. Nicot
article
Phytoma , Groupe France Agricole, 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.
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Differential effect of resistance inducers on the susceptibility of lettuce varieties to Sclerotinia sclerotiorum and Botrytis cinerea
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Asti Irawanti Azis, Magali Duffaud, Claire Troulet, Brigitte Maisonneuve, Efi Toding Tondok, Suryo Wiyono, Marc Bardin, Philippe C. Nicot
article
IOBC WPRS Bulletin, 2016, 115, pp.191-195
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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.
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Brown rot strikes Prunus fruit: an ancient fight almost always lost
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Leandro de Oliveira-Lino, Igor Pacheco, Vincent Mercier, Franco Faoro, Daniele Bassi, Isabelle Bornard, Bénédicte Quilot-Turion
article
Journal of Agricultural and Food Chemistry, American Chemical Society, 2016, 64 (20), pp.4029-4047. ⟨10.1021/acs.jafc.6b00104⟩
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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.
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https://hal.archives-ouvertes.fr/hal-01594477/file/acs.jafc.6b00104_%7BDE6FE245-92E2-4082-A970-1F6511A90758%7D.pdf BibTex
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Premières cartes d’abondance relative de six mustélidés en France
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Clément Calenge, Michel Albaret, François Leger, Jean-Michel Vandel, Joel Chadoeuf, Christophe Giraud, Sylvie Huet, Romain Julliard, Pascal Monestiez, Jeremy Piffady, David Pinaud, Sandrine Ruette
article
Faune Sauvage, Office National de la Chasse et de la 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.
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Le piment : des goûts et des couleurs pour tous les amateurs d’épices
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Anne-Marie Sage-Palloix, Alain Palloix
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Jardins de France, 2016, pp.11-14
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Mais pourquoi tailler les légumes ?
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Michel Javoy, Michel Pitrat, Jean-Daniel Arnaud
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Jardins de France, 2016, pp.19-21
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Guara et Tuono: deux noms pour une variété
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Henri Duval, Federico Dicenta
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Réussir Fruits et Légumes, 2016, pp.44-45
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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.
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Maladies et ravageurs. La génétique au service des résistances
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Michel Pitrat
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Jardins de France, 2016, pp.29-31
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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.
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Pollinisations contrôlées au cours de la création variétale
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Michel Pitrat, Yves Lespinasse
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Jardins de France, 2016, 643, pp.39-42
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Curcubitacées: une sexualité complexe et variée
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Michel Pitrat
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Jardins de France, 2016, pp.22-25
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The andromonoecious sex determination gene predates the separation of cucumis and citrullus genera
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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, Public Library of Science, 2016, 11 (5), pp.e0155444. ⟨10.1371/journal.pone.0155444⟩
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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.
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L'apport des marqueurs moléculaires et de la génomique pour l'utilisation des ressources génétiques chez la tomate
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Christopher Sauvage, Guillaume Bauchet, Mathilde Causse
article
Sélectionneur Français, 2016, pp.29-40
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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.
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Verticillium chez l'aubergine à travers le projet Vasculeg. Recherche de nouveaux moyens de protection (2ième partie)
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Marie-Christine Brand-Daunay, François Villeneuve, F. Latour, Théophile Théry, Christine Fournier, Patricia Erard
article
Infos CTIFL, 2016, pp.45-59
resume
L’aubergine (Solanum melongena L.), est une culture particulièrement sensible aux bioagresseurs telluriques principalement la verticilliose (Verticillium sp.) et les néma- todes à galles (Meloidogyne spp.) en climat tempéré. Utilisé par les producteurs depuis des décennies, le greffage est une solution présentant de nouveaux problèmes. Dès lors, il faut identifier de nouvelles résis- tances et des porte-greffe alternatifs, ainsi, que de nouvelles solutions de protection pour les accompagner. Le projet VASCUlég a eu cet objectif grâce à une collaboration entre le Ctifl, l’INRA, les stations régionales et les firmes semencières de 2011 à 2015. Il a permis d’identifier de nouvelles sources de résistances au Verticillium sp., mais aussi des combinaisons avec des Solanum spp. donnant de bons résultats et des pistes de techniques alternatives de protection
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https://hal.archives-ouvertes.fr/hal-01603029/file/Daunay%20Infos-ctifl%202016%2045-59_1.pdf BibTex
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Efficiency of genomic selection for tomato fruit quality
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Janejira Duangjit, Mathilde Causse, Christopher Sauvage
article
Molecular Breeding, Springer Verlag, 2016, 36 (3), pp.on-line. ⟨10.1007/s11032-016-0453-3⟩
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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.
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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 and Biomolecular Chemistry, Royal Society of Chemistry, 2016, 14 (8), pp.2487-2497. ⟨10.1039/c5ob02483h⟩
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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.
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Dossier Melon - Préserver le gène Vat
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Véronique Bargain, Alexandra Schoeny, Nathalie Boissot
article
Réussir Fruits et Légumes, 2016, 367, pp.64-66
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Dossier Melon - Préserver le gène Vat
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Verticillium chez l'aubergine à travers le projet Vasculeg. Bioagresseurs présents et caractérisation (1ère partie)
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François Villeneuve, François Latour, Théophile Théry, Christine Fournier, Patricia Erard, Veronique Edel-Hermann, Nadine Gautheron, Christian Steinberg, Marie-Christine Daunay
article
Infos CTIFL, 2016, pp.40-48
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Les maladies vasculaires des cultures légumières restent un problème important des producteurs d’aubergine en particulier. Après quelques années d’utilisation de résistance génétique à Verticillium, ils sont de nouveau confrontés aux mêmes problèmes. Le projet VASCUlég a permis d’avoir une idée précise de la situation chez les producteurs. Outre le champignon responsable de la maladie vasculaire, d’autres pathogènes sont présents formant un cortège de bioagresseurs et cela dans les différentes zones de production. La caractérisation des souches isolées est assez complexe du fait de la complexité de Verticillium : nouvelle classification des espèces de Verticillium, identification délicate des races et faible agressivité des souches. V. dahliae n’est qu’une des composantes du complexe parasitaire affectant les plantes greffées avec symptômes.
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Dissecting quantitative trait variation in the resequencing era: Complementarity of bi-parental, multi-parental and association panels
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Laura Pascual, Elise Albert, Christopher Sauvage, Janejira Duangjit, Jean-Paul Bouchet, Frederique Bitton, Nelly Desplat, Dominique Brunel, Marie-Christine Le Paslier, Nicolas Ranc, Laure Bruguier, Betty Chauchard, Philippe Verschave, Mathilde Causse
article
Plant Science, Elsevier, 2016, 242, pp.120-130. ⟨10.1016/j.plantsci.2015.06.017⟩
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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
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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)
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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, Springer Verlag, 2016, 12 (61), pp.1-21. ⟨10.1007/s11295-016-1080-1⟩
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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.
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Reduction of MDHAR activity in cherry tomato suppresses growth and yield and MDHAR activity is correlated with sugar levels under high light
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Vincent Truffault, Noé Gest, Cecile Garchery, Alexandra Florian, Alisdair R Fernie, Hélène Gautier, Rebecca Stevens
article
Plant, Cell and Environment, Wiley, 2016, 39 (6), pp.1279-1292. ⟨10.1111/pce.12663⟩
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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
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Human management of a wild plant modulates the evolutionary dynamics of a gene determining recessive resistance to virus infection.
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Nils Poulicard, Luis Fernández Pacios, Jean-Luc Gallois, Daniel Piñero, Fernando García-Arenal
article
PLoS Genetics, Public Library of Science, 2016, 12 (8), 31 p. ⟨10.1371/journal.pgen.1006214⟩
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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.
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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, BioMed Central, 2016, 16 (25), ⟨10.1186/s12870-016-0708-5⟩
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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.
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Alain Palloix died on 8 March 2016 IN MEMORIAM
auteur
Véronique Lefebvre
article
Fruits, EDP Sciences/CIRAD, 2016, 71 (3), pp.195. ⟨10.1051/fruits/2016009⟩
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Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits
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Elise Albert, Vincent Segura, Justine Gricourt, Julien Bonnefoi, Laurent Derivot, Mathilde Causse
article
Journal of Experimental Botany, Oxford University Press (OUP), 2016, 67 (22), pp.6413-6430. ⟨10.1093/jxb/erw411⟩
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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.
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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, Oxford University Press (OUP), 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.
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Fighting sharka in peach: current limitations and future perspectives
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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, Frontiers, 2016, 7, ⟨10.3389/fpls.2016.01290⟩
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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.
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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, INRA, 2016, pp.Art3-CT87
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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.
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Rationalization of genes for resistance to[i] Bremia lactucae[/i] in lettuce
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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.
