Publications HAL du labo/EPI 37751;1002097

2022

Conference papers

titre
Worldwide Population Structure of Eggplant Identified by SPET Genotyping over 3,400 Accessions
auteur
Lorenzo Barchi, Ezio Portis, Sergio Lanteri, David Alonso, Maria José Diez, Jaime Prohens, Véronique Lefebvre, Jérémy Salinier, Hatice Filiz Boyaci, Laura Toppino, Giuseppe Leonardo, Mark Timothy Rabanus-Wallace, Andreas Boerner, Nils Stein, Richard Finkers, Matthijs Brouwer, Arnaud G. Bovy, Roland Schafleitner, Giuseppe Aprea, Giovanni Giuliano
article
Virtual Plant and Animal Genome XXIX Conference, Jan 2022, San Diego (CA), United States
resume
G2P-SOL (http://www.g2p-sol.eu) is an EU-funded project, bringing together the main European and international genebanks hosting germplasm of the four major Solanaceous crops: potato, tomato, pepper and eggplant. Within the project, about 5,900 eggplant accessions, including wild relatives of the crop, have been inventoried. To provide genomic information on around 3,500 representative accessions, a custom set of 5K SPET probes (single primer enrichment technology, TECAN) was designed targeting SNPs evenly distributed all over the genome but mainly in gene-rich regions. DNA samples were prepared by the genebanks, while library preparation and Illumina sequencing was performed by IGA Technology Services. After quality filtering, reads were aligned to the eggplant reference genome sequence (version 4.1) using BWA-MEM and SNP calling was performed using GATK-4.1.9. By removing accessions with low coverage sequencing data, 3,412 were retained and 120K polymorphic sites identified by applying stringent filtering criteria. Among them, 4,306 were SNPs targeted by the 5K probe set, while the remaining were accessory off-target SNPs. The identified SNPs provided information for identifying putative mislabeled accessions (i.e., wrong species assignment), duplicates within and between genebanks. Moreover, they are exploitable for setting up screening protocols to avoid the acquisition of duplications by ex-situ maintainers. The population structure and genetic relationships of the eggplant accessions were investigated to build up a core collection for GWAS. Furthermore, based on historical phenotypic data available in genebanks, loci associated with key agronomic traits were identified. Our results demonstrate that SPET technology represents a valid alternative to random complexity reduction methods and arrays, proving a suitable tool for the high-throughput genotyping, management, and enhancement of genebank collections.
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Conference papers
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https://hal.inrae.fr/hal-03551609/file/Barchi%202022%20PAG%20San%20Diego%20-%20oral.pdf BibTex
titre
The Human History of Chilli Peppers Told by 10,000 Genebank Samples
auteur
Mark Timothy Rabanus-Wallace, Pasquale Tripodi, Lorenzo Barchi, Sandip Mallikarjun Kale, Alberto Acquadro, Roland Schafleitner, Jaime Prohens, Maria José Diez, Andreas Boerner, Jérémy Salinier, Bernard Caromel, Arnaud G. Bovy, Filiz Boyaci, Ronny Brandt, Axel Himmelbach, Maarten van Zonneveld, Salvatore Esposito, Gancho Pasev, Ezio Portis, Richard Finkers, Sergio Lanteri, Ilan Paran, Véronique Lefebvre, Giovanni Giuliano, Nils Stein
article
Virtual Plant and Animal Genome XXIX Conference, Jan 2022, San Diego (CA), United States
resume
From vindaloo to ratatouille, kung pao to Tex-Mex, chilli peppers and capsicums (Capsicum spp.) are valued staples in cuisines across the globe, prized for their garish aesthetics, diverse flavours, and pungency. First domesticated in South-and Mesoamerica, the Age of Discovery began a dynamic global trade in peppers, resulting in a highly intermixed distribution of pepper varieties across regions of the globe. This high degree of inter-region overlap makes genetic inference on pepper's history a unique challenge, especially with limited sample numbers. Fortunately, genebanks across the globe preserve an excellent representation of pepper diversity in different regions, and the G2P-Sol project (EU) recently completed the GBS sequencing of over 10,000 such accessions. Leveraging this vast dataset, we developed the novel method ReMIXTURE ("Regional Mixture") to complement traditional methods and allow insight into how the kinds of peppers cultivated in various regions overlap with those from various other regions. Despite low genetic differentiation, we were able to detect the signatures of transatlantic maritime trade routes, overland trade in the Americas and Eurasia, and the role of Africa as an important node joining the Americas to the East. The varying degrees of uniqueness of peppers found in each region were quantified, revealing hotspots of potential diversity (Mesoamerica, Southeast Asia, and Africa in particular) exploitable by breeders with an interest in introducing novel genetic variants and phenotypes to breeding efforts. The study also allowed us to assess aspects of genebank management such as duplicate detection, and to identify the influence of recent selective pressures on genes affecting fruit pungency and other qualities.
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Conference papers
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https://hal.inrae.fr/hal-03551615/file/Rabanus-Wallace%202022%20PAG%20San%20Diego%20-%20oral.pdf BibTex

Poster communications

titre
Phenotyping peach orchards with increased accuracy and throughput: perspectives of digital phenotyping
auteur
Morgane Roth, Joss Gillet, Mathias Lefebvre, Alexis Comar, Fabien Miart, Adrien Vielix, Etienne David, Bénédicte Quilot-Turion, Véronique Signoret, Marie Serrie, Sabrina Viret, Raul Lopez Lozano, Sylvain Jay, Marie Weiss
article
X International Peach Symposium, May 2022, Nouassa, Greece
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Poster communications
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titre
Which phloem in Cucumis melo is exploited by Aphis gossypii ?
auteur
Pierre Sadon, Marie-Noëlle Corre, Pascale Mistral, Raphaël Lugan, Olivier Chevallier, Nathalie Boissot, Marie Noëlle Corre
article
Réunion scientifique plénière BAPOA, May 2022, Nice, France
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Poster communications
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https://hal.inrae.fr/hal-03657121/file/20220502%20-%20Poster%20BAPOA%20version%20finale%20%C3%A0%20imprimer.pdf BibTex

2021

Conference papers

titre
Construction and diversity of the G2P-SOL pepper core collection
auteur
Véronique Lefebvre
article
G2P- SOL FINAL WORKSHOP “Multi-omics-based management of plant genetic resources”, Dec 2021, on line, Italy
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titre
Une structure emboîtée universelle pour les interactions quantitatives entre les plantes et leurs parasites ?
auteur
Benoît Moury, Jean-Marc Audergon, Sylvie Baudracco-Arnas, Safa Ben Krima, François Bertrand, Nathalie Boissot, Mireille Buisson, Valérie Caffier, Melissa Cantet, Sylvia Chanéac, Carole Constant, Francois Delmotte, Catherine Dogimont, Juliette Doumayrou, Frédéric Fabre, Sylvain Fournet, Valérie Grimault, Thierry Jaunet, Isabelle Justafré, Véronique Lefebvre, Denis Losdat, Thierry C. Marcel, Josselin Montarry, Cindy E. Morris, Mariem Omrani, Manon Paineau, Sophie Perrot, Marie-Laure Pilet-Nayel, Youna Ruellan
article
Réunion annuelle du réseau E3GP3, Dec 2021, Visioconférence, France
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Conference papers
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https://hal.inrae.fr/hal-03553078/file/Moury_HAL_INRAE.pdf BibTex
titre
Pepper core collection trials and GWAS
auteur
Véronique Lefebvre
article
The advanced Training school II “Using Genetic Resource Data for Breeding”, Oct 2021, on line, Israel
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titre
Experimental evolution of a plant RNA virus: a warning about spurious correlations when studying fitness changes
auteur
Lucie Tamisier, Frédéric Fabre, Marion Szadkowski, Ghislaine Nemouchi, Grégory Girardot, Pauline Millot, Alain Palloix, Benoît Moury
article
18. Rencontres de virologie végétale (RVV 2021), INRAE; CIRAD, Sep 2021, Aussois, France
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Conference papers
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https://hal.inrae.fr/hal-03553147/file/Tamisier_HAL-INRAE.pdf BibTex
titre
Outside the wild: Risks and mechanisms of host jumps of endive necrotic mosaic potyvirus
auteur
Marion Szadkowski, Catherine Wipf-Scheibel, William Billaud, Cecile Desbiez, Jonathan Gaudin, Gregory Girardot, Patrick Gognalons, Judith Hirsch, Thibaud Jayet, Sylvain Piry, Loup Rimbaud, Alexandra Schoeny, Eric Verdin, Raphael Forien, Julien Papaïx, Lionel Roques, Benoît Moury, Karine Berthier
article
18. Rencontres de virologie végétale (RVV 2021), Cirad; INRAE, Sep 2021, Aussois, France
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Conference papers
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https://hal.inrae.fr/hal-03368388/file/2021_Szadkowski_RVV.pdf BibTex
titre
Potato virus Y adaptation to various resistance QTL combinations in pepper and impact on host tolerance
auteur
Thibaud Jayet, William Billaud, Lucie Tamisier, Marion Szadkowski, Catherine Wipf-Scheibel, Loup Rimbaud, Judith Hirsch, Gregory Girardot, Jonathan Gaudin, Alexandra Schoeny, Karine Berthier, Karine Nozeran, Elise Lepage, De-Colle-Guiheneux Sarah, Thomas Pressecq, Véronique Lefebvre, Benoît Moury
article
18. Rencontres de virologie végétale (RVV2021), Cirad; Inrae, Sep 2021, Aussois, France
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https://hal.inrae.fr/hal-03368394/file/Jayet_HAL-INRAE.pdf BibTex
titre
Determinism of virulence of cucumber vein yellowing virus (CVYV) in melon and insights into the durability of resistance
auteur
Cecile Desbiez, Maria Luisa Domingo Calap, Michel Pitrat, Catherine Wipf-Scheibel, Gregory Girardot, Inmaculada Ferriol, Juan Jose Lopez-Moya, Hervé Lecoq
article
18. Rencontres de Virologie Végétale, Sep 2021, Aussois, France
resume
Genetic resistance is a sustainable way of controlling plant viruses, but it requires the presence of resistance genes in the host germplasm. Besides, its durability can be reduced by resistancebreaking isolates, either pre-existing in the environment or emerging after the deployment of the resistance. In the case of cucumber vein yellowing virus (CVYV, genus Ipomovirus), an emerging virus on cucurbits in the Mediterranean Basin, few resistances are available in melon. The accession PI 164323 was found to display complete resistance to the strain CVYV-Esp, and accession HSD 2458 presented a tolerance, i.e. very mild symptoms in spite of virus accumulation in inoculated plants. The resistance is controlled by one dominant allele Cvy-1 1 , while the tolerance is controlled by a recessive allele cvy-2 independent from Cvy-1 1 . Upon inoculation with eight molecularly diverse CVYV isolates, the resistance was found to be strain-specific since many CVYV isolates induced necrosis on PI 164323, whereas the tolerance presented a broader range. A resistance-breaking isolate inducing severe mosaics on PI 164323 was obtained. It differed from the parental strain by a single amino-acid change in the VPg-coding region. The effect on the mutation was confirmed by reverse genetics using a CVYV infectious clone. Competition experiments suggested a fitness cost of the resistancebreaking mutation in susceptible melon. Our results highlight the need to combine cultural practices and/or additional genes to develop a more durable control of CVYV than the use of the Cvy-1 1 allele alone.
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https://hal.inrae.fr/hal-03555763/file/2021-Desbiez-RVV.pdf BibTex
titre
Many different recipes but one flavor: A universal nested structure of quantitative interactions between plant genotypes and their parasites, including viruses
auteur
Benoît Moury, Jean-Marc Audergon, Sylvie Baudracco-Arnas, Safa Ben Krima, François Bertrand, Nathalie Boissot, Mireille Buisson, Valérie Caffier, Melissa Cantet, Sylvia Chanéac, Carole Constant, François Delmotte, Catherine Dogimont, Juliette Doumayrou, Frédéric Fabre, Sylvain Fournet, Valérie Grimault, Thierry Jaunet, Isabelle Justafré, Véronique Lefebvre, Denis Losdat, Thierry C. Marcel, Josselin Montarry, Cindy E. Morris, Mariem Omrani, Manon Paineau, Sophie Perrot, Marie-Laure Pilet-Nayel, Youna Ruellan
article
18. Rencontres de virologie végétale (RVV 2021), INRAE; CIRAD, Sep 2021, Aussois, France
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Conference papers
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https://hal.inrae.fr/hal-03553180/file/Moury_HAL-INRAE.pdf BibTex
titre
Breeding tomato hybrids for flavour: comparison of GWAS on lines and F1 hybrids
auteur
Estelle Bineau, José Rambla, Santiago Priego, Alexandre Hereil, Frédérique Bitton, Clémence Plissonneau, Antonio Granell, Mathilde Causse
article
Online EUCARPIA congress 2021 - Breeding: the key to innovative solutions, WUR, Aug 2021, Online, Netherlands
resume
While breeders face consumer expectations regarding tomato flavour in the F1 hybrid varieties commercialised, no data are available on the inheritance of QTLs for flavour-related trait in heterozygous plant material. Volatile organic compounds (VOCs) are major determinants of tomato lavour. We quantified 46 VOCs in (1) a panel of 121 small fruited tomato accessions (15 S. pimpinellifolium and 106 S. lycopersicum var. cerasiforme) and (2) in a test cross panel involving the previous panel plus 44 elite cherry tomato lines crossed with a common big fruited line. High and consistent heritabilities were assessed for most VOCs in the two panels, and the line and test cross values for VOC content were strongly correlated. In the two panels, cluster analysis on 46 VOC content matched the metabolic pathways known from the literature. Results suggested a global additivity pattern for most VOC genetic control. We performed genome wide association studies (GWAS) on the line and test cross panels separately, along with a third GWAS on the test cross subset carrying the subset of 121 F1 hybrids corresponding to the line panel. We identified 205, 183 and 138 associations, respectively. Although less than 10% associations overlapped between line and F1 hybrid panels, we identified numerous overlapping associations for VOCs belonging to the same metabolic pathway within each panel. With this study, we highlighted the interest of testcross panel to create tasty F1 hybrid varieties. The clusters of associations in the F1 hybrid panel are new levers to improve tomato flavour by regulating several key VOCs simultaneously, while following only a few genomic regions in the breeding material. We selected seven chromosome regions fitting numerous criteria meant to facilitate breeding. For instance, a 4Mbp region on chromosome 3 carried F1 specific associations for 14 different VOCs derived from the lipid metabolism, eight of which having an impact on tomato overall flavour. This region is supported by several candidate genes also highlighted in previous studies.
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Conference papers
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https://hal.inrae.fr/hal-03562573/file/Abstract.Eucarpia.E.Bineau.pdf BibTex
titre
Automated phenotyping provides insights into leaf angle changes in chile pepper response to stress.
auteur
Derek W Barchenger, Roland Schaftleitner, Ilan Paran, Véronique Lefebvre, Pasquale Tripodi, Nils Stein, Richard Finkers, Giovanni Giuliano, Seok-Beom Kang
article
ASHS 2021 Annual Conference, Aug 2021, Denver (Colorado), United States
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https://hal.inrae.fr/hal-03551646/file/Barchenger%202021%20ASHS%20Denver%20-%20oral.pdf BibTex
titre
Recent advances on peach-brown rot interactions: searching solutions to fight in a sustainable manner
auteur
Bénédicte Quilot-Turion
article
ISHS Peach webinar Current trends and challenges on peach fruit production, Jun 2021, Cyprus, Cyprus. pp.1-21
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Conference papers
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https://hal.inrae.fr/hal-03445639/file/ISHS%20Peach%20Webinar%20series%20%28official%20brochure%29.pdf BibTex
titre
Recent advances on peach-brown rot interactions from INRAE's research program
auteur
Bénédicte Quilot-Turion
article
10th ISHS International Peach Symposium A series of 4 HortDialogues webinars on peach 'Current trends and challenges on peach fruit production', International Society for Horticultural Science, Jun 2021, Webinar, Greece
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Conference papers
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https://hal.inrae.fr/hal-03267904/file/Recent%20advances%20on%20peach-brown%20rot_%20BQuilotTurion.pdf BibTex
titre
Adaptation of GWAS models for plant resistance to viruses: from rediscovering major genes to highlighting of new complex traits in breeding germplasm.
auteur
Severine Monnot, Laurence Moreau, Tristan Mary-Huard, Mélissa Cantet, Nathalie Boissot
article
XIIe Eucarpia Meeting on Cucurbit Genetics and Breeding, May 2021, Almeria, Spain. pp.1-16
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titre
UNE HISTOIRE DE LA SÉLECTION DES ESPÈCES LÉGUMIÈRES EN FRANCE
auteur
Mathilde Causse, Michel Pitrat
article
Fruits et Légumes : quelles évolutions, Journées d'études AAF, AEHA et GGEDD, Mar 2021, Paris, France
resume
La sélection met à disposition des producteurs et des consommateurs des variétés qui correspondent aux attentes socio-économiques. Ces attentes varient en fonction du temps. Jusqu'à la fin du XVIII e siècle la société est très majoritairement rurale dans une économie de subsistance. Les légumes les plus consommés sont des légumes-racines (navets), des légumes-feuilles (choux, bettes, poireaux) et des légumes-graines (pois, lentilles, fèves). La sélection et la production de semences sont le fait des producteurs/consommateurs. Nous sommes mal renseignés sur les variétés mais elles sont assez nombreuses et correspondent à une adaptation pédo-climatique locale. Du début du XIX e au milieu du XX e siècle, une économie de marché se développe avec l'exode rural et le développement des transports qui vont entraîner d'une part une localisation des producteurs vers les ceintures vertes des villes et des régions spécialisées et d'autre part le développement des grainetiers avec l'achat des semences. Les variétés se diversifient avec en particulier des efforts d'homogénéisation et une adaptation au forçage sous châssis. Les légumes-fruits deviennent plus importantes (tomate, concombre, courgette). Depuis le milieu du XX e siècle, l'internationalisation des marchés, le développement de l'industrie agro-alimentaire (2 ème à 5 ème gamme), la part prise par la grande distribution dans le commerce des légumes, les évolutions des techniques de production (serres, mécanisation) entraînent le développement de nouvelles variétés répondant à ces demandes. Le secteur de l'innovation variétale et de la production de semences est très dynamique.
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Conference papers
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https://hal.inrae.fr/hal-03562674/file/resume3.pdf BibTex
titre
Résistance à Xanthomonas arboricola pv. pruni chez le pêcher
auteur
Naïma Dlalah, Bénédicte Quilot-Turion, Yannick Montrognon
article
Les Rencontre du GIS, GIS, Jan 2021, webinaire, France
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Conference papers
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https://hal.inrae.fr/hal-03269432/file/19-01-21_GIS%20fruits_ReXapPech.pdf BibTex