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Nematode quantitative resistance conferred by the pepper genetic background presents additive effects and is stable against different isolates of [i]Meloidogyne incognita[/i]
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Fulgencio Sanchez-Solana, Caridad Ros, Carmen María Lacasa, Alain Palloix, Alfredo Lacasa
article
Plant Pathology, Wiley, 2016, 65 (4), pp.673-681. ⟨10.1111/ppa.12459⟩
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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.
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Les saveurs au potager
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Pierre Vaysse, Amélie Devillepoix, Mathilde Causse, Michel Pitrat
article
Jardins de France, 2016, pp.1-6
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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.
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Resistance to root-knot nematodes [i]Meloidogyne[/i] spp. in woody plants
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Simon Bernard Saucet, Cyril van Ghelder, Pierre Abad, Henri Duval, Daniel Esmenjaud
article
New Phytologist, Wiley, 2016, 211 (1), pp.41-56. ⟨10.1111/nph.13933⟩
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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.
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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, INRAE, 2016, 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
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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, Blackwell, 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.
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https://hal.inrae.fr/hal-02633315/file/Thomas_etal_2016_insight_durability_1.pdf 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, Frontiers, 2016, 7:1420, pp.1-18. ⟨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.
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https://hal.archives-ouvertes.fr/hal-01512038/file/Boissot%20Frontiers%20in%20Plant%20Science%202016%201-18_%7BC6845359-1AF1-437B-9291-46217B944035%7D.pdf 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, Springer Verlag/EDP Sciences/INRA, 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.
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https://hal.archives-ouvertes.fr/hal-01512079/file/Palloix_Sage-Palloix%20Agron.%20Sustain.%20Dev.%202016%20in%20press_%7BD3B12097-B202-4937-ACC0-B35CBF2DED74%7D.pdf BibTex
titre
Viruses carried to soil by irrigation can be aerosolized later during windy spells
auteur
Guillaume Girardin, Pierre Renault, Fabienne Bon, Line Capowiez, Joel Chadoeuf, Camille Krawczyk, Dominique Courault
article
Agronomy for Sustainable Development, Springer Verlag/EDP Sciences/INRA, 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.
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https://hal.inrae.fr/hal-02637699/file/Chadoeuf%20Agron.%20Sustain.%20Dev.%202016%201-10_1.pdf 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 , Elsevier, 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.
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Etude des déterminants génétiques et moléculaires de caractères influencés par le changement climatique chez l'abricotier et le cerisier
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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, INRAE, 2016, pp.51-58. ⟨10.15454/1.472108874009284E12⟩
resume
Dans le contexte de l’augmentation des températures liée au changement climatique, une étude sur l’adaptation du cerisier (Prunus avium) et de l’abricotier (Prunus armeniaca) à ces modifications a été conduite avec le concours du Ministère de l’agriculture. Une recherche de QTL a été menée sur des caractères en lien avec la phénologie de la floraison : la date de floraison a été décomposée en besoins en froid et besoins en chaud et la qualité de la floraison a été évaluée par la quantification des nécroses ou des anomalies florales. Pour la date de floraison et ses composantes, des QTL stables et importants ont été détectés sur les groupes de liaison (GL) 4, 1 et 6 chez les deux espèces, confirmant le fort niveau de synténie au sein des Prunus. Les QTL pour les caractères de qualité de floraison étaient moins significatifs et stables, néanmoins, des QTL prometteurs ont été mis en évidence sur les GL1 et 5, uniquement sur l’abricotier. Des gènes-candidats (GC) impliqués dans la phénologie de la floraison ont été identifiés chez le cerisier et seront bientôt validés dans les deux espèces. Les modèles phénologiques classiques, utilisés pour prédire les dates de floraison, ont été optimisés sur abricotier et des analyses similaires sont en cours chez le cerisier. Enfin, les données sur les QTL et les GC mises en évidence sont en cours d’incorporation dans les programmes de sélection assistée par marqueurs (SAM).
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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, Frontiers, 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.
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https://hal.inrae.fr/hal-02639203/file/barbary_2016_frontiersinplantscience_1.pdf 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, Frontiers, 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.
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https://hal.archives-ouvertes.fr/hal-01441597/file/Quilot%20Frontiers%20in%20plant%20sci.%202016%20in%20press_%7BEDF22F1D-E27F-4867-8A1C-A2196B0E625A%7D.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, Frontiers, 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.
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https://hal.archives-ouvertes.fr/hal-01475599/file/2016_Constantinescu_Frontiers%20in%20Plant%20Science_1.pdf BibTex
titre
Abeille domestique: un dépérissement aux multiples causes
auteur
Yves Le Conte, Michel Pitrat
article
Jardins de France, 2016, 643, pp.23-25
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Tomates sous serre et l'envol des bourdons
auteur
Rene Damidaux, Michel Pitrat, Bernard Vaissière
article
Jardins de France, 2016, 643, pp.6
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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-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, Oxford University Press (OUP), 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.
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2015

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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, BioMed Central, 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.
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https://hal.inria.fr/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 Ourry
article
Frontiers in Plant Science, Frontiers, 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.
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https://hal-normandie-univ.archives-ouvertes.fr/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, Paris : Institut national de la recherche agronomique Délégation permanente à l'environnement, 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.
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Cooperative insertion of CO2 in diamine-appended metal-organic frameworks
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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, Nature Publishing Group, 2015, 519 (7543), ⟨10.1038/nature14327⟩
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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
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Pollen tube cell walls of wild and domesticated tomatoes contain arabinosylated and fucosylated xyloglucan
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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, Oxford University Press (OUP), 2015, 115 (1), pp.55-66. ⟨10.1093/aob/mcu218⟩
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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.
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Building high-density peach linkage maps based on the ISPC 9K SNP chip for mapping mendelian traits and QTLS: benefits and drawbacks
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Jehan-Baptiste Mauroux, Bénédicte Quilot-Turion, Thierry Pascal, Patrick Lambert, Michela Troggio, Ignazio Verde, Diego Micheletti, Maria José Aranzana
article
Acta Horticulturae, International Society for Horticultural Science, 2015, 1084, pp.113-118. ⟨10.17660/ActaHortic.2015.1084.13⟩
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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.
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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, International Society for Horticultural Science, 2015, 1102, pp.99-108
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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
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Genomic variation in tomato, from wild ancestors to contemporary breeding accessions
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José Blanca, Javier Montero-Pau, Christopher Sauvage, Guillaume Bauchet, Eudald Illa, María José Díez, David Francis, Mathilde Causse, Esther van der Knaap, Joaquin Canizares
article
BMC Genomics, BioMed Central, 2015, 16, 19 p. ⟨10.1186/s12864-015-1444-1⟩
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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
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A multi-Ievel omic approach of tomato fruit quality
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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 Lepaslier, Mathilde Causse
article
Acta Horticulturae, International Society for Horticultural Science, 2015, 1099, pp.793-800. ⟨10.17660/ActaHortic.2015.1099.100⟩
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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.
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La parthénocarpie : des fruits sans graines
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Michel Pitrat
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Jardins de France, 2015, pp.1-2
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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).
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L’aubergine, de l’état sauvage ancestral à aujourd’hui
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Marie-Christine Daunay
article
Jardins de France, 2015, pp.39-41
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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
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The potential for crop to wild hybridization in eggplant (Solanum melongena; Solanaceae) in southern India
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Priya Davidar, Allison A. Snow, Muthu Rajkumar, Rémy Pasquet, Marie-Christine Daunay, Evans Mutegi
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American Journal of Botany, Botanical Society of America, 2015, 102 (1), pp.129-139. ⟨10.3732/ajb.1400404⟩
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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.
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Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum, Solanaceae) in southern India: implications for conservation
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Evans Mutegi, Allison A. Snow, Muthu Rajkumar, Rémy Pasquet, Hopeland Ponniah, Marie-Christine Daunay, Priya Davidar
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American Journal of Botany, Botanical Society of America, 2015, 102 (1), pp.140-148. ⟨10.3732/ajb.1400403⟩
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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.
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Le greffage des légumes : l’intérêt et la pratique
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Michel Javoy, Michel Pitrat, Jean-Daniel Arnaud
article
Jardins de France, 2015, pp.6-8
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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.
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Les plantes potagères dans les livres de Vilmorin-Andrieux et Cie
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Michel Pitrat
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Jardins de France, 2015, 637
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Efficiency of selection in early generations of potato families with a view toward heat tolerance
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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⟩
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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
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Des légumes qui grimpent
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Michel Pitrat
article
Jardins de France, 2015, pp.24-25
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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.
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Evolution of diversity of fruits and vegetables crops
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Michel Pitrat, Jean Marc Audergon
article
Acta Horticulturae, International Society for Horticultural Science, 2015, 1099, pp.567-576
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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.
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Use of [i]Prunus[/i] genetic diversity for peach rootstocks
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Henri Duval
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Acta Horticulturae, International Society for Horticultural Science, 2015, 1084, pp.277-282
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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.
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Nanoparticles functionalised with an anti-platelet human antibody for in vivo detection of atherosclerotic plaque by magnetic resonance imaging.
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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, Elsevier, 2015, 11 (4), pp.927-937. ⟨10.1016/j.nano.2014.12.006⟩
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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.
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Petites et grandes histoires de l’aubergine
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Marie-Christine Daunay, Harry S. Paris, Jules Janick
article
Jardins de France, 2015, pp.4-6
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Fusarium oxysporum f. sp. melonis chez le melon, enseignements issus du projet VASCUlég
auteur
François Villeneuve, François Latour, Théophile Théry, Veronique Edel-Hermann, Christian Steinberg, Michel Pitrat
article
Infos CTIFL, 2015, pp.45-47
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La fusariose du melon due à Fusarium oxysporum f. sp. melonis (F.o.melonis) reste un problème majeur pour les producteurs. Il a donc été décidé d’élaborer un programme de recherches comprenant 23 partenaires (VASCUlég). L’analyse de la situation révèle une adaptation des bioagresseurs, avec une nette prédominance de F.o.melonis race 1.2 que ce soit seul ou en association avec d’autres pathogènes. La caractérisation moléculaire des souches de F.o.melonis indique une forte diversité génétique. Cependant, de nouvelles sources de résistance à la race 1.2 de F.o.melonis ont été mises en évidence. Ce résultat devra être exploité en interaction avec un certain nombre de techniques complémentaires expérimenté dans le projet, comme le système de culture, la biofumigation, l’utilisation de plantes de service, d’agents de lutte biologique, de stimulateurs de défense des plantes.
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Integrative approach of tomato fruit texture using multiblock analysis
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Rémy Aurand, Mireille Faurobert, Mohamed Hanafi, Gerard Mazerolles, Raphael Tisiot, Laurent Rosso, Brigitte Navez, Nadia Bertin
article
Acta Horticulturae, International Society for Horticultural Science, 2015, 1099, pp.827-834. ⟨10.17660/ActaHortic.2015.1099.105⟩
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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.
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La protection intégrée : alternative efficace au « tout phytosanitaire »
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Maurice Jullian, Véronique Lefebvre
article
Cahier des Techniques de l'INRA, INRA, 2015, pp.1-14
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.
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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, American Phytopathological Society, 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.
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Towards the identification of Type III effectors associated to Ralstonia solanacearum virulence on tomato and eggplant
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Flora Pensec, Aurore Lebeau, Marie-Christine Daunay, Frédéric Chiroleu, Alice Guidot, Emmanuel Wicker
article
Phytopathology, American Phytopathological Society, 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
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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, Microbiology Society, 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
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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 Confolent, Pedro Martínez-Gómez, Henri Duval
article
Scientia Horticulturae, Elsevier, 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’
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A cucurbit androecy gene reveals how unisexual flowers develop and dioecy emerges
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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, American Association for the Advancement of 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
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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, Wiley, 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
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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, Elsevier, 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
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Whole-genome analysis of diversity and SNP-major gene association in peach germplasm
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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, Public Library of Science, 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
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The spatial distribution of [i]Mustelidae[/i] in France.
auteur
Clément Calenge, Joel Chadoeuf, Christophe Giraud, Sylvie Huet, Romain Julliard, Pascal Monestiez, Jérémy Piffady, David Pinaud, Sandrine Ruette
article
PLoS ONE, Public Library of Science, 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.
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https://hal.archives-ouvertes.fr/hal-01139313/file/journal.pone.0121689_%7B9E0313FC-B1B2-4270-AED0-C28F1708ECC1%7D.pdf BibTex

2014

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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, Jerome Balesdent
article
Isotopes in Environmental and Health Studies, Taylor & Francis, 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.
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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.
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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, American Society for Microbiology, 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.
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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, Nature Publishing Group, 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.
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High rates of gene flow by pollen and seed in oak populations across Europe
auteur
Sophie Gerber, Joel 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, Public Library of Science, 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.
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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-Vaslin, Magali Ermel, Philippe Duffe, Anne-Laure Besnard, Bruno Marquer, Isabelle Fudal-Grolier, Juliette Linglin, Joel Chadoeuf, Hortense Brun
article
Infection, Genetics and Evolution, Elsevier, 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
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La coolbox : un système de refroidissement des serres avec de l’eau recyclée
auteur
Patricia Le Crenn, Max Escoffier, Alain Goujon, Jean-Marc Bastien
article
Lettre aux Entreprises - INRA, 2014, N° 65, Juillet 2014
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320 m² de serres, sur les 4 700 m² du parc du domaine de Saint Maurice en Avignon (PACA), sont rafraichies par projection d’eau sur des matelas de copeaux au travers desquels l’air est aspiré. Ce système mis au point au niveau de l’unité GAFL, appelé coolbox, s’inscrit dans une démarche de recherche et d’action pour optimiser l’existant.
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Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era
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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, Wiley, 2014, 13 (4), pp.565-77. ⟨10.1111/pbi.12282⟩
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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
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The relationship between metaheuristics stopping criteria and performances: Cases of NSGA-II and MOPSO-CD for sustainable peach fruit design
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Mohamed Ould Sidi, Bénédicte Quilot-Turion, Abdeslam Kadrani, Michel Génard
article
International Journal of Applied Metaheuristic Computing, IGI Global Publisher, 2014, 5 (3), pp.47-74. ⟨10.4018/ijamc.2014070104⟩
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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
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Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection
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Guillaume Bauchet, Stephane Munos, Christopher Sauvage, Julien Bonnet, Laurent Grivet, Mathilde Causse
article
BMC Plant Biology, BioMed Central, 2014, 14, n.p. ⟨10.1186/s12870-014-0279-2⟩
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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.
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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⟩
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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.
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Lettuce cropping with less pesticides. A review
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Virginie Barrière, François Lecompte, Philippe C. Nicot, Brigitte Maisonneuve, Marc Tchamitchian, Françoise Lescourret
article
Agronomy for Sustainable Development, Springer Verlag/EDP Sciences/INRA, 2014, 34 (1), pp.175-198. ⟨10.1007/s13593-013-0158-5⟩
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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.
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Cloning of the Arabidopsis rwm1 gene for resistance to Watermelon mosaic virus points to a new function for natural virus resistance genes
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Laurence Ouibrahim, Marianne Mazier, Joan Estevan, Gaelle Pagny, Véronique Decroocq, Cecile Desbiez, André Moretti, Jean-Luc Gallois, Carole Caranta
article
Plant Journal, Wiley, 2014, 79 (5), pp.705-716. ⟨10.1111/tpj.12586⟩
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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.
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How to estimate variability in affinity relationships in partially observed groups of domestic herbivores?
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Lia Della-Rossa, Bertrand Dumont, Joel Chadoeuf
article
animal, Published by Elsevier (since 2021) / Cambridge University Press (until 2020), 2014, 8 (5), pp.817-826. ⟨10.1017/S175173111400024X⟩
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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.
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Disease and frost damage of woody plants caused by Pseudomonas syringae: Seeing the forest for the trees
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Jay Ram Lamichhane, Leonardo Varvaro, Luciana Parisi, Jean Marc Audergon, Cindy E. Morris
article
Advances in Agronomy, Elsevier, 2014, 126, pp.235-295. ⟨10.1016/B978-0-12-800132-5.00004-3⟩
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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
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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
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Alexandra Schoeny, Nathalie Boissot, Jérôme Lambion, Catherine Wipf-Scheibel, Pascale Mistral, Patrick Gognalons, Karine Nozeran, Hervé Lecoq
article
Innovations Agronomiques, INRAE, 2014, 40, pp.113-124
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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.
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Gérer les épidémies virales en combinant résistances aux virus et résistances aux pucerons : quel intérêt ?
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Nathalie Boissot, Alexandra Schoeny, Pauline Millot, Catherine Wipf-Scheibel, Karine Nozeran, Hervé Lecoq, Frédéric Fabre
article
Innovations Agronomiques, INRAE, 2014, 46, pp.127-136
resume
Les résistances génétiques ont permis de réduire fortement l’impact des maladies virales chez de nombreuses plantes cultivées. Les résistances peuvent être dirigées directement contre les virus, mais aussi contre leurs pucerons vecteurs. Dans ce travail, nous montrons que la résistance au puceron Aphis gossypii chez le melon permet de réduire significativement les épidémies aussi bien d’un virus transmis selon le mode non persistant, le CMV, que celles d’un virus transmis selon le mode persistant, le CABYV. Par ailleurs, l’utilisation d’un modèle mathématique nous a permis d’explorer l’intérêt d’utiliser conjointement des résistances aux pucerons et au virus pour renforcer le contrôle des épidémies virales dans différents contextes agro-écologiques représentatifs de la culture du melon dans le Sud-Est de la France. Si les effets bénéfiques d’une telle association sont fortement probables dans le cas du CABYV, ils demeurent largement incertains (mais en aucun cas néfastes) pour le contrôle du CMV
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Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization
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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 , National Academy of Sciences, 2014, 111 (14), pp.5135-5140. ⟨10.1073/pnas.1400975111⟩
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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.