Other publications

titre
Une lutte mieux armée face à "Xanthomonas
auteur
Bénédicte Quilot-Turion, Naïma Dlalah, Yannick Montrognon
article
2021, pp.30-31
resume
Dans le cadre d'un projet porté par INRAE d'Avignon et la Sefra, un test ADN a été développé pour cribler efficacement les variétés de pêchers vis à vis de la maladie provoquée par " Xanthomonas". Il représente une aide non négligeable à la sélection et à la caractérisation variétale.
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titre
Des composés de la pêche aux effets fongicides contre la moniliose
auteur
Marie-Noëlle Corre
article
2021
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https://hal.inrae.fr/hal-03298409/file/Corre_ComposesPecheMoniliose_ReussirF_L_2021.jpg BibTex

Preprints, Working Papers, ...

titre
The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions
auteur
Benoît Moury, Jean-Marc Audergon, Sylvie Baudracco-Arnas, Safa Ben Krima, François Bertrand, Nathalie Boissot, Mireille Buisson, Valérie Caffier, Melissa Cantet, Sylvia Chanéac, Carole Constant, François Delmotte, Catherine Dogimont, Juliette Doumayrou, Frédéric Fabre, Sylvain Fournet, Valérie Grimault, Thierry Jaunet, Isabelle Justafré, Véronique Lefebvre, Denis Losdat, Thierry Marcel, Josselin Montarry, Cindy E. Morris, Mariem Omrani, Manon Paineau, Sophie Perrot, Marie-Laure Pilet-Nayel, Youna Ruellan
article
2021
resume
Understanding the relationships between host range and pathogenicity for parasites, and between the efficiency and scope of immunity for hosts are essential to implement efficient disease control strategies. In the case of plant parasites, most studies have focused on describing qualitative interactions and a variety of genetic and evolutionary models has been proposed in this context. Although plant quantitative resistance benefits from advantages in terms of durability, we presently lack models that account for quantitative interactions between plants and their parasites and the evolution of these interactions. Nestedness and modularity are important features to unravel the overall structure of host-parasite interaction matrices. Here, we analysed these two features on 32 matrices of quantitative pathogenicity trait data gathered from 15 plant-parasite pathosystems consisting of either annual or perennial plants along with fungi or oomycetes, bacteria, nematodes, insects and viruses. The performance of several nestedness and modularity algorithms was evaluated through a simulation approach, which helped interpretation of the results. We observed significant modularity in only six of the 32 matrices, with two or three modules detected. For three of these matrices, modules could be related to resistance quantitative trait loci present in the host. In contrast, we found high and significant nestedness in 30 of the 32 matrices. Nestedness was linked to other properties of plant-parasite interactions. First, pathogenicity trait values were explained in majority by a parasite strain effect and a plant accession effect, with no parasite-plant interaction term. Second, correlations between the efficiency and scope of the resistance of plant genotypes, and between the host range breadth and pathogenicity level of parasite strains were overall positive. This latter result questions the efficiency of strategies based on the deployment of several genetically-differentiated cultivars of a given crop species in the case of quantitative plant immunity.
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Preprints, Working Papers, ...
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03169796/file/2021_Moury_bioRxiv.pdf BibTex

2020

Conference papers

titre
A transposable element from the hAT-superfamily is responsible for the absence or globose-shape phenotype of leaf extrafloral nectaries in peach (Prunus persica L. Batsch)
auteur
P Lambert, C Confolent, N Dlalah, Bénédicte Quilot-Turion, V Signoret, T Pascal
article
10th Rosaceae Genomics Conference, centre for research in agricultural genomics, Dec 2020, Barcelona, Spain
resume
Most peach (Prunus persica L. Batsch) cultivars have extrafloral nectaries (EFNs), or leaf-glands, on the leaf petioles, stipules, or margins (Gregory 1915, Okie 1998). From an extensive study, Gregory (1915) observed that the great majority of varieties was found to have well-defined gland shapes. Moreover gland-shapes were generally homogenous on typical shoots, although some cultivars could exhibit mixed glands. This author identified three main types of leaves, those with reniform glands, those with globose glands and glandless leaves. Fruit breeding programs have inadvertently produced peach cultivars with glandless leaves (Okie 1998), yet without determining the effects on either natural enemies or herbivorous pests (Scorza and Sherman 1996). Empirical observations, however, showed that the absence of EFNs resulted in a higher susceptibility to peach powdery mildew (PPM), a major disease of the peach caused by Podosphaera pannosa var. persicae (Weinhold 1961; Monet 1983). As a result, peach seedlings without leaf-glands were systematically discarded in the breeding programs. The Mendelian inheritance of the leaf-gland phenotype (E/e) was first described by Connors (1921) and the E locus was latter mapped on chromosome 7 of the peach (Dettori et al., 2001), but without identifying the genetic factor involved. In order to address the latter point and implement early diagnosis tools, we developed a mapping population of 833 progenies derived from the selfing of 'Malo Konare', a canning peach cultivar with globose leaf-glands, from Bulgarian origin. This population was used to map and investigate the genetic factor underlying the E locus, using additional resources including NGS peach resources and 148 cultivars from various origins. Our findings demonstrated that a MITE-like Moshan transposable element inserted in the gene controlling the character was responsible for the absence or globose-shape phenotype of the EFNs.
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https://hal.inrae.fr/hal-03267833/file/Abstract_lambert_RGC10.pdf BibTex
titre
Wounding nectarine fruit disrupts Monilinia laxa infection: deciphering fruit gene pathway involved and the role of phenolic and volatile compounds
auteur
Bénédicte Quilot-Turion, Marie-Noëlle Corre, Guy Costagliola, Laure Heurtevin, Véronique Signoret, Maria Do Carmo Raseira, Maximiliano Dini Vinoly
article
10th Rosaceae Genomics Conference, Centre for research in agricultural genomics, Dec 2020, Barcelone, Spain
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Conference papers
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https://hal.inrae.fr/hal-03267785/file/RGC10_QuilotTurion.pdf BibTex
titre
Genebank genomics highlights novel centres of diversity and routes of migration in pepper (Capsicum spp.)
auteur
Tripodi P, L Barchi, Kale S, Esposito S, Mt Rabanus-Wallace, A. Acquadro, Schafleitner R, J. Prohens, M.J. Diez, Börner A, A Bovy, Jérémy Salinier, Boyaci H, Pasev G, R Brandt, Axel Himmelbach, E. Portis, Finkers R, S. Lanteri, L Paran, Véronique Lefebvre, Giuliano G, Stein N
article
SOL International Meeting 2020, Nov 2020, on line, United States
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https://hal.inrae.fr/hal-03551675/file/Tripodi%202020%20SOL%20genomics%20on%20line%20-%20%20oral%20.pdf BibTex
titre
Identification de composés naturels de la pêche affectant la pathogénicité de Monilinia Spp.
auteur
Marie-Noëlle Corre
article
Rencontres du GIS Fruits, GIS, Oct 2020, Webinaire, France
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Conference papers
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https://hal.inrae.fr/hal-03269430/file/GIS%20Fruits%20MNCorre_28102020.pdf BibTex
titre
eIF4E-based resistance to potyviruses from natural variation to edited genes
auteur
Jean-Luc Gallois
article
International workshop on plant genome editing, Sep 2020, conférence en ligne, France
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titre
Deciphering the epigenetic variability in S. lycopersicum accessions and their influence on hybrid vigor
auteur
Luisa Bermudez, Estanislao Burgos, Laura Pascual, Mathilde Causse, Magdalena Rossi, Fernando Carrari
article
SOlanaceae Genomics, Sep 2020, Online, Italy
resume
Heterosis is a fundamental biological phenomenon defined by the superior performance of hybrids over its parents in many economically important traits. Even though heterosis has been extensively used in agriculture, both in plants and animals, the underlying molecular basis remains elusive. This lack of knowledge hampers the rational design of hybrids in order to obtain, in a faster and more efficient way, benefits resulting from heterotic effects. Evidence obtained from several species allows hypothesizing that alterations in the epigenetic state, mediated by changes in the DNA methylation pattern, play a role in determining hybrid vigor. Nevertheless, how parental alleles interact in their progeny to influence the epigenome is poorly understood. We analyzed DNA methylomes, siRNAomes and transcriptomes of three tomato hybrids, and their corresponding divergent parents. Interestingly, the parental methylation, siRNAs and transcriptome patterns did not correlate with the genetic distance between the genotypes and several genes involved in key metabolic categories showed to be epigenetically regulated. Evenmore, hybrids displayed non-additive DNA methylation levels throughout the genome. These results add to the growing evidences that point epigenetic mechanisms as key determinants of hybrid performance and make them able to future applications in breeding programs.
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titre
Meta-analysis of GWAS provides new insights into genetic control of tomato flavor
auteur
Jiantao Zhao, Christopher Sauvage, Frédérique Bitton, Mathilde Causse
article
Plant Genome and genomics Conference, Mar 2020, Rotterdam, Netherlands
resume
Tomato flavor has changed over the course of long-term domestication and intensive breeding. To understand the genetic control of flavor related traits, we performed a meta-analysis of genome-wide association studies (GWAS) for 18 traits, using 775 tomato accessions and 2,316,117 SNPs from three GWAS panels (Sauvage et al., 2014; Bauchet et al., 2017 and Tieman et al., 2017). In a first step, we imputed SNP data to increase genome coverage for two out of three panels and ran EMMAX software for each panel separately. From each run, the genomic inflation factor and standard errors of the beta coefficients were implemented in two meta-GWAS models: the inverse variance-weighted fixed effect and the Han Eskin random-effect model that takes heterogeneity across studies into account. Then, from the meta-GWAS results, we conducted a statistical fine-mapping of the candidate loci following a heuristic linkage disequilibrium (LD) approach. We discovered 305 significant associations for the contents of sugars, acids, amino acids and flavor-related volatiles. We showed that fruit citrate and malate contents have been impacted by selection during domestication and improvement, while sugar content has undergone less stringent selection. Results 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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titre
Reducing a model of sugar metabolism in peach fruit to explore genetic diversity
auteur
Hussein Kanso, Bénédicte Quilot-Turion, Mohamed-Mahmoud Memah, Olivier Bernard, Jean-Luc Gouzé, Valentina Baldazzi
article
iCROPM 2020 : Crop modelling for the Future, Feb 2020, Montpellier, France. pp.1-5
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Meta-analysis of GWAS provides new insights into genetic control of tomato flavor.
auteur
Jiantao Zhao, Christopher Sauvage, Frédérique Bitton, Mathilde Causse
article
Plant and Animal Genome 2020, 2020, San Diego, United States
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Poster communications

titre
Small deletion in a photosynthesis-related gene is involved in anthocyanin accumulation in the mesocarp of bf blood-flesh peaches
auteur
Laure Heurtevin, Carole Confolent, Bénédicte Quilot-Turion, Sylvie Bureau, Carine Le Bourvellec, Zhijun Shen, Jacques Lagnel, Thierry Pascal
article
10th Rosaceae Genomics Conference, Dec 2020, Barcelone, Spain
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titre
Research of candidate genes in peach for resistance to root-knot nematodes and resistance to aphids Myzus persicae
auteur
Henri Duval, Laure Heurtevin, Naïma Dlalah, Jacques Lagnel, Caroline Callot
article
10th Rosaceae Genomics Conference, Dec 2020, Barcelona, Spain
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Poster communications
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titre
Apricot processing suitability linked to its macronutrient composition: a part of DeshyFruit project
auteur
Barbara Gouble, Patrice Reling, Adrien Servent, Pierre Brat, Véronique Vidal, Sandrine Laurent, Jean-Marc Audergon
article
Third Symposium on Fruit and Vegetable Processing, Nov 2020, Avignon, France. 1p
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titre
Development of a Snakemake “framework/templates” to study the whole-genome transcriptional profiling from a blood-flesh trait (bf) and non blood-flesh trait (non-bf) cultivars in Prunus persica
auteur
Laure Heurtevin, Thierry Pascal, Bénédicte Quilot-Turion, Martin-Magniette Marie-Laure, Jacques Lagnel
article
JOBIM 2020 Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier, France. ⟨10.13140/RG.2.2.15060.63366⟩
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Reports

titre
Séminaire d’échanges sur les pratiques de recherches interdisciplinaires à INRAE, 7-8 Janvier 2020, Synthèse
auteur
Isabelle Arpin, Olivier Barreteau, Carole Caranta, Christian Ducrot, Patrice Garin, Mourad Hannachi, Isabelle Maillet
article
[Autre] INRAE. 2020, 22 pp
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Preprints, Working Papers, ...

titre
The genomic basis of colour 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 Ben
article
2020
resume
Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechanisms generating and maintaining such phenotypic variation within species is essential to comprehending morphological diversity. A common and conspicuous example of discrete phenotypic variation in natural populations of insects is the occurrence of different colour patterns, which has motivated a rich body of ecological and genetic research. The occurrence of dark, i.e. melanic, forms, displaying discrete colour 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 orange patches on adult elytra varies wildly within species, forming strikingly different complex colour patterns. In the harlequin ladybird Harmonia axyridis, more than 200 distinct colour forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus. Here, we combined whole-genome sequencing, population genomics, gene expression and functional analyses, to establish that the gene pannier controls melanic pattern polymorphism in H. axyridis. We show that pannier, which encodes an evolutionary conserved transcription factor, 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 colour patterns in H. axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of ca. 170 kb in the cis-regulatory regions of pannier with a 50 kb inversion between colour forms. This likely helps maintaining the distinct alleles found in natural populations. Thus we propose that highly variable discrete colour forms can arise in natural populations through cis-regulatory allelic variation of a single gene.
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2019

Conference papers

titre
Within-plant genetic drift to control virus adaptation
auteur
Lucie Tamisier, Ghislaine Nemouchi, Marion Szadkowski, Grégory Girardot, Frédéric Fabre, Alain Palloix, Benoît Moury
article
5. Conférence Jacques Monod, Évolution virale sur le continuum mutualiste – parasite, Oct 2019, Roscoff, France
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titre
Résistance aux virus: Quand la variabilité naturelle guide l'édition de gènes
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Jean-Luc Gallois
article
AFBV 9ème Colloquedes Biotechnologies Végétales, Gœthe Institut. Paris, FRA., Oct 2019, Paris, France
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A reduction strategy to simplify a model of sugar metabolism for application to a large panel of genotypes
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Hussein Kanso, Bénédicte Quilot-Turion, Mohamed-Mahmoud Memah, Olivier Bernard, Jean-Luc Gouzé, Valentina Baldazzi
article
FOSBE 2019 - 8th Conference on Foundations of Systems Biology in Engineering, IFAC, Oct 2019, Valencia, Spain
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titre
Genome-wide association mapping of loci involved in Potato virus Y resistance and tolerance in pepper germplasm
auteur
Lucie Tamisier, Ghislaine Nemouchi, Marion Szadkowski, Véronique Lefebvre, Emmanuel Szadkowski, Gregory Girardot, Renaud Duboscq, Sylvain Santoni, Sarah Gautier, Christopher Sauvage, Alain Palloix, Judith Hirsch, Benoît Moury
article
17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant (2019), Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL). FRA.; Terralia. FRA.; Groupe d'Etude et de Contrôle des Variétés et des Semences (GEVES). FRA., Sep 2019, Avignon, France. 263 p
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titre
Impact of host partial resistance on the gene expression of Phytophthora capsici: consequences for pepper breeding
auteur
Véronique Lefebvre, Gaëtan Maillot, Emmanuel Szadkowski, Bernard Caromel, Anne Massire, Alexandre Bachellez, Nasradin Touhami, Guillem Rigaill, Joel Chadoeuf, Kurt Lamour
article
17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant (2019), Sep 2019, Avignon, France
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Capsicum spp. and eggplant genome sequencing and resequencing provide new tools for the characterization of genetic resources
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L Barchi, Acquadro A, E. Portis, Alonso D, P. Gramazio, Vilanova S, M.J. Diez, Jérémy Salinier, A Unlu, L Toppino, Bassolino L, P Tripodi, D’agostino N, Börner A, Brandt R, D. Scaglione, Dicenta E, S Pinosio, G Aprea, Ferrante P, Finkers R, Boyaci Hf, A Bovy, N Stein, Schafleitner R, M.C. Daunay, Véronique Lefebvre, Lanteri S, J. Prohens, G.L. Rotino, Giuliano Sciara
article
17th Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2019, Avignon, France
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BACKGROUND We report the current state of the art on genome sequencing and resequencing studies in Capsicum annuum L. and Solanum melongena as well as some of their cultivated and wild related species. The availability of high quality genome sequences in both species has opened the way to the characterization of genetic resources through genotyping-by-sequencing (GBS) approaches. Among them, we focus on the recently developed Single Primer Enrichment Technology (SPET) technique, which we have applied for targeted sequencing of a wide collection of S. melongena accessions and representatives of its primary, secondary and tertiary genepools. RESULTS Pepper Since the beginning of 2014, various consortia have released the genome sequences of domesticated and wild Capsicum species. The whole-genome sequences of C. annuum CM334 and C. chinense PI159236, which carry important disease resistance traits and have been widely used as parental lines of mapping populations, were the first to be released [1]. Next, the genome sequences of C. annuum Zunla-1 and of the wild species Chiltepin (C. annuum var. glabriusculum) were published [2]. Both studies highlighted that the pepper genome size is ~3-3.5 Gb, has a high percentage (over 80%) of repetitive elements, and encodes about 35K genes. Later, the improved version of the reference genome of CM334 and C. chinense PI159236, together with the sequencing of the domesticated C. baccatum were also made available, and contributed to deciphering the evolutionary relationships among the three species as well as to estimating the lineage-divergence times occurring in Capsicum [3]. By adopting the linked-read sequencing technology, the genome sequence of an F1 hybrid obtained by crossing CM334 with a nonpungent C. annuum breeding line was also published [4]. The availability of pepper genome sequences has allowed the resequencing of Capsicum accessions at both targeted genomic regions and the whole genome level. By applying a bulk segregant analysis, it has been possible to identify markers tightly linked to the Pvr4 locus, conferring dominant resistance to three pathotypes of Potyvirus (PVY, [5]). Furthermore, after the resequencing of resistant and susceptible cultivars, SNPs and putative alleles related to resistance against powdery mildew and bacterial wilt have also been detected [6,7]. To provide insights into the process of pepper domestication, the Zunla-1 genome sequence was analysed together with resequencing (20-30X) information of 18 cultivated accessions representative of the major varieties of C. annuum and two semi-wild/wild peppers [2]. This resulted in the identification of 115 genomic regions affected by artificial selection in cultivated peppers. Lastly, genome resequencing (30X) of four genotypes, representative of the main varietal types grown in the Mediterranean region, has been performed. Distinctive variations in miRNAs and resistance gene analogues (RGAs) have been highlighted as well as mutations in the coding sequences and regulatory regions of genes affecting fruit size and shape (Barchi et al., SOLCUC meeting 2017). Within the G2P-SOL EU project (www.g2p-sol.eu), the analysis of genome-wide genotyping-by-sequencing (GBS) data on 9,659 pepper accessions retrieved from the major European (CGN, INRA, IPK, UPV) and Asian (AVRDC) gene banks, Universities and Research Centres has been recently performed and the results obtained reported by Tripodi et al. (see Proceedings of this Meeting). Eggplant: In 2014, Hirakawa and co-authors [8] produced the first unanchored draft of the S. melongena genome sequence using the Nakate-Shinkuro accession. The obtained sequence covered about 70% of its projected 1.2 Gb genome size and more than 42K genes were identified. More recently, the Italian Eggplant Genome Consortium (IEGC) [9] developed a high quality and anchored genome assembly of the eggplant line 67/3, the male parent of an F6 RIL (Recombinant Inbred Line) mapping population. A hybrid assembly, covering 1.22 Gb, was obtained by merging Illumina sequencing data and optical mapping. The female parent of the RIL mapping population (line ‘305E40’) was also sequenced (coverage of 34X), and thanks to low coverage resequencing (1X) of the F6 RILs, the genome assembly was anchored to the 12 chromosomes. Recently, based on Illumina sequencing data, a draft genome assembly of 1.02 Gb in size was developed for the cultivated species S. aethiopicum, which contained as for eggplant, about 76% of repetitive sequences. Furthermore, compared to S. melongena, an expansion of gene families involved in drought or salinity tolerance as well as disease resistance including defence responses was identified. Recently, the resequencing of seven eggplant accessions and one accession of the wild relative S. incanum, which are the parents of a MAGIC population, has been performed (Gramazio et al., see Proceedings of this Meeting). The set of identified SNP polymorphisms has been annotated and currently is being used for further analyses in order to efficiently genotype the MAGIC population with the goal of dissecting key agronomic and morphological traits. More recently, 60 genotypes of the cultivated scarlet eggplant (S. aethiopicum) belonging to the varietal groups, “Gilo” and “Shum”, as well as 5 accessions of its ancestor S. anguivi, were sequenced at a coverage of 30-60X, with the goal of investigating the evolution, population demography and domestication history of the species [10]. Population structure of eggplant germplasm based on Single Primer Enrichment Technology (SPET) genotyping : Within the G2P-SOL EU project (www.g2p-sol.eu), which brings together the major European (CGN, INRA, IPK, UPV) and Asian (AVRDC) gene banks, Universities and Research Centres, 2,912 S. melongena, 305 S. aethiopicum and 122 S. macrocarpon accessions as well as a set of 266 accessions belonging to 29 wild species have been inventoried. The Single Primer Enrichment Technology (SPET) genotyping, recently developed by Nugen® was applied for their targeted genotyping. Starting from more than 12K polymorphic sites found in both coding regions and in the introns/UTRs, a set of 5K best performing SPET probes was used for diversity analyses, and a panel of about 25K high confident (min mean read depth of 30 and max missing data of 0.5%) SNPs evenly distributed throughout the genome were detected. The FastSTRUCTURE analysis (Fig. 1) identified 9 main clusters (K), with S. melongena accessions grouping into 6 sub-clusters. Three further clusters were found, including accessions belonging to S. macrocarpon and S. aethiopicum as well as species belonging to the subgenus Solanum, in good agreement with clustering obtained with a maximum likelihood phylogenetic tree. A total of 1,114 accessions were finally classified as admixed. The first two components of the PCA (Fig. 2) explained about 26% of the genetic variation. The first axis, explaining 15% of the genetic variation separated S. macrocarpon from the other species. The second component grouped separately S. melongena and S. aethiopicum as well as species from the Leptostemonum and Solanum subgenera. Several accessions had an unclear assignment, presumably due to misclassifications in the genebanks or gene flow among species. The gathered information was used for the development of a core collection of genotypes for future Genome Wide Association (GWA) studies. For this purpose, 15 S. melongena accessions and 5 wild species will be re-sequenced at 30X with the goal of identifying new SNPs useful for high resolution SPET genotyping.
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Unlocking genomic diversity of pepper (Capsicum spp.) collections held in genebanks: perspectives for breeding and germplasm management
auteur
Tripodi P, L Barchi, Acquadro A, Schafleitner R, J. Prohens, M.J. Diez, Börner A, Bovy As, Jérémy Salinier, Boyaci Hf, Pasev G, Brouwer M, Wallace T, Kale S, Esposito S, Brandt R, E. Portis, Finkers R, Lanteri S, Paran I, Véronique Lefebvre, Giuliano G, Stein N
article
. 17th Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2019, Avignon, France. pp.1-3
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BACKGROUND The genetic diversity present in cultivars, landraces and wild relatives of modern crops, represents the source of agriculturally important genes to be discovered in our attempts of making crops more resilient and better adapted to the challenges of modern agriculture. In this context, genebanks are pivotal for the collection, preservation and distribution of germplasm; however, better knowledge of the available genetic variability would help improve the management of plant genetic resources. Here we report the analysis of genome-wide genotyping-by-sequencing (GBS) data on 9,659 pepper accessions retrieved from the major European (CGN, INRA, IPK, UPV) and Asian (AVRDC) genebanks, universities and research centres. The collection analyzed is so far the largest and the most diverse ever studied in pepper. The main objectives of this study are to: a) evaluate the genetic diversity using a large set of single-nucleotide polymorphism (SNP) data; b) detect the overlaps within collections and between genebanks; c) detect misclassification of accessions; d) develop core collections for association mapping studies. MATERIALS & METHODS Germplasm studied comprised 7,253 C. annuum accessions, 1,795 accessions belonging to the other four domesticated species (C. frutescens, C. chinense, C. baccatum, C. pubescens) and 43 accessions belonging to the wild species (Table 1). About 3% of the collection was represented by unknown species. Passport information and 42 phenotypic descriptors for plant, flower and fruit traits have been provided by genebank curators in order to enhance the description of plant material. A two restriction enzyme GBS protocol was used [1]; PstI-MspI have been selected based on in silico digestion of the reference genome accession (CM334) [2]. RESULTS GeGBS data provided more than 10,000 SNPs evenly distributed on the genome and used to characterize genetic diversity, population structure and phylogenetic relationships. The analysis allowed identifying five main clusters (K) corresponding to the most represented Capsicum species in the whole collection (Figure 1). Capsicum annuum was subdivided into two sub clusters and include admixed samples. Three other clusters were observed for C. baccatum, C. frutescens and C. chinense, respectively. The remaining species, including those corresponding to the group of purple flowers clustered in an admixed group. The principle component analysis (PCA) plot for the first two principal components suggests a geographical differentiation of the Caribbean, Central Asia and European gene-pools, and a distinction of the three main clades according to the most updated classification [3]. Moreover, the observed ~1,000 admixed accessions, and the incomplete separations between C. frutescens and C. chinense, revealed possible taxonomic misclassifications in the genebanks or gene flow between species resulting in introgressions. The genetic and phenotypic variation existing in the collection studied will be exploited for genome-wide association studies (GWAS). 178 Capsicum and Eggplant EUCARPIA Meeting 2019 | BG-O/03 DISCUSSION & CONCLUSION The genetic information provided in this study is appropriate for a deep investigation of the diversity present across the different Capsicum collections maintained by genebanks. Appropriate strategies including “germplasm genomics” can optimize the management of resources, the exchange of material between genebanks and their use for breeding purposes. Beyond genetic diversity, data can be used for the development of core collections to be exploited in GWAS, facilitating the identification of genomic regions associated with valuable traits and enhancing the efforts made by genebanks in the extensive collection and haracterization of Capsicum germplasm resources.
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titre
Comparative demographic study: reconstructing the evolutionary history of Solanaceae species to better understand the domestication process and outcome.
auteur
Stéphanie Arnoux, Christelle Fraïsse, Renaud Duboscq, Mathilde Causse, Christopher Sauvage
article
Capsicum and Eggplant EUCARPIA Meeting 2019, Sep 2019, Avignon, France
resume
Background: The process of domestication is an ideal framework to study the interplay of evolutionary forces that induced molecular changes over short-time scales. These changes can now be tracked at the genome-wide scale, offering a unique opportunity to decipher the most probable demographic scenarios that occurred and characterize them. In this context and for the first time in plant, we performed a comparative genomic approach to infer the parallelism in the evolutionary history of three major crop species of the Solanaceae family, the eggplant, the pepper and the tomato. In each species, we analyzed and compared the summary statistics of two groups of crop and wild accessions, constituting prior knowledge for demographic inferences. Inferring the demographic scenarios of these three species is an unprecedented opportunity to further characterize each domestication event duration, and therefore improve the inference of the demographic history that were hypothesized through indirect means (human and cultivation history of the areas, ancient written records). Material/Methods : To infer the past demographic events, scenarios of domestication were inferred from the comparison of site frequency spectrum in crop and wild groups. We implemented over 10 demographic models to test whether the divergence between the crop and wild groups occurred (i) in the absence/presence of gene flow, (ii) with gradual/instantaneous change in their effective population size, (iii) in one or two steps. For each species, the most probable scenario was selected according to its Akaike Information Criterion, and associated parameters and their precision were estimated. These parameters were translated to human timing by the use of a range of mutation rate to avoid any bias. Abstract: Results (maximum 1300 characters spaces included) : The comparative study of the demographic inferences modeling the domestication of the three species revealed common features of the domestication processes in the Solanaceae family. In the three species the presence of a bottleneck corroborates the stage of domestication related to cultivation. That specific stage induced a reduction in effective size due to the extraction of few individuals from their wild environment to cultivate them in human managed fields. The demographic models inferred the duration of the domestication event such as the divergence time between the crop and their wild relatives, or when occurred the bottleneck. Consequently, using two mutation rates we could provide a range of estimation: the eggplant domestication occurred 5,938-3,087 years ago, the pepper sampled allowed to estimate the stage of cultivation related to a bottleneck at 6,760-3,514 years before common era (BCE), and for the tomato the domestication seems to have occurred between 7,901 and 4,107 years BCE. Another parameter was the asymmetric gene flow between the wild and crop compartment. Our results highlight that both pepper and tomato have experienced a stronger gene flow from the wild to the crop compartment than crop to wild when it is the opposite for eggplant. Discussion and conclusion Overall, our study provides insights into the convergence of the domestication processes in the Solanaceae family. Our results point out the influence of sympatry and allopatry between the crop and the wild compartments to explain the gene flows. These inferences bring as well new details about the timing of domestication and therefore insights into human history and how and when societies domesticated species. It confirms the importance of understanding how plant species respond to human manipulation. By knowing the past behavior of crops facing domestication events, we may potentially improve modern breeding efforts to sustain future crop breeding.
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Mapping the intensity function of a point process in unobserved windows
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Edith Gabriel, Jérôme Coville, Joel Chadoeuf
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GRASPA, Jul 2019, Pescara, Italy
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Predicting the intensity function of point processes inside unobserved windows
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Edith Gabriel, Francisco Rodriguez-Cortes, Jérôme Coville, Jorge Mateu, Joel Chadoeuf
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Spatial statistics, Jul 2019, Sitges, Spain
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Development and validation of an SNP-based new set of markers useful for early selection for Sharka disease in apricot ( P. armeniaca )
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P. Lambert, C. Confolent, G. Roch, N. Dlalah, A. Remay, A. Bernole, Véronique Decroocq, C. Auvinet, J.M. Audergon
article
XVII International Symposium on Apricot Breeding and Culture, ISHS, Jul 2019, Malatya, Turkey. pp.47-52, ⟨10.17660/ActaHortic.2020.1290.9⟩
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Sharka disease, due to the Plum pox virus, is a major threat to apricot trees. Most of the accessions world-wide and particularly those cultivated in Western Europe and the Mediterranean area are susceptible to the disease. A few resistance sources have been identified to date in cultivars developed in the US from a basis of Central Asian germplasm, all of these sharing the same genomic region associated with resistance to sharka in chromosome 1. Based on this, Simple sequence repeats (SSR) markers framing the MATH genes possibly responsible for the resistance have been developed in this region and a set of 2 SSRs (PGS1.21 and PGS1.24) and an indel (ZP002) was selected for identifying and discarding susceptible individuals at the plantlet stage of the apricot breeding process. However SSR markers could be difficult to implement by small teams due to the investment in hands-on time and equipment. As a consequence we turned to single nucleotide polymorphisms (SNP) to develop an alternative set of markers that could be cheaper and more easily implemented. Taking advantage of the numerous apricot genomic-sequences available at the UGAFL, we identified resistant/susceptible SNP/indel haplotypes and developed a set of three primer triplets (SP353, SP870, and SP871) based on the competitive allele-specific PCR (KASP™) technique by LGC genomics. This set was validated using a wide range of apricot accessions from different geographic origins and genetic backgrounds, concurrently with the original set of three SSRs. The new set gave similar results as the SSR-based set, was more convenient and, as a result, is now routinely used for early selection of apricot seedlings in our breeding programs.
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Bioinformatique et reproductibilité au sein de l’unité Génétique et Amélioration des Fruits et Légumes (GAFL): mise en place et retour d'expérience.
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Jacques Lagnel
article
Journées du PEPI IBIS 2019, Jun 2019, Paris, France
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Genomic selection - which prospects in Prunus armeniaca?
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Mariem Nsibi, Carole Confolent, Barbara Gouble, Sylvie Bureau, Alain Blanc, Guillaume Roch, Patrick Lambert, Timothée Flutre, Jean-Luc Regnard, Christopher Sauvage, Jean Marc Audergon
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XVII International Symposium on Apricot Breeding and Culture, Jun 2019, Malatya, Turkey
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Evaluation of apricot fruit quality diversity in two countries, France and New Zealand
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Sylvie Bureau, C Scofield, Barbara Gouble, A Mcglone, H Boldingh, C Clark, Jean-Marc Audergon, J Stanley
article
XVII International Symposium on Apricot Breeding and Culture, Jun 2019, Malatya, Turkey
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Evaluation of apricot fruit quality diversity in two countries, France and New Zealand S. Bureau1, C. Scofield2, B. Gouble1, A. McGlone3, H. Boldingh3, C. Clark3, JM. Audergon4, J. Stanley2. 1 INRA, UMR408 Sécurité et Qualité des Produits d’Origine Végétale, Domaine Saint Paul, 228 Route de l’Aérodrome, CS 40509, F-84000 Avignon, France. 2 The New Zealand Institute for Plant and Food Research Limited, Clyde Research Centre, 990 Earnscleugh Rd, RD1, Alexandra 9391, New Zealand. 3 The New Zealand Institute for Plant and Food Research Limited, Ruakura Research Centre, Private Bag 3123, Hamilton 3240, New Zealand. 4 INRA, UR1052 Génétique et d’Amélioration des Fruits et Légumes, Domaine Saint Maurice, Allée des Chênes, CS 60094, F-84143 Montfavet cedex, France.Abstract New Zealand and French stonefruit industries desire new long-storing, sweet-tasting apricot cultivars. The climacteric nature of apricots (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 range of total soluble solids (TSS). Trials in FR and NZ shared the same research protocols, for optimal comparison and verification. Fifty genotypes representative of fruit diversity in each country were studied in June-July 2016 in FR and January-February 2017 in NZ. For each genotype, six fruit, 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, and skin color; and fruit tissue samples: Mid Infrared Spectroscopy (MIRS), TSS, titratable acidity (TA), and individual sugar and organic acid contents. A large diversity was observed for firmness, from 2 to 55 N in NZ and 2 to 36 N in FR. Ethylene production ranged from 0 to 996 nmol/h.kg in NZ and 0 to 3000 nmol/h.kg in FR, and discriminated between known low- and 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 3 to 514 meq/kg in NZ and 22 to 350 meq/kg in FR. Acceptable prediction of TSS and TA was observed for NIRS and of TSS, TA, and individual sugar and organic acid contents for MIRS. NIRS and MIRS have the ability for rapid fruit characterization and discrimination across countries. The fruit genetic variability opens new opportunities for the breeding programs.
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https://hal.inrae.fr/hal-03601883/file/Turq19_Gouble_FR%20NZ%20apricot%20fruit%20diversity_abstract.pdf BibTex
titre
Tomato breeding advances in genomic era
auteur
Mathilde Causse
article
Tomato News Conference, May 2019, Avignon, France
resume
The main advances in tomato breeding are presented
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titre
Analysis of the Tomato spotted wilt virus RNA-dependent RNA polymerase adaptative evolution and constrained domains using homology protein structure modeling
auteur
Zoé Terret, Grégori Bonnet, Benoît Moury, Jean-Luc Gallois
article
17. Rencontres de Virologie Végétale (RVV 2019), Jan 2019, Aussois, France. 127 p
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https://hal.inrae.fr/hal-02735593/file/2019_Terret_RVV_1.pdf BibTex
titre
Genome-wide association mapping of loci implied in Potato virus Y resistance and tolerance in the pepper germplasm
auteur
Lucie Tamisier, Ghislaine Nemouchi, Marion Szadkowski, Gregory Girardot, Renaud Duboscq, Sylvain Santoni, Sarah Gautier, Christopher Sauvage, Alain Palloix, Judith Hirsch, Benoît Moury
article
17. Rencontres de Virologie Végétale (RVV 2019), Jan 2019, Aussois, France. 127 p
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https://hal.inrae.fr/hal-02734804/file/2019_Tamisier_RVV_1.pdf BibTex
titre
Single Primer Enrichment Genotyping Highlights the Worldwide Population Structure of Tomato and Eggplant Germplasm.
auteur
Lorenzo Barchi, Alberto Acquadro, Ezio Portis, Sergio Lanteri, David Alonso, Pietro Gramazio, Santiago Vilanova, Maria Díez, Jaime Prohens, Jeremy Salinier, Véronique Lefebvre, Gancho Pasev, Stanislava Grozeva, Hatice Filiz Boyaci, Abdullah Unlu, Laura Toppino, Laura Bassolino, Giuseppe Rotino, Andreas Boerner, Ronny Brandt, Nils Stein, Richard Finkers, Arnaud Bovy, Roland Schafleitner, Davide Scaglione, Eleonora Di Centa, Sara Pinosio, Giuseppe Aprea, Paola Ferrante, Giovanni Giuliano
article
XXVII Plant and Animal Genome Conference, Jan 2019, San Diego (CA), United States
resume
G2P-SOL (http://www.g2p-sol.eu) is an EU-funded project, bringing together the main European and international genebanks hosting germplasm of the four major Solanaceous crops: potato, tomato, pepper and eggplant. 23,900 tomato and 5,900 eggplant accessions, including wild relatives of both crops, have been inventoried within the project. To gain information about population structure of the collections, the novel Single Primer Enrichment Technology (SPET, US Patent 9,650,628) developed by NuGEN was used for genotyping. An SNP/indel panel was developed by assaying 14k probes for tomato and 11k for eggplant, evenly distributed in the gene-rich regions, and selecting the 5k best performing probes for each species. DNA samples were prepared by the genebanks using pre-tested protocols, and genotyping partners (ENEA for tomato and University of Torino for eggplant) performed QC and sample normalization. Genotyping and sequencing was performed by IGA Technology Services. Reads were aligned to the eggplant and tomato reference genomes using BWA-MEM and SNP calling was performed using GATK-4.0. We report on the assessment of the genetic relationships in a wide set of tomato and eggplant accessions maintained in genebanks as well as the extent of duplications and possible mis-classifications. The results suggest that SPET genotyping is a reliable, high-throughput, low cost technology for genetic fingerprinting of crops, with a high degree of cross-transferability to their wild relatives. SPET-based higher density genotyping is being developed to characterize the core collections developed in G2P-SOL for GWAS analyses.
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https://hal.inrae.fr/hal-03551688/file/Barchi%202019%20PAG%20San%20Diego%20-%20oral.pdf BibTex