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Variability of morphological charters among Tunisian apricot germplasm
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Lamia Krichen, Jean Marc Audergon, Neïla Trifi-Farah
article
Scientia Horticulturae, Elsevier, 2014, 179, pp.328-339. ⟨10.1016/j.scienta.2014.09.054⟩
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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.
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Genomic analyses provide insights into the history of tomato breeding
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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 Causse, Zhangjun Fei, James J. Giovannoni, Roger T. Chetelat, Dani Zamir, Thomas Staedler, Jingfu Li, Zhibiao Ye, Yongchen Du, Sanwen Huang
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Nature Genetics, Nature Publishing Group, 2014, 46 (11), pp.1220 - 1226. ⟨10.1038/ng.3117⟩
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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.
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High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae
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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⟩
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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.
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High-resolution mapping of the RMia gene for resistance to root-knot nematodes in peach
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Henri Duval, Mathilde Hoerter, Joel Polidori, Carole Confolent, Martin Masse, André Moretti, Cyril van Ghelder, Daniel Esmenjaud
article
Tree Genetics and Genomes, Springer Verlag, 2014, on-line, 10 p. ⟨10.1007/s11295-013-0683-z⟩
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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
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QTL hotspots in eggplant (Solanum melongena) detected with a high resolution map and CIM analysis
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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⟩
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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
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Assessing the genetic diversity and population structure of Tunisian apricot germplasm
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L. Krichen, Jean Marc Audergon, N. Trifi-Farah
article
Scientia Horticulturae, Elsevier, 2014, 172, pp.86-100. ⟨10.1016/j.scienta.2014.03.038⟩
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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
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Inter individual variations of the fish skin microbiota: Host genetics basis of mutualism?
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Sébastien Boutin, Christopher Sauvage, Louis Bernatchez, Céline Audet, Nicolas Derôme
article
PLoS ONE, Public Library of Science, 2014, 9 (7), 17 p. ⟨10.1371/journal.pone.0102649⟩
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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
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Comparison of evolutionary and swarm intelligence-based approaches in the improvement of peach fruit quality
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A. Kadrani, Bénédicte Quilot-Turion, Michel Génard, Francoise Lescourret, Mohamed Ould Sidi
article
Annals of Management Science, 2014, 3 (1), pp.129-142
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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.
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Variation in Tomato Fruit Ascorbate Levels and Consequences of Manipulation of Ascorbate Metabolism on Drought Stress Tolerance
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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⟩
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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.
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Profiling sugar metabolism during fruit development in a peach progeny with different fructose-to-glucose ratios.
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Elsa Desnoues, Yves Gibon, Valentina Baldazzi, Veronique Signoret, Michel Génard, Bénédicte Quilot-Turion
article
BMC Plant Biology, BioMed Central, 2014, 14 (1), pp.336 : 1-12. ⟨10.1186/s12870-014-0336-x⟩
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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.
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Comment rationaliser le stockage d’échantillons dans les congélateurs - 80°C ?
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Veronique Signoret, Esther Pelpoir, Elsa Desnoues
article
Cahier des Techniques de l'INRA, INRA, 2014, 82 (2), pp.1-5
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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
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Pyramiding resistances based on translation initiation factors in Arabidopsis is impaired by male gametophyte lethality
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Caroline Callot, Jean-Luc Gallois
article
Plant Signaling and Behavior, Taylor & Francis, 2014, 9, pp.e27940;
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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
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Specific requirement for translation initiation factor 4E or its isoform drives plant host susceptibility to tobacco etch virus.
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Joan Estevan, Aramata Marena, Caroline Callot, Séverine Lacombe, André Moretti, Carole Caranta, Jean-Luc Gallois
article
BMC Plant Biology, BioMed Central, 2014, 14 (67), 10 p. ⟨10.1186/1471-2229-14-67⟩
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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
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Genome-wide association in tomato Reveals 44 candidate loci for fruit metabolic traits
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Christopher Sauvage, Vincent Segura, Guillaume Bauchet, Rebecca Stevens, Phuc Thi Do, Zoran Nikoloski, Alisdair R Fernie, Mathilde Causse
article
Plant Physiology, American Society of Plant Biologists, 2014, 165 (3), pp.1120-1132. ⟨10.1104/pp.114.241521⟩
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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
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Resource competition modulates the seed number-fruit size relationship in a genotype-dependent manner: a modeling approach in grape and tomato
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Marion Prudent, Zhanwu Dai, Michel Génard, Nadia Bertin, Mathilde Causse, Philippe Vivin
article
Ecological Modelling, Elsevier, 2014, 290, pp.54-64. ⟨10.1016/j.ecolmodel.2013.10.023⟩
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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
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Pyramiding, alternating or mixing: comparative performances of deployment strategies of nematode resistance genes to promote plant resistance efficiency and durability
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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
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BMC Plant Biology, BioMed Central, 2014, 14, ⟨10.1186/1471-2229-14-53⟩
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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.
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Varietal and technical innovations for the sustainable and integrated management of root-knot nematodes
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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, Society of Nematologists, 2014, 46 (2), pp.154
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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.
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Special Issue for the Plant Resistance Sustainability International Conference, La Colle sur Loup, France, 16-19 October 2012
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Carole Caranta, Francois-Christophe Coleno, Charles-Eric Durel, Marie-Helene Jeuffroy, Christian Lannou, Benoît Moury, Alain Palloix
article
Infection, Genetics and Evolution, Elsevier, 2014, 27, pp.445. ⟨10.1016/j.meegid.2014.09.011⟩
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absent
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The Vat locus encodes for a CC-NBS-LRR protein that confers resistance to Aphis gossypii infestation and A. gossypii-mediated virus resistance
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Catherine Dogimont, Veronique Chovelon, Jérôme Pauquet, Adnane Boualem, Abdelhafid Bendahmane
article
Plant Journal, Wiley, 2014, 80 (6), pp.993-1004. ⟨10.1111/tpj.12690⟩
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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.
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Bottleneck and gene flow effects impact the genetic structure of seed-propagated apricot populations in Moroccan oasis agroecosystems
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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, Cambridge University Press (CUP), 2014, pp.1-11. ⟨10.1017/S1479262113000543⟩
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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
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Nouvelles sources de résistance au puceron Aphis gossypii chez le melon
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Nathalie Boissot, Sophie Thomas, Pascale Mistral, Virginie Chareyron
article
Innovations Agronomiques, INRAE, 2014, 35, pp.89-95
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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
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Variétés et systèmes de culture de tomate : les apports conjoints de la génétique et de l'agronomie
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François Lecompte, Mathilde Causse
article
Agronomie, Environnement & Sociétés, Association Française d'Agronomie (Afa), 2014, 4 (2), pp.23-34
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La tomate est produite dans des conditions variées, du champ aux cultures hors-sol sous serre. Cette diversification a suivi l'évolution variétale et les innovations techniques des dernières décennies. Les variétés ont été acclimatées pour la culture sous abri tout au long de l'année. Des résistances variétales aux bioagresseurs ont été introgressées à partir des espèces sauvages. L'offre variétale a été perfectionnée pour aboutir aujourd'hui à une gamme permettant l’adaptation fine, sous serre, des conduites climatiques. La diversification variétale pour différents segments de marché est un objectif majeur des sélectionneurs. Les ruptures dans les systèmes de culture ont aussi été nombreuses, notamment la généralisation de la culture hors sol, le développement des outils de pilotage et la lutte biologique. Les évolutions rapides des méthodes d’amélioration des plantes, couplées au décryptage du génome de la tomate et à la modélisation, préfigurent des évolutions majeures des variétés et des systèmes de culture
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Understanding dormancy release in apricot flower buds ([i]Prunus armeniaca[/i] L.) using several process-based phenological models
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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
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Agricultural and Forest Meteorology, Elsevier Masson, 2014, 184, pp.210- 219. ⟨10.1016/j.agrformet.2013.10.005⟩
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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.