Other publications

titre
Carole Caranta, a smooth strategist
auteur
Carole Caranta, Nicole Ladet, Inge Laino
article
2019
resume
Head of a scientific division that brings together more than 70% of researchers in plant biology and breeding nationwide, Carole Caranta plays a key role in INRA’s research and partnership strategies. Her career is marked by a passion for science, openness to others, striking a balance between fundamental and targeted research, and forging socio-economic partnerships.
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titre
Gestion durable des résistances aux maladies chez la plante : quelle stratégie choisir ?
auteur
Elsa Ballini, Judith Hirsch, Benoît Moury, Loup Rimbaud, Anne-Marie Sage-Palloix
article
2019
resume
A l'INRA, l'équipe de recherche "Virologie" de Benoît Moury pose la question de l’efficacité des différentes stratégies d’utilisation des gènes de résistance aux maladies : pyramidage, rotation, mosaïque, mélange variétal…
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Poster communications

titre
Resistance against melon chlorotic mosaic virus and tomato leaf curl New Delhi virus in melon
auteur
Cecile Desbiez, Gustavo Romay, Hervé Lecoq, Catherine Wipf-Scheibel, Pauline Millot, Gregory Girardot, Michel Pitrat
article
International Advances in Plant Virology 2019, Oct 2019, Rome, Italy. 128 p., 2019, International Advances in Plant Virology 2019 at Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca Difesa e Certificazion Via C.G. Bertero 22, 00156 Roma Italy. Programme, abstracts & delegate list. 29-31 October 2019
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https://hal.inrae.fr/hal-02735214/file/2019_Desbiez_IntAdvPlantVirol_1.pdf BibTex
titre
Diversity of Tobacco etch virus pathotypes faced with pepper resistance sources and durability potential of resistance genes
auteur
Benoît Moury, Bülent B. Arpacı, Vincent Simon, Alain Palloix
article
17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2019, Avignon, France. INRA, Centre de recherche Provence-Alpes-Côte d’Azur, 263 p., 2019, Innovations in Genetics and Breeding of Capsicum and Eggplant. Proceedings of the 17th EUCARPIA Meeting on Genetics and Breeding of Capsicum and Eggplant September 11-13, 2019 | Avignon - France
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titre
Development of genome-wide KASPar markers from a comparative transcriptomic analysis for mapping QTLs associated with the pungent trait of pepper (Capsicum annuum L.)
auteur
Lihao Wang, J.P. Bouchet, Wang N, Zhang Z, A.M. Sage-Palloix, Y Cao, Zhang B, Alain Palloix, Véronique Lefebvre
article
17th Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2019, Avignon, France
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BACKGROUND Pepper (Capsicum spp.), belonging to the Solanaceae family, is an important vegetable crop worldwide owing to its nutritional value and flavor. There are five domesticated pepper species (C. annuum L., C. frutescens L., C. chinense Jacq., C. baccatum L., and C. pubescens Ruiz et Pav.) and more than 20 wild relative species. Global pepper production is approximately 34.5 million tons annually.Under the threat of a changing environment, new varieties with enhanced resistance to biotic and abiotic stresses are demanded by farmers. Marker-assisted selection (MAS) has been used to introduce new and desirable characters into plants, such as disease resistance. The lack of sufficient molecular markers for pepper has been a bottleneck for genetic and linkage studies [1]. MATERIALS & METHODS Transcriptomes from five C. annuum L. accessions (Yolo Wonder, CM334, Perennial, PM687 and PM217) were sequenced. Unigenes of CM334, Perennial, PM687, and PM217 were mapped to the reference transcriptome of Yolo wonder [1]. Positions of SNPs and their flanking sequences were extracted to design KASPar markers. A genetic map based on KASPars was constructed by using Joinmap 4 thanks to 113 F9-recombinant-inbred-lines (RIL) issued from the intraspecific cross ‘Perennial x 83-58’. Capsaicin and dihydrocapsaicin were quantified in the RIL progeny by ultra-high performance liquid chromatography (UPLC, Waters, USA) and a QTL analysis was performed by using the software MapQTL3.0. RESULTS Comparison of the erennial transcriptome with the Yolo Wonder transcriptome revealed 9,037 SNPs corresponding to 4,333 unigenes. Comparison of the transcriptomes of CM334, PM687, and PM217 with the Perennial transcriptome revealed 2,077 SNPs corresponding to 1,674 unigenes. We developed KBioscience Competitive Allele-Specific PCR (KASPar) markers for a set of SNPs. Out of the 975 KASPars developed, 303 (31%) were polymorphic between Perennial and 83-58. We constructed a genetic linkage map with 372 markers (including 278 KASPars) and detected quantitative trait loci (QTL) for the pungent trait (capsaicin and dihydrocapsaicin content) using the F9 RIL progeny. Four QTLs determining the capsaicin and dihydrocapsaicin content were identified. For traits related to the capsaicin content, one major QTL was located between marker BD76366 and Pun1 on chromosome P2; it explained 29% to 41.5% of the phenotyptic variation. Two minor QTLs located on chromosome P2 and P12 explained 8.0% and 11.0%. For the dihydrocapsaicin content, one major and two minor QTLs were located at the same positions as the QTLs of capsaicin content on chromosomes P2 and P12; an additional minor QTL located on chromosome P12 explained 9.9% of the phenotypic variation. DISCUSSION & CONCLUSION This research identified thousands of polymorphic positions among the genomes of pepper accessions. We developed KASPar markers covering the whole-genome and that can be used to locate QTLs or genes at any position. 31% of 975 KASPar markers were polymorphic; they were used to construct a molecular linkage map and identified QTLs associated with the pungent trait. The KASPar markers we have developed have potential value for pepper crop improvement and breeding for altered capsaicin content.
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https://hal.inrae.fr/hal-03551775/file/WangL%20%202019%20Eucarpia%20poster.pdf BibTex
titre
Phytophthora capsici aggressiveness toward pepper and tomato
auteur
Emmanuel Szadkowski, Alexandre Bachellez, Nasradin Touhami, Anne Massire, Dylan Storey, Kurt Lamour, Véronique Lefebvre
article
17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant (2019), Sep 2019, Avignon, France. 2019
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The fascinating diversity of pepper and eggplant collections held at the INRA Centre for Vegetable Germplasm
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Jérémy Salinier, Marie-Christine Brand-Daunay, J Goussopoulos, C Gros, Véronique Lefebvre
article
17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant (2019), Sep 2019, Avignon, France
resume
The INRA Unit for Genetics and Breeding of Fruit and Vegetables has carried out genetic research and breeding on pepper (Capsicum annuum L.) and eggplant (Solanum melongena L.) since 1962 and has progressively gathered numerous genetic resources, which are now managed by the INRA Centre for Vegetable Germplasm. Our goal is to present a comprehensive overview of the current content of both collections, including their wild and cultivated relatives.
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https://hal.inrae.fr/hal-02958665/file/The%20Fascinating%20Diversity%20of%20Pepper%20and%20Eggplant%20Collections%20held%20at%20the%20INRA%20Centre%20for%20Vegetable%20Germplasm.pdf BibTex
titre
Deciphering the genetic basis of tolerance to Cucumber mosaic virus in pepper
auteur
Judith Hirsch, Marion Szadkowski, Gregory Girardot, Allan Kampfer, Maxime Louis, Sandra Martin, Sabrina Azehaf, Yseult Cardona, Alexandra Schoeny, Pauline Millot, Catherine Wipf-Scheibel, Patrick Gognalons, Cecile Desbiez, Karine Nozeran, Eric Verdin, Alain Palloix, Benoît Moury
article
17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2019, Avignon, France. INRA, Centre de recherche Provence-Alpes-Côte d’Azur, pp.88, 2019, Innovations in Genetics and Breeding of Capsicum and Eggplant. Proceedings of the 17th EUCARPIA Meeting on Genetics and Breeding of Capsicum and Eggplant September 11-13, 2019 | Avignon - France
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https://hal.inrae.fr/hal-02737621/file/2019_Hirsch_Eucarpia_Capsicum_and_Eggplant.pdf BibTex
titre
Genetic architecture of robustness in Capsicum annuum for resistance to Phytophthora capsici and Potato virus Y under a temperature stress
auteur
Valentin Ribaut, Anne Massire, Judith Hirsch, Emmanuel Szadkowski, Loup Rimbaud, Bernard Caromel, Alexandre Bachellez, Nasradin Touhami, Marion Szadkowski, Benoît Moury, Véronique Lefebvre
article
17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2019, Avignon, France. INRA, Centre de recherche Provence-Alpes-Côte d’Azur, 263 p., 2019, Innovations in Genetics and Breeding of Capsicum and Eggplant. Proceedings of the 17th EUCARPIA Meeting on Genetics and Breeding of Capsicum and Eggplant September 11-13, 2019 | Avignon - France
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https://hal.inrae.fr/hal-02736058/file/2019_Ribaut_Eucarpia_1.pdf BibTex
titre
A high-density genotyping strategy based on gene capture in pepper: perspectives for genome wide association study and genetic mapping
auteur
Sonia Elbelt, Jacques Lagnel, Bernard Caromel, Jacques David, Judith Hirsch, Emmanuel Szadkowski, Benoît Moury, Caroline Caporalino, N. Stein, G. Giuliano, Véronique Lefebvre
article
17. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2019, Avignon, France. INRA, Centre de recherche Provence-Alpes-Côte d’Azur, 263 p., 2019, Innovations in Genetics and Breeding of Capsicum and Eggplant. Proceedings of the 17th EUCARPIA Meeting on Genetics and Breeding of Capsicum and Eggplant September 11-13, 2019 | Avignon - France
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https://hal.inrae.fr/hal-02737663/file/2019_Elbelt_Eucarpia_1.pdf BibTex
titre
COMPARISON BETWEEN TRADITIONAL AND MODERN FRESH MARKET TOMATO VARIETIES IN THREE EUROPEAN COUNTRIES: SENSORY ANALYSIS AND GENE EXPRESSION PROFILING
auteur
Fiorella Sinesio, Brigitte Navez, Mathilde Causse, Joan Casals, Romero del Castillo, Saggia Civitelli, Valentine Cottet, Antonio Granell, Silvana Grandillo
article
LXIII SIGA ANNUAL CONGRESS, Sep 2019, Napoli, Italy
resume
Tomato (Solanum lycopersicum L.) is one of the most important crops worldwide. Sensory quality of fresh market tomatoes is defined by numerous traits relating to appearance, flavour (taste and aroma) and textural properties. Widespread consumer complaints with the flavor quality of many modern commercial tomato varieties for fresh market have urged sensory quality to become a major breeding objective, and have also fostered the development of niche markets for heirloom, local or traditional varieties. In order to meet consumers’ demand, new breeding targets should be identified based on consumers’ preferences. To gain further insights into the factors underlying tomato sensory quality and driving consumers’ liking, within the framework of the European TRADITOM project (http://traditom.eu/), 17 traditional and modern fresh market tomato varieties, belonging to the typologies “Oxheart”, “Marmande” and “Round” were selected and different partially overlapping sets were grown and evaluated in France, Italy and Spain. Two different growing conditions were tested in France (soilless under greenhouse (HS) vs. soil under plastic tunnel (S)) and in Spain (open air (OA) vs. soil under greenhouse (G)), while in Italy the products were grown in soil under plastic tunnel, and were evaluated at two different ripening stages. In each country fruit quality was assessed at three levels: objective description of sensory properties by trained panels, consumer preference tests and physico-chemical measurements. To determine how consumers perceived the sensory characteristics of the different products, after the overall liking (OL), they were asked to answer a Check-All-That-Apply (CATA) survey, with 24 questions related to fruit appearance, flavor and texture. Principal component analysis (PCA) was carried out to describe the relationships between physicochemical and sensory variables and to identify sample groups. Overall a strong genotype effect on consumer OL was observed; while the effect of different growing conditions on OL was not significant. Correspondence Analysis run on the contingency tables of CATA attributes from each country allowed finding associations between tomato varieties and CATA attributes. Finally, transcriptional profiling of selected genes was conducted on all the samples by a mid-throughput Fluidigm RT-PCR platform. The main sensory and transcriptional profiling results will be discussed. This work was supported by the European Commission Horizon 2020 program (TRADITOM grant agreement no. 634561).
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titre
Development and validation of an SNP-based new set of markers useful for early selection for sharka disease in apricot (P. armeniaca)
auteur
Patrick Lambert, Carole Confolent, Guillaume Roch, Naïma Dlalah, Arnaud Remay, Anne Bernole, Véronique Decroocq, Clarisse Auvinet, Jean Marc Audergon
article
17. International Symposium on Apricot Breeding and Culture, Jul 2019, Malatya, Turkey. pp.1, 2019
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https://hal.inrae.fr/hal-02790319/file/SAM%20sharka_XVII%20apricot%20symposium_Lambert_1.pdf BibTex
titre
AllMine, a flexible pipeline for allele mining
auteur
Thomas Bersez, Jean-Luc Gallois, Jacques Lagnel
article
JOBIM (Journées Ouvertes Biologie, Informatique et Mathématiques), Jul 2019, Nantes, France
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titre
Lettuce lines with potyvirus resistance: differential set for study of strains and new genitors of resistance
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Brigitte Maisonneuve, Yannick Bellec, Eric Martin, Hervé Lot, Patrick Gognalons, Benoît Moury
article
9. International conference on genetics and breeding of leafy vegetables. Eucarpia Leafy Vegetables 2019, Jun 2019, Olomouc, Czech Republic. JOLA, v.o.s., pp.44-45, 2019, 9th International Conference on Genetics and Breeding of Leafy Vegetables. Eucarpia Leafy Vegetables 2019. Programme and Proceedings of Abstracts
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https://hal.inrae.fr/hal-03553254/file/Maisonneuve_HAL-INRAE.pdf BibTex
titre
Selections issued from CEP Innovation and CENTREX and INRA - Innovative apricot breeding program in France.
auteur
C Auvinet, C Pitiot, G Roch, A Blanc, F Gilles, G Clauzel, J Broquaire, B Gouble, S Bureau, Jean-Marc Audergon
article
XVII International Symposium on Apricot Breeding and Culture, Jun 2019, Malatya, Turkey. 1p
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https://hal.inrae.fr/hal-03600730/file/Turq19_Auvinet_Innovating%20breeding_poster.pdf BibTex
titre
Deciphering the genetic basis of tolerance to Cucumber mosaic virus in pepper
auteur
Judith Hirsch, Marion Szadkowski, Gregory Girardot, Allan Kampfer, Maxime Louis, Sandra Martin, Sabrina Azehaf, Yseult Cardona, Alexandra Schoeny, Pauline Millot, Catherine Wipf-Scheibel, Patrick Gognalons, Cecile Desbiez, Karine Nozeran, Eric Verdin, Alain Palloix, Benoît Moury
article
17. Rencontres de Virologie Végétale (RVV 2019), Jan 2019, Aussois, France. 127 p., 2019, 17èmes Rencontres de Virologie Végétale : RVV 2019
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titre
Identification and characterization of new resistance to viruses in Cucurbitaceae
auteur
Aimeric Agaoua, Cecile Desbiez, Verane Sarnette, Vincent Rittener, Catherine Dogimont
article
17. Rencontres de Virologie Végétale (RVV 2019), Jan 2019, Aussois, France. 127 p., 2019, 17èmes Rencontres de Virologie Végétale : RVV 2019
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Reports

titre
Réflexion prospective interdisciplinaire. Approches prédictives pour la biologie et l’écologie. Rapport de synthèse.
auteur
Carole Caranta, Hervé Monod, Hugues Berry, Michaël Chelle, Michel Génard, Fabien Jourdan, Christian Lannou, Emmanuelle Maguin, Françoise Médale, Sylvie Oddou-Muratorio, Claire Rogel Gaillard, Jan Traas
article
[Autre] INRA. 2019, 40 pp
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https://hal.inrae.fr/hal-02791153/file/0-RapportBiolPredict_Dec2019_final.pdf BibTex