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Evolution of plant eukaryotic initiation factor 4E (eIF4E) and potyvirus genome-linked protein (VPg): A game of mirrors impacting resistance spectrum and durability
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Benoît Moury, Carine Charron, Bérenger Janzac, Vincent Simon, Jean-Luc Gallois, Alain Palloix, Carole Caranta
article
Infection, Genetics and Evolution, Elsevier, 2014, 27, pp.472-480. ⟨10.1016/j.meegid.2013.11.024⟩
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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
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Le génome de la tomate séquencé, une manne pour les sélectionneurs
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Mondher Bouzayen, Mathilde Causse
article
Jardins de France, 2014, pp.71
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Histological and cell wall polysaccharide chemical variability among apricot varieties
auteur
Marc Lahaye, Xavier Falourd, Bernard Quemener, Marie Francoise Devaux, Jean Marc Audergon
article
LWT - Food Science and Technology, Elsevier, 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
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Selecting with markers linked to the PPVres major QTL is not sufficient to predict resistance to Plum Pox Virus (PPV) in apricot
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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, Springer Verlag, 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.
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The plant genetic background affects the efficiency of the pepper major nematode resistance genes Me1 and Me3
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Arnaud Barbary, Alain Palloix, Ariane Fazari, Nathalie Marteu, Philippe Castagnone-Sereno, Caroline Djian-Caporalino
article
TAG Theoretical and Applied Genetics, Springer Verlag, 2014, 127 (2), pp.499-507. ⟨10.1007/s00122-013-2235-1⟩
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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.
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2013

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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⟩
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This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are
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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, Springer Verlag, 2013
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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, Wiley, 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.
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Potato virus Y: a major crop pathogen that has provided major insights into the evolution of viral pathogenicity
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Julie Quenouille, Nikon Vassilakos, Benoît Moury
article
Molecular Plant Pathology, Wiley, 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.
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Quelques exemples d’intérêts et de limites de la sélection assistée par marqueurs chez la pomme de terre
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Marie-Claire Kerlan, Sylvie Marhadour, Bernard Caromel, E. Bonnel, Sarah Danan, Véronique Lefebvre, Jean-Eric Chauvin
article
Innovations Agronomiques, INRAE, 2013, 27, pp.111-122
resume
La sélection assistée par marqueurs (SAM) n’est possible que si les marqueurs moléculaires sont facilement utilisables et informatifs. Chez la pomme de terre, espèce tétraploïde et hétérozygote, la SAM est encore assez peu développée pour le moment. Notre démarche a été, d’une part, de rechercher des marqueurs moléculaires liés à des caractères d’intérêt à partir de populations diploïdes en ségrégation et de tester leur transférabilité au niveau tétraploïde et, d’autre part, de tester des marqueurs moléculaires déjà publiés dans des fonds génétiques tétraploïdes différents. Les modèles retenus étaient la résistance aux bioagresseurs (le mildiou du feuillage causé par Phytophthora infestans, la résistance aux nématodes à kyste Globodera rostochiensis et G. pallida, la résistance au virus Y) et la teneur en glycoalcaloïdes des tubercules. Dans le cas d’un déterminisme génétique simple (cas du gène Ry conférant la résistance au virus Y issu de Solanum stoloniferum ou du gène R1 de résistance au mildiou issu de S. demissum), les marqueurs publiés ont pu être validés dans différents fonds génétiques. Pour le gène H1 conférant la résistance à G. rostochiensis, le marqueur disponible au moment du projet s’est avéré ne pas être lié à la résistance dans notre matériel mais d’autres marqueurs ont été validés depuis. Dans le cas d’une résistance oligogénique, illustrée par la résistance à G. pallida dont le déterminisme génétique est sous le contrôle de 2 QTL, la portabilité de 4 marqueurs permettant de suivre le QTL à effet fort GpaVspl dans différents fonds génétiques tétraploïdes a été testée. Deux marqueurs permettant de suivre le QTL à effet faible GpaXIspl ont également été validés. L’ensemble des marqueurs a été transféré aux partenaires professionnels qui les utilisent désormais à des échelles différentes dans leurs schémas de sélection. Pour les caractères à déterminisme polygénique (résistance au mildiou du feuillage et teneur en glycoalcaloïdes), il semble actuellement prématuré d’envisager la SAM.
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Whole genome resequencing in tomato reveals variation associated with introgression and breeding events
auteur
Mathilde Causse, Nelly Desplat, Laura Pascual-Banuls, Marie-Christine Le Paslier, Christopher Sauvage, Guillaume Bauchet, Aurélie Berard, Rémi Bounon, Maria Tchoumakov, Dominique Brunel, Jean-Paul Bouchet
article
BMC Genomics, BioMed Central, 2013, 14 (791), 14 p. ⟨10.1186/1471-2164-14-791⟩
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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
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Medieval iconography of watermelons in Mediterranean Europe
auteur
Harry S. Paris, M-Christin Daunay, Jules Janick
article
Annals of Botany, Oxford University Press (OUP), 2013, 112 (5), pp.867-879. ⟨10.1093/aob/mct151⟩
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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.
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Des plantes alimentaires aquatiques
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Michel Pitrat
article
Jardins de France, 2013
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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.
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Effect of plant genotype on the efficacy of stimulators of plant defences in two horticultural pathosystems
auteur
Brigitte Maisonneuve, Caroline Allen-Aubouard, Michel Pitrat
article
IOBC WPRS Bulletin, 2013, 89, pp.327-331
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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
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Role of vernalization and of duplicated FLOWERING LOCUS C in the perennial Arabidopsis lyrata
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Ulla Kemi, Anne Niittyvuopio, Tuomas Toivainen, Anu Pasanen, Bénédicte Quilot-Turion, Karl Holm, Ulf Lagercrantz, Outi Savolainen, Helmi Kuittinen
article
New Phytologist, Wiley, 2013, 197 (1), pp.323-335. ⟨10.1111/j.1469-8137.2012.04378.x⟩
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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.
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Exploitation of natural genetic diversity to study plant-virus interactions: what can we learn from Arabidopsis thaliana?
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Laurence Ouibrahim, Carole Caranta
article
Molecular Plant Pathology, Wiley, 2013, 14 (8), pp.844-854. ⟨10.1111/mpp.12052⟩
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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.
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Proteomic analysis of tomato (Solanum lycopersicum) secretome
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Emadeldin Konozy, Helene Rogniaux, Mathilde Causse, Mireille Faurobert
article
Journal of Plant Research, Springer Verlag, 2013, 126, pp.251-266. ⟨10.1007/s10265-012-0516-4⟩
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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.
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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
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Yariv Brotman, Michael Normantovich, Zachi Goldenberg, Zvi Zvirin, Irina Kovalski, Nastacia Stovbun, Tirza Doniger, Anthony M. Bolger, Christelle Troadec, Abdelhafid Bendahmane, Roni Cohen, Nurit Katzir, Michel Pitrat, Catherine Dogimont, Rafael Perl-Treves
article
Molecular Plant, Cell Press/Oxford UP, 2013, 6 (1), pp.235-238. ⟨10.1093/mp/sss121⟩
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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.
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Multi-trait and multi-environment QTL analyses of yield and a set of physiological traits in pepper
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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, Springer Verlag, 2013, 126 (10), pp.2597-2625. ⟨10.1007/s00122-013-2160-3⟩
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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.
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Susceptibility of Prunus rootstocks against Marcus and Dideron isolates of Plum pox virus by graft-inoculation
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M. Rubio, F. Dicenta, Martin Masse, Henri Duval
article
Annals of Applied Biology, Wiley, 2013, 162 (2), pp.214 - 220. ⟨10.1111/aab.12015⟩
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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.
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Phenotypic diversity in wild and cultivated melons (Cucumis melo)
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Michel Pitrat
article
Plant Biotechnology, Japanese Society for Plant Cell and Molecular Biology, 2013, 30 (3), pp.273 - 278. ⟨10.5511/plantbiotechnology.13.0813a⟩
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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.
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Genetic changes in flowering and morphology in response to adaptation to a high-latitude environment in Arabidopsis lyrata
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Bénédicte Quilot-Turion, Johanna Leppälä, Paivi H. Leinonen, Patrik Waldmann, Outi Savolainen, Helmi Kuittinen
article
Annals of Botany, Oxford University Press (OUP), 2013, 111 (5), pp.957-968. ⟨10.1093/aob/mct055⟩
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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.
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Protein and mineral nutrient contents in kernels from 72 sweet almond cultivars and accessions grown in France, Greece and Italy
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Pavlina D. Drogoudi, Georgios Pantelidis, Loretta Bacchetta, Donato de Giorgio, Henri Duval, Ioannis Metzidakis, Daniella Spera
article
International Journal of Food Sciences and Nutrition, Taylor & Francis, 2013, 64 (2), pp.202-209. ⟨10.3109/09637486.2012.728202⟩
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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.