2018

Conference papers

titre
Contribution of Oxford NanoPore technology for the de novo genome assembly of nonmodel species: the case of the Asian ladybird Harmonia axyridis
auteur
Jacques Lagnel, Arnaud Estoup, Cecile Donnadieu, Celine Lopez-Roques, Maxime Manno, Anne Loiseau, Mathieu Gautier
article
Réunion France Génomique, Nov 2018, Evry, France
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Aphid triggered immunity in melon: key determinants for durable resistance to virus and aphids
auteur
Nathalie Boissot
article
Cucurbitaceae 2018, University of California [Davis] (UC Davis). USA., Nov 2018, Davis, United States
resume
The Vat gene in melon is unique in conferring resistance to both A. gossypii and the viruses it transmits. This double phenotype is controlled by a cluster of genes including a 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 Vat gene structure suggests a functioning so called effector-triggered immunity (ETI), with separate recognition and response phases. During the recognition phase, the VAT protein is thought to interact (likely indirectly) with an aphid effector introduced by aphid salivation within the plant cells. 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, the levels of miRNAs are modified. At the plant level, resistance to aphids is quantitative (aphids escape the plant and display low rates of reproduction). ‘Aphid-ETI’ has qualitative and local effect against non circulative viruses (CMV, ZYMV, WMV) and but quantitative effect against circulative virus such as CABYVs. Durability of ETI is highly variable. At population level, ‘Aphid-ETI’ reduces aphid density and genetic diversity, and durability of the ‘Aphid-ETI’ strongly depends on the agro-ecosystem. Some clones are adapted to Vat resistance, putatively either by introducing a polymorphic effector not triggering ETI, or by adapting to the defenses they triggered. Several ways to enhance ‘Aphid-ETI’ durability will be proposed. ‘Aphid-ETI’ against viruses decreases the intensity of Cucumber Mosaic Virus (CMV) and Cucurbit aphid-borne yellows virus (CABYV) epidemics. Laboratory experiments strongly suggested that non circulative viruses cannot adapt to ‘Aphid-ETI’ and therefore durability of ‘Aphid-ETI’ against CMV is predicted long. Field experiments combined to modelling suggested that highly durable resistance against CABYV could be obtained by combining within a same melon genotype the Vat gene with recessive genes conferring resistance to CABYV. Extension of those results to any other circulative viruses will be discussed.
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https://hal.inrae.fr/hal-02734670/file/Cucurbit%202018%20Summary%20NBoissot_1.pdf BibTex
titre
The G2P-SOL project: harnessing the genetic and phenotypic diversity of the four major Solanaceae crops
auteur
Giovanni Giuliano, Véronique Lefebvre, , On Behalf of The G2p-Sol Consortium
article
15th Solanaceae Conference, Sep 2018, Chiang Mai, Thailand
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titre
Single Primer Enrichment genotyping highlights the worldwide population structure of tomato and eggplant germplasm.
auteur
Lorenzo Barchi, A. Acquadro, Ezio Portis, Sergio Lanteri, David Alonso, P. Gramazio, Santiago Vilanova, Maria José Diez, Jaime Prohens, Jérémy Salinier, Véronique Lefebvre, Laura Toppino, L. Bassolino, Giuseppe Rotino, D. Scaglione, Dicenta E., S. Pinosio, Giuseppe Aprea, Paola Ferrante, Giovanni Giuliano
article
15th Solanaceae Conference, Sep 2018, Chiang Mai, Thailand
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titre
Impact of heating location, forced ventilation and screens on the energy efficiency and condensation risks inside a cucumber greenhouse.
auteur
Pierre-Emmanuel Bournet, Eric Brajeul, Vincent Truffault, Etienne Chantoiseau, R. Naccour
article
XXX International Horticultural Congress IHC2018: III International Symposium on Innovation and New Technologies in Protected Cultivation, International Society for Horticultural Science: ISHS, Aug 2018, Istambul, Turkey. 8p., ⟨10.17660/ActaHortic.2020.1271.4⟩
resume
In the West of France, greenhouse cucumber production is largely developed. Heating makes it possible to maintain a high level of production, but with high energy costs. Growers therefore try to implement new crop management practices to increase the energetic efficiency while keeping good productivity and quality. In this prospect, two treatments were tested considering two greenhouse compartments (307 m2): one with heating tubes at the upper limit of the canopy and a thermal screen (control) and the second one with heating tubes at low position inside the canopy, mechanical ventilation (5 volumes h-1) and thermal + shading screens (innovative). These compartments were equipped with sensor chains, each with four pairs of temperature and humidity probes at four levels. Additional thermocouples measured fruit temperatures. The energy consumption of the compartments was also assessed. Measurements were conducted over a three-month period of time. Results show that a better homogenization of the distributed climate was reached inside the innovative treatment. Also, the innovative treatment made it possible to significantly reduce risks of condensation on fruit compared to the control. Finally, in the innovative compartment, the energy efficiency was notably increased compared to the conventional management, generating the same yield, but saving 17% of the energy. The innovative crop management therefore demonstrated the benefits of the fans combined with low level heating and double screens.
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OSCAR, a national observatory to support the deployment of new grapevine disease resistant varieties in France
auteur
François Delmotte, Soizic Guimier, Isabelle Demeaux, Carole Couture, Christophe J. Schneider, Rémy Cailliatte, Laurent Audeguin, Frédéric Fabre, Laurent Deliere
article
12. International Conference on Grapevine Breeding and Genetics (ICGBG), Jul 2018, Bordeaux, France. 306 p
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Apport de la technologie Oxford NanoPore pour l’assemblage de novo du génome d’espèces non-modèles : le cas de la coccinelle asiatique Harmonia axyridis
auteur
Jacques Lagnel, Arnaud Estoup, Cecile Donnadieu, Celine Lopez-Roques, Maxime Manno, Anne Loiseau, Mathieu Gautier
article
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM 2018), Société Française de Bio-Informatique (SFBI). FRA. GdR 3003 Bioinformatique Moléculaire (GdR BiM), FRA. Institut Français de Bioinformatique (IFB), FRA. Aix Marseille Université (AMU), FRA. Institut National de la Santé et de la Recherche Médicale (INSERM), FRA. Centre National de la Recherche Scientifique (CNRS), FRA., Jul 2018, Marseille, France
resume
La technologie de séquençage long fragments d'Oxford NanoPore (ONT) est basée sur le séquençage des acides nucléiques via le passage de molécules uniques au travers de nano pores protéiques et permet l’obtention de séquences de plusieurs dizaines de kilobases. Elle a très récemment connu une phase exponentielle de développement et son champ d'application s’est élargi à de nombreux domaines de la génomique et notamment l’assemblage de génome de novo. La coccinelle H. axyridis originaire d'Asie, a été introduite pour être utilisée comme agent de lutte biologique mais a établi des populations invasives en Amérique, en Europe et Afrique du Sud. H. axyridis est devenue une espèce modèle pour l’exploration du déterminisme génétique des caractères impliqués dans le succès invasif de certaines populations. D’autre part, avec plus de 200 morphes de couleur d'élytres contrôlés par un seul locus multi-alléliques, H. axyridis est également une espèce emblématique pour l’étude du déterminisme génétique du polymorphisme de couleur. Néanmoins, mener à bien la caractérisation de l’architecture génétique de ces différents caractères d’intérêt nécessite de disposer de ressources génomiques riches et notamment d’assemblages de génome de bonne qualité (la taille haploïde du génome de H. axyrridis étant estimée à 400 Mb). Suite aux résultats relativement décevants en termes de qualité d’assemblage obtenus à partir de données Illumina classiques (séquençage de banques en PE et MP), nous avons généré des séquences longues issues de la technologie ONT (4 flowcells MinIon, 65X, GeT-PlaGe, INRA-Genotoul, France). Un assemblage de novo a été réalisé en combinant ces longs reads ONT avec des reads courts d’Illumina. Plus précisément, le pipeline d'assemblage comprenait une correction des reads initiaux avec le programme bioinformatique Canu suivi d’un assemblage avec SMARTdenovo. L’assemblage ainsi généré présentant un taux riche en délétions d'homopolymères, une étape de polissage a été réalisée avec des lectures Illumina (banques PE et MP). In fine, la contiguïté de notre assemblage est 200 fois supérieure à notre assemblage initial. La moitié du génome obtenu est contenue dans des séquences génomiques de plus de 1,4 Mb avec une complétude évaluée par l’alignement de gènes orthologues conservés (BUSCO) de plus de 95.5%. Enfin, un contig de 1.3Mb nous a permis une résolution moléculaire fine d’une région du génome de 200 kb caractérisée par un grand nombre de SNPs signant des variations moléculaires importantes spécifiques des différents morphes de couleur d’H. axyridis. L’utilisation de la technologie ONT pour l’assemblage de novo de notre espèce non-modèle s’est ainsi révélée d’un excellent rapport qualité/prix.
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Exploring the genetic variability of peach skin phenolics and triterpenoids as natural defenses against brown rot
auteur
Bénédicte Quilot-Turion, Silvia Scariotto, Marie Noëlle Corre, Leandro de Oliveira-Lino, Véronique Signoret, Maximiliano Dini Vinoly, Lorraine Latchoumane, Maria Do Carmo Raseira, Jean-Luc Poëssel
article
9. International Rosaceae Genomics Conference, Nanjing Agricultural University (NAU). Nanjing, CHN., Jun 2018, Nanjing, China
resume
Brown rot caused by Monilinia spp. provokes dramatic losses of peach in all production regions. In this context, the general objective of our work is to develop sustainable ways to fight against this damaging disease. This study explored phenolic and triterpenoid diversity of fruit skin together with brown rot resistance. A Brazilian peach collection and an interspecific cross between P. davidiana and P. persica, each of 120 genotyped individuals, have been screened for 3 years, for susceptibility to M. fructicola and to M. laxa respectively. Some genotypes of the two populations showed low or null infection the 3 years. Secondary compounds of fruit skin of all genotypes were analyzed two years by HPLC-DAD. Depending on the genotypes, 30 to 40 compounds including triterpenoids, hydroxycinnamic derivatives and flavonoids, were quantified and around 20 were identified by mass spectrometry. Among these, phenolic esters of triterpenoids were identified for the first time in peach fruit. The correlation of quantitative data between years showed their robustness. A large diversity in contents of the compounds was observed. The association and QTL analyses proved to be complementary and led to assumptions about the co-locations of loci controlling different traits, especially for compounds with differential levels in the skin of peaches and nectarines. These analyses will help deciphering the genetic control of fruit skin phenolics and triterpenoids and pave the way to the identification of the underlying genes. Detection of loci related to resistance will provide tools for the implementation of marker assisted selection. Correlations between compounds and infection traits led us to hypothesize that some compounds from peach skin could play a role in the brown rot control. The fungicide activity of these compounds is being tested in vitro.
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https://hal.inrae.fr/hal-02791339/file/C387B32D-49F8-4752-8155-1DE74807FE2F_1 https://hal.inrae.fr/hal-02791339/file/Abstract_2 BibTex
titre
Genomic selection - which prospects in Prunus armeniaca? Preliminary results issued from fruit quality traits and phenology
auteur
Mariem Nsibi, Carole Confolent, Barbara Gouble, Sylvie Bureau, Alain Blanc, Guillaume Roch, Patrick Lambert, Timothée Flutre, Jean-Luc Regnard, Christopher Sauvage, Jean Marc Audergon
article
9. International Rosaceae Genomics Conference, Jun 2018, Nanjing, China
resume
Genomic selection (GS) refers to a selection method which intends to assess individuals according to their genomic values using genome-wide dense markers. Particularly efficient in animal improvement strategies, opening interesting perspective in crops, it is already engaged in perennial species such as apple where, genetic gain was maximized for fruit quality traits quantitatively inherited by comparison with conventional breeding strategy. In the present work, GS was applied on a biparental apricot population (184 individuals) characterized over two consecutive years for phenology (blooming and maturity dates) and fruit quality traits (fruit weight, color, sugar nd acidity content, ethylene production). A ridge regression (RR-BLUP) modelling has been used. The performance of GS was assessed by cross validation using the accuracy defined as the correlation between true phenotypes values and the estimated ones. The effects of markers density and number, training set size and composition as well as the heritability of the investigated traits were evaluated on the accuracy of the model. The main results issued from the two years multi-annual modelling approach are showing that (i) genomic predictions are accurate even with a little number of markers (>100 markers), (ii) the accuracy increases with the training population’s size and with high heritability traits, (iii) and the optimization of the training set improves the performance of genomic selection model. To conclude, a clear interest exists in continuing the evaluation of the genomic selection in biparental apricot populations even for traits that are difficult to measure. The robustness of the approach needs to be tested both on other progenies and on a large set of genetic resources
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https://hal.archives-ouvertes.fr/hal-01830311/file/Apricot%20Selgen_MNsibi_Abstract_1.pdf BibTex
titre
Resistance to sharka in Stone Fruit trees : Genetic and genomic technologies for new breeding strategies
auteur
Véronique Decroocq, Stephane Decroocq, David Tricon, Timothée Flutre, Thierry Pascal, Christophe Tuero, J. Salava, S. Liu, W.S. Liu, J. Rubio, E. Sanchez, H. Prieto
article
9. International Rosaceae Genomics Conference, Jun 2018, Nanjing, China
resume
Resistance to sharka in Stone Fruit trees : Genetic and genomic technologies for new breeding strategies. 9. International Rosaceae Genomics Conference
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https://hal.archives-ouvertes.fr/hal-01819033/file/DecroocqV%20Resistance%20to%20sharka%20in%20Stone%20Fruit%20trees_1.pdf BibTex
titre
Lutte contre les pucerons des cultures maraichères sous abris : Méthode de production d’auxiliaires
auteur
Christophe Giraud
article
Rencontre EMBA (Ecological Management of Bioagressors in Agroecosystems) 2018, Jun 2018, Montpellier, France
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Towards an integrative modeling approach for peach ideotype design adapted to sustainable agriculture
auteur
Bénédicte Quilot-Turion
article
2. trilateral INUPRAG symposium, Umea Plant Science Centre (UPSC). SWE., Jun 2018, Barcelone, Spain
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https://hal.inrae.fr/hal-02791337/file/UNIPRAG%202018%20Meeting%20Program_1 BibTex
titre
Pest and pathogen resistance in peach
auteur
Patrick Lambert
article
Organic Farming Reasearch and Perspectives (ORGANIST), May 2018, Milan, Italy. pp.24
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https://hal.inrae.fr/hal-02791308/file/2018_Lambert_Organist_1.pdf BibTex
titre
eIF4E-mediated resistance to viruses: from natural variation to synthetic alleles
auteur
Jean-Luc Gallois, Anna Bastet, Camille Gauffier, Christophe Robaglia, Carole Caranta
article
Embo workshop Target of rapamycin (TOR) signaling in photosynthetic organisms, EMBO. Heidelberg, DEU., May 2018, Bischoffsheim, France
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Genotype by environment interaction in tomato grown under several abiotic stresses and the genetic basis of plasticity
auteur
Isidore Diouf, Laurent Derivot, Shai Koussevitzky, Yolande Carretero, Frédérique Bitton, Mathilde Causse
article
XIX EUCARPIA Meeting of the Tomato Working Group, May 2018, Napoli, Italy
resume
Abiotic stresses and cultural conditions can lead to different performances of a given genotype when exposed to different environments. The ability of a genotype to change its phenotype is called phenotypic plasticity and has received great interest these last decades. Plant geneticists are aware of the importance of measuring phenotypic plasticity and assessing its genetic basis for breeding purposes. In order to analyse the impact of several stress conditions at the genetic level, we grew a multi-parental tomato population in12 distinct environments. The environments that were located in Israel, France and Morocco comprised optimal cultural conditions and water deficit, salinity and heat stress conditions. Quantitative trait loci (QTL) mapping analysis was performed on these data in three step: (i) main effect QTL were mapped on the trait means for each environment separately; (ii) QTL x Treatment effect were mapped on ‘Treatment specific plasticity’ measured as the difference between the optimal and stressed treatment; (iii) plasticity QTL were mapped based on the Finlay–Wilkinson’s regression slope. Results of phenotypic analysis and QTL detection will be presented as well as some attempt at identifying candidate genes for QTL for plasticity traits.
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https://hal.inrae.fr/hal-03562885/file/Causse_oral_Abstract_form_EUCARPIA%20TOMATO%202018.pdf BibTex
titre
Genomic selection for fruit quality and yield in tomato.
auteur
Jiantao Zhao, Christopher Sauvage, Mathilde Causse
article
XIX EUCARPIA Meeting of the Tomato Working Group., May 2018, Napoli, Italy
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https://hal.inrae.fr/hal-03543135/file/Zhao_Abstract_form_EUCARPIA%20TOMATO%202018.pdf BibTex
titre
Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance
auteur
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
20. Journées Francophones de Virologie 2018, Société Française de Virologie (SFV). FRA., Mar 2018, Paris, France
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Apport de la technologie Oxford NanoPore pour l’assemblage de novo du génome d’espèces non-modèles : le cas de la coccinelle asiatique Harmonia axyridis
auteur
Jacques Lagnel, Arnaud Estoup, Cecile Donnadieu, Celine Lopez-Roques, Maxime Manno, Anne Loiseau, Mathieu Gautier
article
Montpellier Omics days 2018, Université de Montpellier (UM). Montpellier, FRA., Feb 2018, Montpellier, France
resume
La technologie de séquençage long fragments d'Oxford NanoPore (ONT) est basée sur le séquençage des acides nucléiques via le passage de molécules uniques au travers de nano pores protéiques et permet l’obtention de séquences de plusieurs dizaines de kilobases. Elle a très récemment connu une phase exponentielle de développement et son champ d'application s’est élargi à de nombreux domaines de la génomique et notamment l’assemblage de génome de novo. La coccinelle H. axyridis originaire d'Asie, a été introduite pour être utilisée comme agent de lutte biologique mais a établi des populations invasives en Amérique, en Europe et Afrique du Sud. H. axyridis est devenue une espèce modèle pour l’exploration du déterminisme génétique des caractères impliqués dans le succès invasif de certaines populations. D’autre part, avec plus de 200 morphes de couleur d'élytres contrôlés par un seul locus multi-alléliques, H. axyridis est également une espèce emblématique pour l’étude du déterminisme génétique du polymorphisme de couleur. Néanmoins, mener à bien la caractérisation de l’architecture génétique de ces différents caractères d’intérêt nécessite de disposer de ressources génomiques riches et notamment d’assemblages de génome de bonne qualité (la taille haploïde du génome de H. axyrridis étant estimée à 400 Mb). Suite aux résultats relativement décevants en termes de qualité d’assemblage obtenus à partir de données Illumina classiques (séquençage de banques en PE et MP), nous avons généré des séquences longues issues de la technologie ONT (4 flowcells MinIon, 65X, GeT-PlaGe, INRA-Genotoul, France). Un assemblage de novo a été réalisé en combinant ces longs reads ONT avec des reads courts d’Illumina. Plus précisément, le pipeline d'assemblage comprenait une correction des reads initiaux avec le programme bioinformatique Canu suivi d’un assemblage avec SMARTdenovo. L’assemblage ainsi généré présentant un taux riche en délétions d'homopolymères, une étape de polissage a été réalisée avec des lectures Illumina (banques PE et MP). In fine, la contiguïté de notre assemblage est 200 fois supérieure à notre assemblage initial. La moitié du génome obtenu est contenue dans des séquences génomiques de plus de 1,4 Mb avec une complétude évaluée par l’alignement de gènes orthologues conservés (BUSCO) de plus de 95.5%. Enfin, un contig de 1.3Mb nous a permis une résolution moléculaire fine d’une région du génome de 200 kb caractérisée par un grand nombre de SNPs signant des variations moléculaires importantes spécifiques des différents morphes de couleur d’H. axyridis. L’utilisation de la technologie ONT pour l’assemblage de novo de notre espèce non-modèle s’est ainsi révélée d’un excellent rapport qualité/prix.
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titre
VARIATION GENETIQUE ET POTENTIEL D’AMELIORATION DE LA QUALITE NUTRITIONNELLE DES LEGUMES
auteur
Mathilde Causse
article
Association des Sélectionneurs Francais, Feb 2018, Paris, France
resume
Les espèces potagères représentent un groupe d’espèces très hétérogènes, présentant des compositions en phytonutriments très variées. Leur consommation est reconnue comme favorable à l’équilibre nutritionnel et la santé. De nombreuses sources de variation des teneurs en phytonutrients existent (d’ordre physiologique, génétique ou liées aux conditions de production, de récolte, de conservation et de consommation), mais la variation génétique en est souvent la principale. La sélection directe a surtout porté sur l’élimination de composés antinutritionnels ou défavorables plutot que sur l’améliration de teneurs en composés spécifiques. Avec l’avènement des marqueurs moléculaires et de la génomique, les voies de synthèse de la plupart des composés importants ont été disséquées, notamment chez la tomate et de nombreux QTL cartographiés. Quelques gènes ont pu être caractérisés. Le recours aux biotechnologies pour la biofortification a également été envisagé.
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https://hal.inrae.fr/hal-03562894/file/ASF2018_Causse.pdf BibTex
titre
Infrared spectroscopy as a rapid tool to assess apricot fruit quality: comparison of two strategies for a model establishment
auteur
Sylvie Bureau, Catherine Renard, Z. Fakhfackh, Jean Marc Audergon
article
16. International Symposium on Apricot Breeding and Culture, International Society for Horticultural Science (ISHS). INT., 2018, Shenyang, China. pp.5, ⟨10.17660/ActaHortic.2018.1214.24⟩
resume
Infrared spectroscopy is known as a rapid tool to study apricot fruit quality, non-destructively by near-infrared ( NIR, 800-2500 nm) range and destructively on fruit puree by mid-infrared ( MIR, 4000-650 cm(-1)) range. These techniques appear suitable for the determination of soluble solids content ( SSC) and titratable acidity ( TA). However, a major drawback is the need to repeatedly establish calibration equations, which can depend on cultivar, year, etc. The objective here was to evaluate the robustness of NIR and MIR techniques and to determine the best strategy: is it more efficient to build models every year or to build global models combining all years? Eight apricot cultivars, representative of the known apricot diversity for quality traits, have been analysed between 2005 and 2011. The most efficient strategy ( i. e., reliable calibration with a minimum of calibration) was a multi-year model, integrating a limited amount of fruit per year but incremented each year.
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Other publications