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An extensive proteome map of tomato (Solanum lycopersicum) fruit pericarp
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Jiaxin Xu, Laura Pascual-Banuls, Rémy Aurand, Jean-Paul Bouchet, Benoit Valot, Michel Zivy, Mathilde Causse, Mireille Faurobert
article
Proteomics, Wiley-VCH Verlag, 2013, 13 (20), pp.3059 - 3063. ⟨10.1002/pmic.201200438⟩
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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.
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Effect of salinity and calcium on tomato fruit proteome
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Arafet Manaa, Mireille Faurobert, Benoit Valot, Jean-Paul Bouchet, Dominique Grasselly, Mathilde Causse, Hela Ben Ahmed
article
OMICS, Mary Ann Liebert, 2013, 17 (6), 15 p. ⟨10.1089/omi.2012.0108⟩
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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.
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https://hal.inrae.fr/hal-02648418/file/Effect%20of%20Salinity%20and%20Calcium%20on%20Tomato%20Fruit%20Proteome%20%281%29_1.pdf BibTex
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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.
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Sylvie Bureau, Bénédicte Quilot-Turion, Véonique Signoret, Christel Renaud, Mickael Maucourt, Doriane Bancel, Catherine Renard
article
Analytical Chemistry, American Chemical Society, 2013, 85 (23), pp.11312-11318. ⟨10.1021/ac402428s⟩
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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.
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High temperature inhibits ascorbate recycling and light stimulation of the ascorbate pool in tomato despite increased expression of biosynthesis genes
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Capucine Massot, Doriane Bancel, Félicie Lopez Lauri, Vincent Truffault, Pierre Baldet, Rebecca Stevens, Hélène Gautier
article
PLoS ONE, Public Library of Science, 2013, 8 (12), 13 p. ⟨10.1371/journal.pone.0084474⟩
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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.
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Identification of reference genes for normalizing RNA expression in potato roots infected with cyst nematodes
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Patricio Castro Quezada, Jawad Aarrouf, Michel Claverie, Bruno Favery, Didier Mugniery, Véronique Lefebvre, Bernard Caromel
article
Plant Molecular Biology Reporter, Springer Verlag, 2013, 31 (4), pp.936-945. ⟨10.1007/s11105-013-0566-3⟩
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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. .
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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, Springer Verlag, 2013, 32 (2), pp.349-364. ⟨10.1007/s11032-013-9875-3⟩
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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.
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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
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Maryse Nicolaï, Melissa Cantet, Véronique Lefebvre, Anne-Marie Sage-Palloix, Alain Palloix
article
Genetic Resources and Crop Evolution, Springer Verlag, 2013, 60 (8), pp.2375-2390. ⟨10.1007/s10722-013-0006-0⟩
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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.
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Genetic and QTL analyses of yield and a set of physiological traits in pepper
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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⟩
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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.
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A cytochrome P450 regulates a domestication trait in cultivated tomato
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Manohar Chakrabarti, Na Zhang, Christopher Sauvage, Stephane Munos, José Blanca, Joaquin Canizares, María José Díez, Rhiannon Schneider, Michael Mazourek, Jammi Mcclead, Mathilde Causse, Esther van der Knaap
article
Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2013, 110 (42), pp.17125-17130. ⟨10.1073/pnas.1307313110⟩
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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.
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Ascorbate as seen through plant evolution: the rise of a successful molecule?
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Noé Gest, Hélène Gautier, Rebecca Stevens
article
Journal of Experimental Botany, Oxford University Press (OUP), 2013, 64 (1), pp.33 - 53. ⟨10.1093/jxb/ers297⟩
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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.
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Deciphering genetic diversity and inheritance of tomato fruit weight and composition through a systems biology approach
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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, Oxford University Press (OUP), 2013, 64 (18), pp.1-16. ⟨10.1093/jxb/ert349⟩
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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.
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https://hal.archives-ouvertes.fr/hal-01208665/file/Pascual_Xu_Integration%20MS_modif%20R2-2_1.pdf https://hal.archives-ouvertes.fr/hal-01208665/file/2013_Pascual_Journal%20of%20Experimental%20Botany_2.pdf BibTex
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Closely related poleroviruses depend on distinct translation Initiation factors to infect Arabidopsis thaliana
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Catherine Reinbold, Séverine Lacombe, Véronique Ziegler-Graff, D Scheidecker, Louis Wiss, Monique Beuve, Carole Caranta, Veronique Brault
article
Molecular Plant-Microbe Interactions, American Phytopathological Society, 2013, 26 (2), pp.257-265. ⟨10.1094/MPMI-07-12-0174-R.⟩
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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.
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Closely related poleroviruses depend on distinct translation initiation factors to infect Arabidopsis thaliana
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Catherine Reinbold, Séverine Lacombe, Véronique Ziegler-Graff, Danièle Scheidecker, Louis Wiss, Monique Beuve, Carole Caranta, Veronique Brault
article
Molecular Plant-Microbe Interactions, American Phytopathological Society, 2013, 26 (2), pp.257-265. ⟨10.1094/MPMI-07-12-0174-R⟩
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In addition to being essential for translation of eukaryotic mRNA, translation initiation factors are also key components of plant–virus interactions. In order to address the involvement of these factors in the infectious cycle of poleroviruses (aphid-transmitted, phloem-limited viruses), the accumulation of three poleroviruses was followed in Arabidopsis thaliana mutant lines impaired in the synthesis of translation initiation factors in the eIF4E and eIF4G families. We found that efficient accumulation of Turnip yellows virus (TuYV) in A. thaliana relies on the presence of eIF (iso)4G1, whereas Beet mild yellowing virus (BMYV) and Beet western yellows virus-USA (BWYV-USA) rely, instead, on eIF4E1. A role for these factors in the infectious processes of TuYV and BMYV was confirmed by direct interaction in yeast between these specific factors and the 5′ viral genome-linked protein of the related virus. Although the underlying molecular mechanism is still unknown, this study reveals a totally unforeseen situation in which closely related viruses belonging to the same genus use different translation initiation factors for efficient infection of A. thaliana.
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Genetic mapping of a major dominant gene for resistance to ralstonia solanacearum in eggplant
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Aurore Lebeau, Matthieu Gouy, Marie-Christine Daunay, Emmanuel Wicker, Frédéric Chiroleu, Philippe Prior, Anne Frary, Jacques Dintinger
article
TAG Theoretical and Applied Genetics, Springer Verlag, 2013, 126 (1), pp.143 - 158. ⟨10.1007/s00122-012-1969-5⟩
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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.
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A diminution in ascorbate oxidase activity affects carbon allocation and improves yield in tomato under water deficit
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Cécile Garchery, Noé Gest, Phuc Thi Do, Moftah Alhagdow, Pierre Baldet, Guillaume Menard, Christophe Rothan, Capucine Massot, Hélène Gautier, Jawad Aarrouf, Alisdair R. Fernie, Rebecca Stevens
article
Plant, Cell and Environment, Wiley, 2013, 36 (1), pp.159-175. ⟨10.1111/j.1365-3040.2012.02564.x⟩
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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.
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Functional characterization of the plant ubiquitin regulatory X (UBX) domain-containing protein AtPUX7 in Arabidopsis thaliana
auteur
Jean-Luc Gallois, Jan Drouaud, Alain Lecureuil, Anouchka Debast Guyon, Sandrine Bonhomme, Philippe Guerche
article
Gene, Elsevier, 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.
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Characterization and genetic mapping of a new blood-flesh trait controlled by the single dominant locus DBF in peach
auteur
Zhijun Shen, Carole Confolent, Patrick Lambert, Jean-Luc Poessel, Bénédicte Quilot-Turion, Mingliang Yu, Ruijan Ma, Thierry Pascal
article
Tree Genetics and Genomes, Springer Verlag, 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.
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Méthodes de lutte contre les Phytophthora en cultures maraîchères : quel apport des core-collections microbiennes dans un processus de sélection ?
auteur
Marie-Line Kuhn, Anne Massire, Melissa Cantet, Rene Damidaux, Elvina Gibowski, Youna Ruellan, Véronique Lefebvre, Franck Panabières
article
Innovations Agronomiques, INRAE, 2013, 27, pp.47-58
resume
Parmi les Solanacées maraîchères, le piment et la tomate sont confrontés aux attaques de nombreux agents pathogènes, dont Phytophthora capsici et Phytophthora infestans. Des gènes majeurs de résistance ont été identifiés chez la tomate vis-à-vis de P. infestans, et sont fréquemment contournés par des populations virulentes. La résistance du piment à l’égard de P. capsici est conférée par des locus à effet quantitatif (QTL). Pour exploiter efficacement ces résistances quantitatives en sélection variétale, il est nécessaire d’évaluer leur spectre d’action pour prédire leur durabilité. Cette démarche nécessite une bonne connaissance de la diversité des populations pathogènes et de leurs capacités évolutives. La constitution de core-collections représentatives de la diversité intraspécifique de Phytophthora pourrait constituer un outil particulièrement utile pour évaluer a priori la durabilité des résistances variétales. Les résultats des recherches menées à l’INRA révèlent les limites de cette stratégie : elle est utilisable dans un contexte local, exige une bonne connaissance des populations d’agents pathogènes, dépend largement des propriétés épidémiologiques des espèces étudiées, et repose sur la mise en place de protocoles éprouvés de conservation des souches.
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https://hal.inrae.fr/hal-02642876/file/Vol27-6-Panabieres_1.pdf BibTex
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Home conservation strategies for tomato (Solanum lycopersicum): Storage temperature vs. duration – Is there a compromise for better aroma preservation?
auteur
Christian Ginies, Barbara Gouble, Sylvie Bureau, Mathilde Causse, Catherine Renard
article
Food Chemistry, Elsevier, 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.
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https://hal.archives-ouvertes.fr/hal-01328646/file/2013%20-%20Renard-Ginies-Gouble-Bureau_1.pdf BibTex
titre
Home conservation strategies for tomato (Solanum lycopersicum): Storage temperature vs. duration – Is there a compromise for better aroma preservation?
auteur
Christian Ginies, Barbara Gouble, Sylvie Bureau, Mathilde Causse, Catherine Renard
article
Food Chemistry, Elsevier, 2013, ⟨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.
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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, Elsevier, 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.
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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, Elsevier, 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.
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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 Berthomé, Claire Lurin
article
RNA Biology, Taylor & Francis, 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.
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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, Wiley, 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.
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Pericarp tissue microstructure and cell wall polysaccharide chemistry are differently affected in lines of tomato with contrasted firmness
auteur
Marc Lahaye, Marie Francoise Devaux, Mervin Poole, Graham B. Seymour, Mathilde Causse
article
Postharvest Biology and Technology, Elsevier, 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.
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Identification et marquage des facteurs génétiques de résistance à la Sharka chez l’abricotier et le Prunus davidiana
auteur
David Tricon, Patrick Lambert, Jean Marc Audergon, Thierry Pascal, Guillaume Roch, Véronique Decroocq
article
Innovations Agronomiques, INRAE, 2013, 27, pp.31-35
resume
La sharka, maladie provoquée par le Plum Pox Virus (PPV), affecte gravement les arbres fruitiers à noyaux du genre Prunus. Le PPV est largement répandu en Europe de l’Est et dans les régions méditerranéennes. Il affecte, entre autre, fortement la qualité des fruits, les rendant impropres à la commercialisation. A ce jour, aucun cultivar de pêchers n’est résistant et la majorité des variétés cultivées d'abricotiers sont également sensibles. Cependant, des sources de résistance ont été identifiées chez Prunus davidiana, espèce apparentée au pêcher et chez quelques cultivars d’abricotiers. L’étude de la ségrégation de ce caractère dans des populations F1 et F2 a permis d’identifier plusieurs QTL chez chacune de ces espèces et de développer des marqueurs moléculaires utilisables en Sélection Assistée par Marqueurs. De plus, nous avons pu vérifier la robustesse de ces QTL dans différents fonds génétiques et la stabilité de la résistance selon l’inoculum et le type d’inoculations utilisés.
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Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species
auteur
Jiaxin Xu, Nicolas Ranc, Stephane Munos, Sophie Rolland, Jean-Paul Bouchet, Nelly Desplat, Marie-Christine Le Paslier, Yan Liang, Dominique Brunel, Mathilde Causse
article
TAG Theoretical and Applied Genetics, Springer Verlag, 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.
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2012

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titre
A diminution in ascorbate oxidase activity affects carbon allocation and improves yield in tomato under water deficit
auteur
Cécile Garchery, Noé Gest, Phuc Do, Moftah Alhagdow, Pierre Baldet, Guillaume Menard, Christophe Rothan, Capucine Massot, Hélène Gautier, Jawad Aarrouf, Alisdair Fernie, Rebecca Stevens
article
Plant, Cell and Environment, 2012, 36 (1), pp.159 - 175. ⟨10.1111/j.1365-3040.2012.02564.x⟩
resume
The regulation of carbon allocation between photosynthetic 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 stomatal 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. Ascorbate oxidase may therefore be a target for strategies aimed at improving water productivity in crop species.
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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 Derome, Céline Audet, Louis Bernatchez
article
G3, Genetics Society of America, 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.
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https://hal.archives-ouvertes.fr/hal-02107010/file/49868_20120323015132794_1.pdf BibTex
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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, Springer Verlag, 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
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https://hal.archives-ouvertes.fr/hal-01332298/file/2012_Aarrouf_Plant%20Cell%20Reports%20%28Postprint%29_2 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, Mary Ann Liebert, 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.
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https://hal.inrae.fr/hal-02649667/file/Faurobert%202012%20OMICS%20343-356_1.pdf 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, Nature Publishing Group, 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.
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Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis)
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Christopher Sauvage, Marie Vagner, Nicolas Derôme, Céline Audet, Louis Bernatchez
article
G3, Genetics Society of America, 2012, 2 (6), pp.707 - 720. ⟨10.1534/g3.112.001990⟩
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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,
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Association between Aphis gossypii genotype and phenotype on melon accessions
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Sophie Thomas, Catherine Dogimont, Nathalie Boissot
article
Arthropod-Plant Interactions, Springer Verlag, 2012, 6 (1), pp.93-101. ⟨10.1007/s11829-011-9155-2⟩
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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
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Occidental diffusion of cucumber (Cucumis sativus) 500-1300 CE: two routes to Europe
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Harry S. Paris, M-Christin Daunay, Jules Janick
article
Annals of Botany, Oxford University Press (OUP), 2012, 109 (1), pp.117-126. ⟨10.1093/aob/mcr281⟩
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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.
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SPICY: towards automated phenotyping of large pepper plants in the greenhouse
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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, CSIRO Publishing, 2012, 39 (10-11), pp.870 - 877. ⟨10.1071/FP12019⟩
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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.
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Variabilité génétique de réactivité aux stimulateurs de défense des plantes (SDP)
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Brigitte Maisonneuve, Michel Pitrat
article
Vents du Sud (INRA - PACA), 2012, 1 p
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Cell wall glycosidase activities and protein content variations during fruit development and ripening in three texture contrasted tomato cultivars
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Emadeldin Konozy, Mathilde Causse, Mireille Faurobert
article
Saudi Journal of Biological Sciences, 2012, 19 (3), pp.277 - 283. ⟨10.1016/j.sjbs.2012.04.006⟩
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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.
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The cucurbits and nightshades of renaissance England: John Gerard and William Shakespeare
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Jules Janick, Harry S. Paris, M-Christin Daunay
article
Horticultural Reviews, 2012, 40, pp.215-257. ⟨10.1002/9781118351871.ch6⟩
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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.
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Dossier pêche : Création variétale Inra. Transmissions du public au privé
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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
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Effet de différentes doses d’UV-C sur l’aspect visuel et les paramètres de fluorescence chlorophyllienne de la laitue Romaine.
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Chayma Ouhibi, H Attia, Laurent Urban, Mokhtar Lachaâl, Jawad Aarrouf
article
Tunisian Journal of Medicinal Plants and Natural Products , 2012
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Optimization of parameters of the ‘Virtual Fruit’ model to design peach genotype for sustainable production systems
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Bénédicte Quilot-Turion, Mohamed Mahmoud Ould Sidi, Abdeslam Kadrani, Nadine Hilgert, Michel Génard, Francoise Lescourret
article
European Journal of Agronomy, Elsevier, 2012, 42, pp.34-38. ⟨10.1016/j.eja.2011.11.008⟩
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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.
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Application of a SUGAR model to analyse sugar accumulation in peach cultivars that differ in glucose–fructose ratio
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B.H. Wu, Bénédicte Quilot-Turion, Michel Génard, S.H. Li, J.B. Zhao, J. Yang, Y.Q. Wang
article
Journal of Agricultural Science, Cambridge University Press (CUP), 2012, 150, pp.53-63. ⟨10.1017/S0021859611000438⟩
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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
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Relative efficiency of morphological characters and molecular markers in the establishment of an apricot core collection
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L. Krichen, Jean Marc Audergon, N. Trifi-Farah
article
Hereditas, Mendelian Society of Lund, 2012, 149 (5), pp.163 - 172. ⟨10.1111/j.1601-5223.2012.02245.x⟩
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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.
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Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis)
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Fabien C. Lamaze, Christopher Sauvage, Amandine Marie, Dany Garant, Louis Bernatchez
article
Molecular Ecology, Wiley, 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.