titre
Explore the best sugar factory: the fruit
auteur
Elsa Desnoues, Michel Génard, Bénédicte Quilot-Turion, Valentina Baldazzi
article
2018
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https://hal.inria.fr/hal-01953091/file/Desnoues_TheScienceBreaker18.pdf BibTex

Poster communications

titre
Projets IVD INRA-AgriObtentions variétales pour les légumineuses à graines
auteur
Nathalie Moutier, Mathieu Floriot, Eric Hanocq, Pascal Marget, Rémy Cailliatte, Isabelle Lejeune-Henaut
article
RFL2 Rencontres Francophones Légumineuses, Oct 2018, Toulouse, France. 2018
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titre
eIF4E-mediated resistance to viruses: from natural variation to synthetic alleles
auteur
Jean-Luc Gallois, Anna Bastet, Nathalie Giovinazzo, Camille Gauffier, Christophe Robaglia
article
International Conference on Arabidopsis Research ICAR 2018, Jun 2018, TURKU, Finland. 2018
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. As a proof of concept, we show in Arabidopsis how such trans-species synthetic gene design allows resistance pyramiding and broad spectrum engineering of virus resistance in plants at no yield loss.
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Poster communications
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https://hal.inrae.fr/hal-02734736/file/Gallois%20ICAR%202018_1.pdf BibTex
titre
Genome-wide association study of partial resistance to bacterial canker of apricot
auteur
Mariem Omrani, Guillaume Roch, Alain Blanc, Cindy E. Morris, Jean Marc Audergon
article
PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. 2018
resume
Apricot, a highly valuable crop is threatened by the growing importance of bacterial canker caused by Pseudomonas syringae. Among the key factors able to control the disease, genetic improvement is a promising measure. The variability of susceptibility on branches and the characterization of genetic determinants through a genome wide association study were thus investigated on a core-collection. 73 accessions were annually inoculated in the orchard with an aggressive strain of the bacterium for 4 years. Phenotypic data about the length of both external canker (lgc) and superficial browning (bs) of tissues were collected. The analysis displayed a highly environmental-dependent genetic variation with broad-sense heritabilities of lgc and bs reaching respectively 59% and 78% for the most severe year. Considering the two variance-maximizing years, genetic (G) and genetic x year (GxY) BLUP were predicted for each variable using a linear mixed model. Association analysis were performed with a 63,236 SNP set through both a multi-variate (GEMMA) and a multi-locus genome-wide analysis. By exploiting the between-years (multi-locus model on G and GxY terms) and between-phenotypes (multivariate model on lgc-bs G terms) correlations, 11 significant associations have been detected. Among them, two SNP impacting both lgc and bs expressions over the two studied years and explaining 41% and 31% of the total phenotypic variance were identified on chromosomes 5 and 6. A long-range linkage disequilibrium had been noticed between these two markers suggesting a co-selection effect. The associated SNP reported from this work will open up new opportunities for a Marker-assisted selection strategy.
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Reports

titre
Compte rendu de fin de contrat de recherche, Contrat LactuMel CTPS-CASDAR C-2013-02 : Recherche de résistance aux nématodes à galles chez la laitue
auteur
Brigitte Maisonneuve
article
[Contrat] Gautier semences; Rijk Zwaan; Association Provençale de Recherche et d'Expérimentation Légumière (APREL); Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL); Groupe de Recherche en Agriculture Biologique (GRAB). 2018
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Preprints, Working Papers, ...

titre
Characterization of the early response of Arabidopsis thaliana to Dickeya dadantii infection using expression profiling.
auteur
Frédérique van Gijsegem, Frederique Bitton, Anne-Laure Laborie, Yvan Kraepiel, Jacques Pédron
article
2018
resume
To draw a global view of plant responses to interactions with the phytopathogenic enterobacterale Dickeya dadantii, a causal agent of soft rot diseases on many plant species, we analysed the early Arabidopsis responses to D. dadantii infection. We performed a genome-wide analysis of the Arabidopsis thaliana transcriptome during D. dadantii infection and conducted a genetic study of identified responses. A limited set of genes related to plant defence or interactions with the environment were induced at an early stage of infection, with an over-representation of genes involved in both the metabolism of indole glucosinolates (IGs) and the jasmonate (JA) defence pathway. Bacterial type I and type II secretion systems are required to trigger the induction of IG and JA-related genes while the type III secretion system appears to partially inhibit these defence pathways. Using Arabidopsis mutants impaired in JA biosynthesis or perception, we showed that induction of some IG metabolism genes was COI1-dependent but, surprisingly, JA-independent. Moreover, characterisation of D. dadantii disease progression in Arabidopsis mutants impaired in JA or IG pathways showed that JA triggers an efficient plant defence response that does not involve IGs. The induction of the IG pathway by bacterial pathogens has been reported several times in vitro. This study shows for the first time, that this induction does indeed occur in planta, but also that this line of defence is ineffective against D. dadantii infection, in contrast to its role to counteract herbivorous or fungal pathogen attacks.
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https://hal.inrae.fr/hal-02786599/file/2018-van-gijsegem-BioRxiv_1.pdf BibTex