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Sensitivity of peach cultivars against a Dideron isolate of Plum pox virus
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Manuel Rubio, Pedro Martínez-Gómez, Jesus Garcia-Brunton, Thierry Pascal, Ana Garcia-Ibarra, Federico Dicenta
article
Scientia Horticulturae, Elsevier, 2012, 144, pp.81 - 86. ⟨10.1016/j.scienta.2012.06.038⟩
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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.
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Co-localisation of host plant resistance QTLs affecting the performance and feeding behaviour of the aphid Myzus persicae in the peach tree
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Marie-Hélène Sauge, Patrick Lambert, Thierry Pascal
article
Heredity, Nature Publishing Group, 2012, 108 (3), pp.292-301. ⟨10.1038/hdy.2011.74⟩
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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
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Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato
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Sung-Chur Sim, Gregor Durstewitz, Joerg Plieske, Ralf Wieseke, Martin W. Ganal, Allen van Deynze, John P. Hamilton, C. Robin Buell, Mathilde Causse, Saranga Wijeratne, David M. Francis
article
PLoS ONE, Public Library of Science, 2012, 7 (7), ⟨10.1371/journal.pone.0040563⟩
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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.
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Genetic linkage map and diversity analysis of tahitian vanilla (Vanilla ×tahitensis, Orchidaceae)
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Sandra Lepers-Andrzejewski, Sandrine Causse, Bernard Caromel, Maurice Wong, Michel Dron
article
Crop Science, Crop Science Society of America, 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.
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Sensibilité variétale aux maladies et ravageurs. Fiche n° 5: la tavelure
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Laurent Brun, Armand Guillermin, Guy Clauzel, Vincent Mercier, Jm Broquaire, Jean Marc Audergon
article
Arboriculture Fruitière, 2012, 1 p
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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
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Light affects ascorbate content and ascorbate-related gene expression in tomato leaves more than in fruits
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Capucine Massot, Rebecca Stevens, Michel Génard, Jean Jacques Longuenesse, Hélène Gautier
article
Planta, Springer Verlag, 2012, 235 (1), pp.153-163. ⟨10.1007/s00425-011-1493-x⟩
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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
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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
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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⟩
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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.
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High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus
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Natalie H. Chapman, Julien Bonnet, Laurent Grivet, James Lynn, Neil Graham, Rebecca Smith, Guiping Sun, Peter G. Walley, Mervin Poole, Mathilde Causse, Graham J. King, Charles Baxter, Graham B. Seymour
article
Plant Physiology, American Society of Plant Biologists, 2012, 159 (4), pp.1644 - 1657. ⟨10.1104/pp.112.200634⟩
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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.
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Genome-Wide Association Mapping in Tomato (Solanum lycopersicum) Is Possible Using Genome Admixture of Solanum lycopersicum var. cerasiforme
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Nicolas Ranc, Stephane Munos, Jiaxin Xu, Marie-Christine Le Paslier, Aurelie Chauveau, Rémi Bounon, Sophie Rolland, Jean-Paul Bouchet, Dominique Brunel, Mathilde Causse
article
G3, Genetics Society of America, 2012, 2 (8), pp.853 - 864. ⟨10.1534/g3.112.002667⟩
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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.
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https://hal.inrae.fr/hal-02652089/file/2012_Ranc_G3%20-%20Genes%20Genomes%20Genetics_1.pdf BibTex
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What do spring migrants reveal about sex and host selection in the melon aphid?
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Sophie Thomas, Nathalie Boissot, Flavie Vanlerberghe-Masutti
article
BMC Evolutionary Biology, BioMed Central, 2012, 12 (47), 16 p. ⟨10.1186/1471-2148-12-47⟩
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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.
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https://hal.inrae.fr/hal-02650759/file/Thomas-BMC-EvolBiol-2012_1.pdf BibTex
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Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)
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Maryse Nicolaï, Cedric Pisani, Jean-Paul Bouchet, M. Vuylsteke, Alain Palloix
article
Genetics and molecular research : GMR, Ribeirão Preto foundation for Scientific Research (FUNPEC), 2012, 11 (3), pp.2295-2300. ⟨10.4238/2012.August.13.3⟩
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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.
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https://hal.inrae.fr/hal-02650422/file/2012_Nicolai_Genetics%20and%20Molecular%20Research_1.pdf BibTex
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Regulation of the fruit-specific PEP Carboxylase SlPPC2 promoter at early stages of tomato fruit development
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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, Public Library of Science, 2012, 7 (5), pp.1-11. ⟨10.1371/journal.pone.0036795⟩
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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.
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https://hal.archives-ouvertes.fr/hal-01136957/file/PLoS%20One%20SlPPC2%202012_%7B86E0B881-F91A-41A1-9579-A5A5B7F7D244%7D.pdf BibTex
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Obtention de laitues résistantes au chlorsulfuron par régénération de protoplastes irradiés aux UV
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M-Christine Chupeau, Yannick Bellec, Brigitte Maisonneuve, Yves Chupeau
article
Cahiers des Techniques de l'INRA, INRA, 2012, 77 (3), pp.1-7
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
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https://hal.archives-ouvertes.fr/hal-01019541/file/Maisonneuve_2012%20Le%20Cahier%20des%20Techniques%20de%20l%27INRA_1.pdf BibTex
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Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence
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Amandine Delteil, Melisande Blein-Nicolas, Odile Faivre-Rampant, Amira Guellim, Joan Estevan, Judith Hirsch, Rosangela Bevitori, Corinne Michel, Jean-Benoit Morel
article
Molecular Plant Pathology, Wiley, 2012, 13 (1), pp.72-82. ⟨10.1111/j.1364-3703.2011.00731.x⟩
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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.
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Particle swarm optimization to design ideotypes for sustainable fruit production systems
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Abdeslam Kadrani, Mohamed Mahmoud Ould Sidi, Bénédicte Quilot-Turion, Michel Génard, Francoise Lescourret
article
International Journal of Swarm Intelligence Research, IGI Global, 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.
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Apricot cell wall composition: Relation with the intra-fruit texture heterogeneity and impact of cooking
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Crepin Ella Missang, Jean Francois Maingonnat, Catherine Renard, Jean Marc Audergon
article
Food Chemistry, Elsevier, 2012, 133, pp.45-54. ⟨10.1016/j.foodchem.2011.12.059⟩
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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.
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Anatomical and biochemical trait network underlying genetic variations in tomato fruit texture
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Rémy Aurand, Mireille Faurobert, David Page, Jean Francois Maingonnat, Béatrice Brunel, Mathilde Causse, Nadia Bertin
article
Euphytica, 2012, 187 (1), pp.99 - 116. ⟨10.1007/s10681-012-0760-7⟩
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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.
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Apricot cell wall composition: Relation with the intra-fruit texture heterogeneity and impact of cooking.
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Crepin Ella Missang, Jean Francois Maingonnat, Catherine Renard, Jean Marc Audergon
article
Food Chemistry, Elsevier, 2012
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Anatomical and biochemical trait network underlying genetic variations in tomato fruit texture.
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Rémy Aurand, Mireille Faurobert, David Page, Jean Francois Maingonnat, Béatrice Brunel, Mathilde Causse, Nadia Bertin
article
Euphytica, 2012
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Genetic diversity and differentiation of grafted and seed propagated apricot (Prunus armeniaca L.) in the Maghreb region
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Hedia Bourguiba, Jean Marc Audergon, Lamia Krichen, Neila Trifi-Farah, Ali Mamouni, Samia Trabelsi, Bouchaib Khadari
article
Scientia Horticulturae, Elsevier, 2012, 142, pp.7-13. ⟨10.1016/j.scienta.2012.04.024⟩
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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.
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Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin
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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, BioMed Central, 2012, 12, ⟨10.1186/1471-2229-12-49⟩
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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.
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https://hal.archives-ouvertes.fr/hal-01191293/file/Publis012-agap-030_Bourguiba_BMC%20PlantBiol_Loss%20genetic%20diversity%20Mediterranean%20Basin_%7B22D40E1C-CC1A-496F-8E60-CB5D34BA61A5%7D.pdf BibTex
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Virus adaptation to quantitative plant resistance: erosion or breakdown?
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Josselin Montarry, Elodie Cartier, Mireille Jacquemond, Alain Palloix, Benoît Moury
article
Journal of Evolutionary Biology, Wiley, 2012, 25 (11), pp.2242-2252. ⟨10.1111/j.1420-9101.2012.02600.x⟩
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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.
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Inheritance of Fruit Quality Traits in Apricot Progenies
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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 Renard, Luca Dondini, Stefano Tartarini
article
Acta Horticulturae, International Society for Horticultural Science, 2012, 966, pp.89-99. ⟨10.17660/ActaHortic.2012.966.14⟩
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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.
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