2017

Conference papers

titre
Contournement de la résistance Vat : un peu, beaucoup, pas du tout
auteur
Nathalie Boissot, Pascale Mistral, Virginie Chareyron, Alexandra Schoeny, Hervé Lecoq, Pauline Millot, Flavie Vanlerberghe-Masutti
article
10. journées réseau Biologie et Adaptation des Pucerons et Organismes Associés (BAPOA), Nov 2017, Colmar, France
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titre
Résistance aux pucerons chez le melon et durabilité
auteur
Nathalie Boissot, Alexandra Schoeny, Cecile Desbiez, Frédéric Fabre, Flavie Vanlerberghe-Masutti
article
10. Rencontres du GIS PICLég, Groupement d'Intérêt Scientifique pour la Production Intégrée en Cultures légumières (Gis Piclèg). FRA., Nov 2017, Marseille, France
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https://hal.inrae.fr/hal-02789645/file/Gis%20Picleg%202017_1 BibTex
titre
Characterization of the RMja resistance gene to root-knot nematodes from the Alnem almond rootstocK
auteur
Henri Duval
article
7. ISHS symposium on Almond, International Society for Horticultural Science (ISHS). INT., Nov 2017, Adélaïde, Australia
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titre
Projet LactuMel, Recherche de résistance aux nématodes à galles chez la laitue
auteur
Brigitte Maisonneuve
article
Restitution de Projets CTPS (CASDAR semences), Comité Technique Permanent de la Sélection (CTPS). FRA. Institut National de la Recherche Agronomique (INRA), FRA., Oct 2017, Paris, France
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titre
Evaluer la sélection génomique au sein de croisements bi-parentaux d’espèces pérennes fruitières génotypés par séquençage : point d’étape du projet FruitSelGen
auteur
Timothée Flutre, Amandine Launay, Caroline Denance, Helene Muranty, Jean Marc Audergon, Carole Confolent, Patrick Lambert, Bénédicte Quilot-Turion, Pierre-François Bert, Elisa Marguerit, Elisabeth Dirlewanger, José Quero-Garcia, Stephane Decroocq, Véronique Decroocq, Gisele Butterlin, Eric Duchêne, Evelyne Costes, Jean-Jacques Kelner, Benoit Pallas, Pierre Mournet
article
Séminaire SelGen 2017 : "La sélection génomique, bilan et perspectives", Sep 2017, Paris, France. pp.1
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https://hal.archives-ouvertes.fr/hal-01819030/file/2017-09_TFlutre_s%C3%A9minaire-Selgen-Paris_poster-FruitSelGen_1.pdf BibTex
titre
InnoVarTom. Dégradation de la qualité gustative des tomates : un problème de réputation collective ?
auteur
Olivier Bonroy, Mathilde Causse, Aline Fugeray-Scarbel
article
Séminaire SelGen 2017 : "La sélection génomique, bilan et perspectives", Sep 2017, Clichy, France. 1 p
resume
La sélection génomique pourrait permettre de mieux sélectionner les tomates sur le critère de la qualité gustative. Or actuellement, quand une innovation « gustative » (nouvelle typologie de tomate orientée goût) est mise sur le marché, elle perd au fil du temps sa qualité. L’objectif du projet InnoVarTom est de déterminer, à partir d’entretiens semi-directifs, si cette dégradation de la qualité gustative des tomates peut être liée à un problème de détérioration de la réputation collective dans la filière. Nous montrons que les conditions de dégradation de la réputation collective se vérifient effectivement dans la filière tomate.
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https://hal.archives-ouvertes.fr/hal-01595680/file/Poster-Innovartom-Bonroy2017_1.pdf BibTex
titre
Variation in phenylpropanoid intermediates associated with adaptation to abiotic stress in the perennial tree species Prunus persica and P. armeniaca
auteur
A. O. Conrad, T. Zhebentyayeva, M. Staton, Jean Marc Audergon, Véronique Decroocq, Z. Liu, C. D. Dardick, C. D. Nelson, A. Abbott
article
Annual Meeting the American-Phytopathological-Society (APS), The American Phytopathological Society (APS). USA., Aug 2017, San Antonio, United States. pp.1
resume
Phenological traits, e.g. dormancy, are mechanisms by which perennial tree species have adapted to stressful conditions that are unfavorable for growth. While there are many mechanisms by which trees adapt and respond to stress, the phenylpropanoid pathway in particular is known to be associated with tree stress response. In this study, Prunus persica (peach) and P. armeniaca (apricot) were used as models to explore the relationship between phenylpropanoids and adaptive trait variation. Concentrations of eight phenylpropanoid intermediates were measured throughout dormancy in floral buds of trees that differed genotypically and phenotypically in chill requirement (peach) and bloom date (apricot). There was a significant interaction effect of time and genotype on the concentration of each of the compounds (mixed ANOVA, P < 0.05). Moreover, concentrations of the flavonoid aglycones, apigenin, kaempferol, and quercetin, dropped precipitously in high chill peach and late flowering apricot, around the endodormancy-ecodormancy transition and at the time when buds began to show signs of blooming (e.g. presence of sepals and petals). These results suggest a potential role of phenylpropanoid intermediates in mediating the resumption of growth and development following winter dormancy. A better understanding of tree responses to stress, will be critical for tree improvement programs aimed at identifying and breeding trees more suitable for rapidly changing environments.
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titre
Deciphering regulation levels of sugar metabolism during peach fruit development through metabolic, enzymatic, genetic analyses and kinetic modeling
auteur
Bénédicte Quilot-Turion, Elsa Desnoues, Valentina Baldazzi, Michel Génard, Veronique Signoret, Patrick Lambert, Carole Confolent, Laure Heurtevin
article
ISHS 9. International Peach Symposium, International Society for Horticultural Science (ISHS). INT., Jul 2017, Bucarest, Romania
resume
Deciphering regulation levels of sugar metabolism during peach fruit development through metabolic, enzymatic, genetic analyses and kinetic modeling. ISHS 9. International Peach Symposium
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titre
Advances in pyramiding resistance genes to root-knot nematodes in Prunus rootstocks
auteur
Henri Duval, Cyril van Ghelder, Guillaume Roch, Daniel Esmenjaud
article
9. International Peach symposiumHS, International Society for Horticultural Science (ISHS). INT., Jul 2017, Bucarest, Romania
resume
Advances in pyramiding resistance genes to root-knot nematodes in Prunus rootstocks. 9. International Peach symposiumHS
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titre
Differential gene expression analysis in the threatened sponge Spongia officinalis following exposure to different temperature conditions.
auteur
V Koutsouveli, Tereza Manousaki, Jacques Lagnel, S Kollias, Costas Tsigenopoulos, C Arvanitidis, C Dounas, Antonios Magoulas, Ana Riesgo, Thanos Dailianis
article
10. World Sponge Conference, National University of Ireland Galway. IRL., Jun 2017, Galway, Ireland
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titre
Genetic diversity and architecture of gene expression in response to water deficit in tomato
auteur
Elise Albert, Christopher Sauvage, Jean-Paul Bouchet, Frederique Bitton, Matthieu Beukers, Renaud Duboscq, Yolande Carretero, Mathilde Causse
article
Improving Agriculture through Genomics CROPS 2017, Jun 2017, Huntsville, United States
resume
Tomato is both a model species thanks to the large genetic and genomic resources available and an important crop. Tomato fruit quality is characterized by a large number of components influenced by the genotypes and the environment, notably water status. In order to unravel the genetic control of these components, quantitative trait loci for transcript amount (eQTL), metabolic and phenotypic traits (phQTL) have been mapped under control and water deficit conditions. We used a RIL population derived from an intraspecific cross between a cherry tomato line and a large fruited line. The genomes of both parents were sequenced and differ by more than 2 million SNPs. RNAseq of parental lines revealed a number of functions affected by water stress, but also some major differences according to the parents. On the RIL population we harvested fruit and leaf samples and performed eQTL mapping for 270 differentially expressed genes using the fluidigm technology. Several eQTL were mapped, some with strong effects, a majority of which acting as cis eQTL, and clusters of eQTL and pQTL were demonstrated. Analysis of the transcriptome of the F1 hybrid allowed the quantification of allele specific expression and identification of almost 2000 cis-regulated genes and 1,450 trans regulated genes. Contrary to trans regulatory divergences, cis regulatory divergences were strongly conserved between organs and between watering regimes. Results will be discussed in regard to the gene functions and co-localisations with metabolite or phenotype pQTLs.
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https://hal.archives-ouvertes.fr/hal-01607155/file/CROPS_abstract-eQTL_1.pdf https://hal.archives-ouvertes.fr/hal-01607155/file/CROPS_abstract-eQTL_2.docx BibTex
titre
Allier géostatistique et algorithme EM pour cartographier la date d’apparition des hommes
auteur
Edith Gabriel, Frédérik Saltré, Joel Chadoeuf
article
49èmes journées de statistique, May 2017, Avignon, France
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titre
Des résistances aux nématodes à galles du genre Meloidogyne dans le genre Lactuca : espoir pour la sélection de la laitue
auteur
Brigitte Maisonneuve
article
Rencontres techniques phytosanitaires SDQSPV/ Ctifl, légumes et fraise, Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL). FRA., Jan 2017, Bellegarde, France
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titre
Impact of selection, genetic drift and viral accumulation on the evolution of a plant RNA virus
auteur
Lucie Tamisier, Gregory Girardot, Ghislaine Nemouchi, Marion Szadkowski, Alain Palloix, Benoît Moury
article
16. Rencontres de Virologie Végétale (RVV 2017), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD). FRA., Jan 2017, Aussois, France. 137 p
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https://hal.archives-ouvertes.fr/hal-01606407/file/2017_Tamisier_RVV_1.pdf BibTex
titre
A new eIF4E1 allele characterized by RNAseq data mining is associated with resistance to PVY in tomato albeit with a low durability
auteur
Caroline Lebaron, Aurélie Rosado, Christopher Sauvage, Camille Gauffier, Sylvie German-Retana, Benoît Moury, Jean-Luc Gallois
article
16. Rencontres de Virologie Végétale (RVV 2017), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD). FRA., Jan 2017, Aussois, France. 137 p
resume
Allele mining on susceptibility factors offers opportunities to find new sources of resistance among crop wild relatives for breeding purposes. As a proof of concept, we used available RNAseq data to investigate polymorphisms among the four tomato genes encoding translation initiation factors (eIF4E1 and eIF4E2, eIFiso4E and the related gene New Cap-binding Protein -nCBP) to look for new potential resistance alleles to potyviruses. By analyzing polymorphism among RNAseq data obtained for 20 tomato accessions, ten belonging to the cultivated type Solanum lycopersicum and 10 belonging to the closest related wild species Solanum pimpinellifolium, we isolated one new eIF4E1 allele, in the Solanum pimpinellifolium LA0411 accession, which encodes a potential new resistance allele, mainly due to a polymorphism associated with an amino acid change within eIF4E1 region II. We confirmed that this new allele, pot1², is indeed associated with resistance to PVY, although with a restricted resistance spectrum and a very low durability potential. This suggests that mutations occurring in eIF4E region II only may not be sufficient to provide efficient and durable resistance in plants. However, our study emphasizes the opportunity brought by RNAseq data to mine for new resistance alleles. Moreover, this approach could be extended to seek for putative new resistance alleles by screening for variant forms of susceptibility genes encoding plant host proteins known to interact with viral proteins.
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titre
Integration of QTL, eQTL and allele specific expression to unravel genotype by watering regime interaction in cultivated tomato
auteur
Elise Albert, Christopher Sauvage, Jean-Paul Bouchet, Frederique Bitton, Matthieu Beukers, Yolande Carretero, Mathilde Causse
article
24. Plant and Animal Genome Conference (PAG), Plant & Animal Genome (PAG). USA., Jan 2017, San Diego, United States
resume
Tomato is both a model species and important crop. Tomato fruit quality is characterized by a large number of components influenced by the genotypes and the environment, notably water status. In order to unravel the genetic control of these components, quantitative trait loci for metabolic and phenotypic traits (pQTL) have been mapped under control and drought conditions. We used a RIL population derived from an intraspecific cross between a cherry tomato line and a large fruited line. The genomes of both parents were sequenced and differ by more than 2 million SNPs. RNAseq of parental lines revealed a number of functions affected by water stress, but also some major differences according to the parents. On the RIL population we harvested fruit and leaf samples and performed eQTL mapping for 100 differentially expressed genes using the fluidigm technology. Several eQTL were mapped, some with strong effects, a majority of which acting as cis eQTL, and clusters of eQTL and pQTL were demonstrated. Analysis of the transcriptome of the F1 hybrid allowed the quantification of allele specific expression and identification of other strong effect cis eQTL. Results will be discussed in regard to the gene functions and co-localisations with metabolite or phenotype pQTLs.
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titre
Discovering peach QTLs with multiple progeny analysis
auteur
J.R. Hernández Mora, D. Micheletti, Mc.A.M. Bink, W.E. van de Weg, D. Bassi, N. Nazzicari, A. Caprera, M.T. Dettori, S. Micali, Elisabeth Dirlewanger, Patrick Lambert, Thierry Pascal, E. Banchi, M. Troggio, L. Rossini, I. Verde, Bénédicte Quilot-Turion, Francois Laurens, P. Arus, M.J. Aranzana
article
14. EUCARPIA Symposium on Fruit Breeding and Genetics, 2017, Bologne, Italy. ⟨10.17660/ActaHortic.2017.1172.77⟩
resume
Although many peach QTLs responsible for the variability of traits have been identified and published so far, the number of molecular markers currently used in breeding is still limited. One of the reasons is the large QTL intervals produced, in part, by the limited progeny size. Here we report a QTL mapping approach that enlarges the progeny size by analyzing jointly multiple progenies. Our analysis included 1467 individuals from eighteen Prunus progenies, 13 from intra-specific crosses and five inter-specific between peach and closely related species. The progenies were grown in five locations, with no duplication between orchards. Data from phenology, tree, flower and fruit traits, fruit quality and yield measured in different locations and years were subjected to different standardization methods and integrated in a single data file. The populations were genotyped with the 9K SNP Illumina array, which increased considerably the marker density compared to previous studies. The QTL analysis was conducted with FlexQTLTM software. Here we describe and discuss the preliminary QTLs obtained for some of the traits analyzed (maturity date, percentage of red skin color and soluble solid content). The identification of donors of favorable alleles will represent an important tool for marker-assisted breeding. This study has been conducted in the frame of the Fruit Breedomics European project.
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Other publications

titre
Recherche de résistance aux nématodes à galles chez la laitue
auteur
Brigitte Maisonneuve
article
2017
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Cépages résistants : la vigne contre-attaque
auteur
Laurent Deliere, Christophe Schneider, Laurent Audeguin, Loïc Le Cunff, Rémy Cailliatte, Emilce Prado, Christine Onimus, Isabelle Demeaux, Soizic Guimier, Frédéric Fabre, François Delmotte
article
2017, pp.34-37
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Poster communications

titre
Study of the graft-compatibility of almond on myrobalan (Prunus cerasifera) rootstocks
auteur
Henri Duval, Patrice Duvivier
article
7. ISHS symposium on Almond, Nov 2017, Adélaïde, Australia. 2017
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titre
Sélection génomique - Quelles perspectives chez les Prunus ?
auteur
Mariem N'Sibi, Carole Confolent, Patrick Lambert, Sylvie Bureau, Barbara Gouble, Alain Blanc, Guillaume Roch, Mariem Omrani, Timothée Flutre, Christopher Sauvage, Jean Marc Audergon
article
Séminaire SelGen 2017 : "La sélection génomique, bilan et perspectives", Sep 2017, Paris, France. 1 p, 2017
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Poster communications
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https://hal.inrae.fr/hal-02789979/file/2017_FruitSelGen-Abricotier_v1_1.pdf BibTex
titre
Are sown flower strips an efficient tool to limit aphid colonization and viral epidemics in melon crops?
auteur
Alexandra Schoeny, Nathalie Boissot, Catherine Wipf-Scheibel, Karine Nozeran, Pascale Mistral, Patrick Gognalons, Pauline Millot, Hervé Lecoq
article
10. Conférence de la Société française de phytopathologie, 12. European foundation for plant pathology conference, May 2017, Malo-les-Bains, France. 2017, Deepen knowledge in plant pathology for innovative agro-ecology
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https://hal.archives-ouvertes.fr/hal-01605708/file/2017_Schoeny_EFPP_Poster_1 https://hal.archives-ouvertes.fr/hal-01605708/file/2017_Schoeny_EFPP_Poster2_2.pdf BibTex
titre
Finding loss-of-susceptibility resistance gene toward tospoviruses in Solanaceae
auteur
Zoé Terret, Grégori Bonnet, Laure Didierlaurent, Jean-Luc Gallois
article
16. Rencontres de Virologie Végétale (RVV 2017), Jan 2017, Aussois, France. 2017
resume
Tospovirus is the only member of the Bunyavirus family which infects plants (the other members infecting animals and humans). Tomato spotted wilt virus (TSWV), the most famous tospovirus, is a major pathogen for tomato and pepper cultures. Because there is no chemical treatment against viruses, the only way to fight them is to develop genetic resistance. Genetic resistances to tospoviruses are available, but are largely overcome. Therefore, there is an urgent need to characterize new sources of resistance. The aim of my PhD is to find new genetic resistances based on susceptibility factors, which are proteins required by the virus to accomplish its cycle and infect the plant. As a first step, I will develop a 3D model of the TSWV RNA-dependent RNA polymerase (RdRp), a key viral protein for its infectious cycle. Based on this model, a part of the RdRp protein will be selected as bait in order to identify plant protein interactors by yeast-two hybrid screening. Finally, I will search for new tomato alleles encoding variant forms of those tomato susceptibility factors. If those variants impair the interaction between the plant factor and the viral protein, those alleles are very likely to be associated with the crop resistance to the pathogen.
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https://hal.archives-ouvertes.fr/hal-01604721/file/Terret_Gallois%20Aussois%202017%20Poster_1.pdf https://hal.archives-ouvertes.fr/hal-01604721/file/Terret_Gallois%20Aussois%202017%20Poster_2.docx BibTex
titre
A synthetic eIF4E1 resistance allele allows resistance pyramiding and broad resistance spectrum to potyviruses in Arabidopsis thaliana
auteur
Anna Bastet, Baptiste Lederer, Nathalie Giovinazzo, Joan Estevan, Christophe Robaglia, Jean-Luc Gallois
article
16. Rencontres de Virologie Végétale (RVV 2017), Jan 2017, Aussois, France. 2017
resume
Developing genetic resistance is an important alternative to the use of pesticides in order to avoid viral infections in crops. However, this approach can be limited by the lack of natural resistant alleles available for plant breeding. Biotechnologies can supply for this lack by altering susceptibility host factors used by viruses. However, strategies relying on knocking out plant host factors can be undermined by associated developmental default, or gene redundancy (Gauffier et al., 2016). Synthetic biology could offer the opportunity to develop functional synthetic alleles associated with plant resistance at no developmental cost. The translation initiation factors (eIF4E), that are associated with resistance to most single strand positive RNA (including the major group of potyviruses), are the ideal targets to validate such approaches. We focused on the Arabidopsis thaliana eIF4E1 gene that encodes a susceptibility factor to a potyvirus, the Clover yellow vein virus. Artificial resistance alleles were created by directed mutagenesis and used to complement loss-of-function eif4e1 plants for assessing in planta both their functionality and resistance efficiency. By combining these synthetic resistance alleles with others eIF4E factors-mediated resistance, a broad resistance spectrum to potyviruses is expected as well as increased resistance durability. This study will make proof of the feasibility of this approach to obtaining large resistance spectrum in plants with the perspective of extending it to crops.
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Poster communications
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https://hal.archives-ouvertes.fr/hal-01594565/file/Bastet_Gallois%20Aussois%202017_1.pdf https://hal.archives-ouvertes.fr/hal-01594565/file/Bastet_Gallois%20Aussois%202017_2.docx BibTex
titre
Exploring plant tolerance to viruses as a sustainable means of disease control
auteur
Judith Hirsch, Gregory Girardot, Sandra Martin, Jawad Aarrouf, Alain Palloix, Benoît Moury
article
16. Rencontres de Virologie Végétale (RVV 2017), Jan 2017, Aussois, France. 137 p., 2017, 16ièmes Rencontres de Virologie Végétale - 15 -19 janvier 2017 - Aussois - France
resume
Exploring plant tolerance to viruses as a sustainable means of disease control. 16. Rencontres de Virologie Végétale (RVV 2017)
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https://hal.archives-ouvertes.fr/hal-01605629/file/2017_Hirsch_RVV_1.pdf BibTex

Videos

titre
Restitution du programme LactuMel
auteur
Brigitte Maisonneuve
article
2017
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Videos
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https://hal.inrae.fr/hal-02786257/file/11_Lactumel_Maisonneuve_V02.mp4 BibTex

2016

Conference papers

titre
Durabilité des résistances médiées par Vat
auteur
Alexandra Schoeny, Nathalie Boissot
article
Rencontre Ecophyto Melon Sud-Est, Dec 2016, Avignon, France. 15 p
resume
Durabilité des résistances médiées par Vat. Rencontre Ecophyto Melon Sud-Est
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titre
Projet LactuMel (2014-2016): Recherche de résistance aux nématodes à galles chez la laitue
auteur
Brigitte Maisonneuve
article
Rencontres du GIS PIClég, Groupement d'Intérêt Scientifique pour la Production Intégrée en Cultures légumières (Gis Piclèg). FRA., Nov 2016, Nantes, France
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titre
Screening a priori durable resistance in tomato to Phytophthora infestans using its pathogenicity effectors
auteur
Emmanuel Szadkowski, Gaëtan Maillot, Alexandre Bachellez, Dorine Achard, Anne Massire, Bernard Caromel, Véronique Lefebvre
article
Effectome meeting 2016, Nov 2016, Lauret, France
resume
Screening a priori durable resistance in tomato to Phytophthora infestans using its pathogenicity effectors. Effectome meeting 2016
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titre
Les porte-greffes de l'amandier
auteur
Henri Duval
article
1. journée de l'amande, Nov 2016, Plan d'Orgon (13), France
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Conference papers
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https://hal.inrae.fr/hal-02743311/file/6_porte-greffes2016_1.pdf https://hal.inrae.fr/hal-02743311/file/Referentiel_amande_2016_2017_2.pdf BibTex
titre
Effet sur la démographie et la composition génétique des populations de pucerons dans les cultures de melons résistants vs sensibles
auteur
Nathalie Boissot
article
3. Meeting Resistance, Nov 2016, Lauret, France
resume
absent
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titre
La recherche et le développement : une nouvelle organisation au service de nos producteurs. Enjeux et questions posées à la filière fruits à noyau
auteur
Jean Marc Audergon
article
Séminaire AOP Pêches et Abricots de France, Nov 2016, Baillargues, France. 14 p
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Conference papers
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https://hal.inrae.fr/hal-02793499/file/Audergon%20S%C3%A9minaire%20AOP%202016_1.pptx https://hal.inrae.fr/hal-02793499/file/Audergon%20S%C3%A9minaire%20AOP%202016_2.pptx BibTex
titre
ARDU. ARboriculture Durable: approches interdisciplinaires
auteur
Claire Lamine, Sylvaine Simon, Jean Marc Audergon
article
Métaprogramme INRA Gestion durable de la santé des cultures, Oct 2016, Paris, France. 21 p
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https://hal.inrae.fr/hal-02801861/file/2016_Lamine_ARDUSmash_1.pdf BibTex
titre
A systems biology study in tomato fruit reveals signaling from the ascorbate pool and links with translation and the heat-shock response
auteur
Rebecca Stevens, Pierre Baldet, Jean-Paul Bouchet, Mathilde Causse
article
Annual Conference COST FA1106 “Quality Fruit”, Oct 2016, Porto, Portugal. 36 p
resume
Plants with lowered activity of enzymes catalyzing the final step of ascorbate synthesis or the equilibrium between reduced and oxidized forms have highly pleiotropic phenotypes suggesting regulatory roles for ascorbate and its oxidized forms. Network analysis of the transcriptome, proteome and key metabolites of RNAi lines for ascorbate oxidase, monodehydroascorbate reductase and galactonolactone dehydrogenase has been carried out in orange fruit pericarp of tomato (Solanum lycopersicum). We show a transcriptional switch-type response with expression profiles in ascorbate oxidase lines being inversed compared to the monodehydroascorbate reductase and galactonolactone dehydrogenase lines. Differentially expressed genes are linked to ribosome biogenesis and translation. The inversion between the transcriptome signatures is not specific to tomato fruit as it is conserved in Arabidopsis. The transcriptome response is not correlated with accumulated proteins which, with the metabolites, are correlated to the activity of the ascorbate redox enzymes. Differentially accumulated proteins include metacaspase, protein disulphide isomerase, chaperone DnaK and carbonic anhydrase and the metabolites chlorogenic acid, dehydroascorbate and alanine. Hub genes are related to signaling, the heat-shock response and ribosome biogenesis. This study in a non-photosynthetic tissue reveals signaling from the ascorbate pool related to the heat-shock response, translation and protein synthesis.
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titre
Analyse agroclimatique du contexte de la floraison de l'abricotier (Var Bergeron). Quelques éléments d'analyse à partir d'un retour sur plusieurs décennies
auteur
Patrick Bertuzzi, Jean Marc Audergon, I. García de Cortázar-Atauri
article
Présentation Sefra, Sep 2016, Gotheron, France. 28 p
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https://hal.inrae.fr/hal-02794141/file/Audergon%20Presentation_SEFRA%202016_1.pdf BibTex
titre
A compartmental epidemiological model for brown rot spreading in stone fruits orchard
auteur
Danièle Bevacqua, Michel Génard, Bénédicte Quilot-Turion, Leandro Oliveira Lino, Vincent Mercier, Françoise Lescourret
article
Hortimodel2016, 19-22 Septembre, Avignon, Sep 2016, Avignon, France. pp.1-40
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Conference papers
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https://hal.inrae.fr/hal-03587185/file/HORTIMODEL_AbstractBook.pdf BibTex
titre
A model-based approach for peach fruit transpiration process and its genetic variability
auteur
M. Memmah, Bénédicte Quilot-Turion, Michel Génard, Imen Soula
article
Hortimodel2016, 19-22 Septembre, Avignon, Sep 2016, Avignon, France. pp.1-40
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Conference papers
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https://hal.inrae.fr/hal-03587187/file/HORTIMODEL_AbstractBook.pdf BibTex
titre
A kinetic model of sugar metabolism in peach fruit allows the exploration of genetic variability
auteur
Elsa Desnoues, Bénédicte Quilot-Turion, Michel Génard, Valentina Baldazzi
article
Hortimodel2016, 19-22 Septembre, Avignon, Sep 2016, Avignon, France. pp.1-39
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Conference papers
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https://hal.inrae.fr/hal-03587210/file/HORTIMODEL_AbstractBook.pdf BibTex
titre
Screening of solanaceous wild relatives for graft affinity with eggplant (Solanum melongena L.)
auteur
François Villeneuve, François Latour, Théophile Théry, Patricia Erard, Christine Fournier, Marie-Christine Daunay
article
16. Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary. 9 p
resume
Eggplant (Solanum melongena L.), an important solanaceous crop in tbe world, is susceptible to soilbome bio-agressors, the main of which, in temperate areas, being Verticillium wilt (Verticillium sp.) and root knot nematodes (Meloidogyne spp.). Grafting on resistant rootstock is an alternative rnethod to soil disinfection. In France, the generalization of grafting spread over the 2000's. After several years of utilization of resistant tornato rootstocks for eggplant production, and to a lesser extent, of Solanum torvum rootstocks, damaging wilt-like-symptoms are often observed by growers. Renee it is necessary to identify alternative rootstocks, able to sustain the soil pathogenic cornplex by a combination of vigor and genetic resistance. However, graft affinity between potential rootstocks and eggplant (scion) is the fust step to investigate. Solanaceae family offers a wide choice of candidate rootstock species. The objective ofthis research was to identify solanaceous species baving a good graft affinity with eggplant, Screening of a wide set of genetic resources was carried out at the Centre Technique Interprofessionnel des Fruits et Légumes -Ctifl- (Lanxade and Balandran center) in collaboration with INRA. Experirnents were carried out during a five years period (2011-2015). Several So/anum species displayed a good graft affinity with eggplant and are candidates for further agronomie evaluation.
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https://hal.inrae.fr/hal-02794118/file/Daunay%2016th%20eucarpia%202016%20152-160_1.pdf BibTex
titre
Genetic mapping of broad-spectrum QTLs and strain-specific major QTL for resistance to Ralstonia solanacearum in eggplant using GBS
auteur
Sylvia Salgon, Cyril Jourda, Christopher Sauvage, Marie-Christine Brand-Daunay, Emmanuel Wicker, Jacques Dintinger
article
16. Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary
resume
Genetic mapping of broad-spectrum QTLs and strain-specific major QTL for resistance to [i]Ralstonia solanacearum[/i] in eggplant using GBS. 16. Eucarpia Capsicum and Eggplant Meeting
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https://hal.archives-ouvertes.fr/hal-01512188/file/Sauvage_Daunay%2016th%20eucarpia%202016%20246_1.pdf BibTex
titre
Eggplant resistance to bacterial wilt and to Fusarium wilt: Is there a link?
auteur
Marie-Christine Daunay, Jean Winoc Hennart, Sylvia Salgon, Jacques Dintinger
article
16. Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary. 14 p
resume
INRA URI 052 maintains a germplasm collection of S. melongena and related species. The accessions of this collection that are described in the literature as resistant to Ralstonia solanacearum, agent responsible ofbacterial wilt, were screened at plantlet stage against Fusarium oxysporum f.sp. melongenae on the basis of the number ofleaves wilted and vessels browning. Results show that the panel of accessions tested display phenotypes ranging from fully resistant to fully susceptible to Fusarium wilt, with ail intermediate resistance levels. Results are discussed on the basis ofthe complexity ofresistance evaluation and of what is known in tomato about a link between resistances to both vascular diseases.
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https://hal.inrae.fr/hal-02801124/file/Daunay%2016th%20eucarpia%202016%2099-111_1.pdf BibTex
titre
Greenhouse eggplant production in France: Success and failures of grafting for controlling Verticillium sp.
auteur
François Villeneuve, François Latour, Théophile Théry, Christian Steinberg, Véronique Edel-Hermann, Marie-Christine Brand-Daunay
article
16. Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary. 6 p
resume
After many years of utilisation of grafting on Verticillium wilt resistant rootstocks, mainly tomato rootstocks, growers observe new wilt like symptoms on their grafted eggplants. Accordingly, Ctifl, in close collaboration with lNRA, regional extension services, and seed companies, set up a research designed to get a general picture of the various soil borne phytosanitary problems, and to identify their causees). The princip le of the study was to monitor pathogen distribution changes in eggplant crops in the two main production regions in France. The results show the prevalence of Verticillium wilt and, in the majority of cases and a1l production areas, the simultaneous presence of a number of other bioagressors, including fungi and nematodes. The isolates of Verticillium were identified at the species level (V. dahliae, V. isaacii) and characterized for their race (0 or 1) and their aggressiveness. Surprisingly, the aggressiveness ofmost isolates was relatively low. To our knowledge, this is the first report of V. isaacii in France, but its impact on production across France is unknown at this time.
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https://hal.archives-ouvertes.fr/hal-01595652/file/Daunay%2016th%20eucarpia%202016%20poster%20455-460_1.pdf BibTex
titre
Quantitative trait loci in pepper genome 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, Frédéric Fabre, Benoît Moury, Alain Palloix
article
16. Eucarpia Capsicum and Eggplant meeting, Szent István University. Gödöllo, HUN., Sep 2016, Kecskemét, Hungary. 591 p
resume
Infection of plants by viruses is a complex process that involves several steps: inoculation into plant cells, replication in inoculated cells, cell-to-cell movement during leaf colonization and long-distance movement during systemic infection. The success of the different steps is conditioned by the effective viral population size (Ne) defined as the number of individuals that pass their genes to the next generation. During the infection cycle, the virus population will endure several bottlenecks leading to drastic reductions in Ne and to the random loss of sorne virus variants. If strong enough, these bottlenecks could act against selection by eliminating the fittest variants. Therefore, a better understanding of how plant affects Ne rnay contribute to the developrnent of durable virus-resistant cultivars. We aimed to (i) identify plant genetic factors that control Ne at the inoculation step, (ii) understand the mechanisms used by the plant to control Ne and (iii) compare these genetic factors with other genes controlling virus life cycle and plant resistance durability. The virus effective population size was measured in a segregating population of 152 doubled-haploid lines of Capsicum annuum. Plants were inoculated mechanically either with a Patata virus Y (PVY) construct expressing the green fluorescent protein (OFP), or a necrotic variant of Cucumber mosaic virus (CMV), the CMV-N strain of Fulton. Ne was assessed by counting the number ofprimary infection foci observed on inoculated cotyledons under UV light for PVY -OFP or the number of necrotic local lesionsobserved on inoculated leaves for CMY-N. The numbers of primary infection foci and locallesions were correlated arnong the doubled-haploid lines (r=0.57) and showed a high heritability (h2=0.93 and 0.98 for PVY and CMV, respectively). The effective population size of the two viruses was shown to be controlled by botb common quantitative trait loci (QTLs) and virus-specifie QTLs, indicating the contribution ofboth general and specifie mechanisms. The PVY-specific QTL colocalizes with a QTL that had previously been shown to be involved in PVY accumulation and capacity to break amajor-effect resistance gene down.
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Conference papers
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https://hal.inrae.fr/hal-02738767/file/Tamisier_Palloix%2016th%20eucarpia%202016%20169-176_1.pdf BibTex
titre
Plant genetic background increasing the efficiency and durability of major resistance genes to root knot nematodes can be resolved into a few resistance QTLs
auteur
Arnaud Barbary, Caroline Djian-Caporalino, Philippe Castagnone-Sereno, Nathalie Marteu, Ariane Fazari, Bernard Caromel, Alain Palloix
article
16. Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary. 4 p
resume
With the banning of most chemical nematicides, the control of root knot nematodes (RKNs) in vegetable crops is mainly based on the deployment of single-major resistance genes (R-genes). However, these genes are rare and their efficiency is threatened by RKNs capacities of adaptation. ln pepper, several dominant R-genes are efficient against RKNs, but their efficiency and durability were shown to be increased in partially resistant genetic background. A QTL analysis was performed in such a genetic background, using a F2:3population from the cross between Yolo Wonder, a partially resistant to resistant accession depending on RKN species, and Doux Long des Landes, a susceptible one. The genetic linkage map was constructed from 130 F2 individuals and the 130 F3 families were tested forresistance to the three main RKNs species, M incognita, M arenaria and Mjavanica. Four new major QTLs were mapped into two clusters. The cluster on chromosome Pl includes three tightly linked QTLs with specifie effects against each RKN species. The fourth QTL, specifie of resistance to M javanica, mapped on the pepper chromosome P9, which is known to carry multiple NBS-LRR repeats with major resistance genes to nematodes and other pathogens. The newly discovered cluster on chromosome Pl, displays a broad spectrum of action with major additive effects on resistance. Therefore, it provides innovative potential for breeding new cultivars or rootstocks combining quantitative resistance and major resistance genes and increasing the efficiency as weil as the durability ofRKNs genetic control.
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Conference papers
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https://hal.inrae.fr/hal-02792960/file/Caromel-Palloix%2016th%20eucarpia%202016%20poster%20523-527_1.pdf BibTex
titre
A TILLING approach to generate broad-spectrum resistance to potyviruses in tomato is hampered by eIF4E gene redundancy
auteur
Jean-Luc Gallois, Camille Gauffier, Caroline Lebaron, Anna Bastet, Carole Caranta
article
International Advances in Plant Virology, Association of applied biologists, Sep 2016, London, United Kingdom
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https://hal.inrae.fr/hal-03195976/file/virology_2016_ann_pbf.pdf BibTex
titre
Linking genetics, physiology and modelling to gain insight in peach fruit quality
auteur
Bénédicte Quilot-Turion
article
11. National Meeting of the SFBV, Jul 2016, Angers, France
resume
absent
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https://hal.archives-ouvertes.fr/hal-01343638/file/Quilot-Turion%20SFBV%202016_1.pdf https://hal.archives-ouvertes.fr/hal-01343638/file/Quilot-Turion%20SFBV%202016_2.docx BibTex
titre
From domestication to modern breeding: what have learned from genetic resources in tomato?
auteur
Christopher Sauvage, Mathilde Causse
article
11. National Meeting of the SFBV, Jul 2016, Angers, France
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https://hal.inrae.fr/hal-02792606/file/Sauvage%20SFBV%202016_1.pdf https://hal.inrae.fr/hal-02792606/file/Sauvage%20SFBV%202016_2.docx BibTex
titre
The type III effector RipAX2 confers avirulence of [i]Ralstonia solanacearum[/i] to the eggplant AG91-25, carrying the resistance gene Ers1
auteur
Jérémy Guinard, Keke Wang, Fabien Lonjon, Lakshmi Sujeeun, Marco E. Mechan Llontop, Anne-Claire Noel, Patrick Barberis, Stéphane Genin, Marie-Christine Brand-Daunay, Jacques Dintinger, Stéphane Poussier, Boris Vinatzer, Nemo Peeters, Emmanuel Wicker
article
6. International Bacterial Wilt Symposium (IBWS), Jul 2016, Toulouse, France
resume
absent
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https://hal.archives-ouvertes.fr/hal-01343635/file/Daunay%206th%20IBWS%202016%20Poster_1.pdf BibTex
titre
From gene to phenotype: genetic control and modeling of sugar metabolism during peach fruit development
auteur
Elsa Desnoues, Valentina Baldazzi, Michel Génard, Patrick Lambert, Carole Confolent, Laure Heurtevin, Bénédicte Quilot-Turion
article
8. International Rosaceae Genomics Conference, Jun 2016, Angers, France
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https://hal.inrae.fr/hal-02798866/file/Quilot-Turion%208.%20Inter.%20Rosa.%20Geno.%20Conf.%202016_1.pdf https://hal.inrae.fr/hal-02798866/file/Quilot-Turion%208.%20Inter.%20Rosa.%20Geno.%20Conf.%202016_2.docx BibTex
titre
Impact of selection, genetic drift and viral accumulation on the evolution of a plant RNA virus
auteur
Lucie Tamisier, Gregory Girardot, Ghislaine Nemouchi, Marion Szadkowski, Alain Palloix, Benoît Moury
article
13. International plant virus epidemiology symposium, Jun 2016, Avignon, France. 165 p
resume
Genetic control is an efficient way to fight against crop disease, but this method is limited by the pathogen ability to evolve and break the resistance down. In the pepper-Potato virus Y (PVY) pathosystem, studies have demonstrated that the plant genetic background can increase the durability of the major resistance gene (Palloix et al., 2009), especially by constraining pathogen evolution (Quenouille et al., 2013). We conducted an experimental evolution to (i) measure the pathogen ability to adapt to plants combining major resistance gene and partially resistant genetic background and (ii) identify the role of the evolutionary forces induced by the genetic background on virus evolution.
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https://hal.inrae.fr/hal-02739150/file/2016_Tamisier_Avignon_1 BibTex
titre
Joint estimation of effective population size and selection coefficient without neutrel markers: method validation and application to experimental evolution of viruses
auteur
Elsa Rousseau, Benoît Moury, Ludovic Mailleret, Rachid Senoussi, Alain Palloix, Vincent Simon, Frédéric Grognard, Sophie Valière, Frédéric Fabre
article
13. International plant virus epidemiology symposium, Jun 2016, Avignon, France. 165 p
resume
Experimental evolution studies deserve considerable attention to the estimation of basic evolutionary forces such as selection and genetic drift. With the advent of high-throughput sequencing techniques, these studies gained a renewed attention. However the joint estimation of selection and genetic drift still remain challenging when no neutral markers are available, a common situation with many microbes, such as viruses, due to their small tightly packed genomes.
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Conference papers
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https://hal.inrae.fr/hal-02739698/file/Palloix%2013.int.%20plant%20virus%20epid.%20sympo.%202016%2016_1.pdf BibTex
titre
A priori durable resistance in tomato to Phytophthora infestans using its pathogenicity effectors
auteur
Emmanuel Szadkowski, Gaëtan Maillot, Alexandre Bachellez, Anne Massire, Bernard Caromel, Véronique Lefebvre
article
Journées Jeunes Chercheurs du DBAP, Institut National de Recherche Agronomique (INRA). UMR Institut Jean-Pierre BOURGIN (1318)., Apr 2016, Lyon, France
resume
A priori durable resistance in tomato to Phytophthora infestans using its pathogenicity effectors. Journées Jeunes Chercheurs du DBAP
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titre
Prunus - Réalités et perspectives de l'écologisation en arboriculture fruitière
auteur
Claire Lamine, Servane Penvern, Lucile Garcon, Sibylle Bui, Jean Pluvinage, Sylvaine Simon, Guy Clauzel, Jean Marc Audergon
article
PRUNUS, Mar 2016, Saint Marcel lès Valence, France. 12 p
resume
Le projet « PRUNUS- Réalités et perspectives de l’écologisation en arboriculture fruitière » a été financé par le programme Pesticides* du ministère de l’environnement sur la période 2013-2015 avec pour objectif d’identifier les effets de verrouillage et les leviers de transition vers une écologisation des pratiques agricoles (réduction des pesticides) dans les vergers de pêchers et d’abricotiers de la basse Vallée du Rhône.
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https://hal.archives-ouvertes.fr/hal-01313366/file/2016_Lamine_Prunus.pdf BibTex
titre
Mise en place d'un réseau national d'observations harmonisées de la phénologie chez les espèces fruitières.
auteur
Marc Bonhomme, Pascale Guillermin, Jean-Michel Legave, José Quero-Garcia, Teresa Barreneche, Gilles Orain, Jean-Marc Ebel, V. Mathieu, Jean Marc Audergon
article
Séminaire ACCAF "Recherche et Adaptation au Changement Climatique", Mar 2016, Magny le Hongre, France. 1 p
resume
Dans le cadre du projet ACCAF PerPheClim, la phénologie a été étudiée en tant qu’indicateur de l’impact des changements climatiques. Pour appréhender son évolution, la mise en place d’observatoires implantés en des sites contrastés et suivis sur le long terme est apparue particulièrement utile. De tels observatoires, existaient pour la vigne et les espèces forestières mais pas pour les espèces fruitières (Domergues et al.,2004). Il a donc été décidé de mettre en place un dispositif national en réseau adapté à révéler les interactions génotype x environnement chez les espèces fruitières (Legave, 2009) et d’accompagner le dispositif par la mise en oeuvre de protocoles de suivis harmonisés.
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titre
Caractérisation variétale de la texture des abricots, réponse à la cuisson et analyse des mécanismes
auteur
Barbara Gouble, Albert Ribas-Agusti, Patrice Reling, Sylvie Bureau, Carine Le Bourvellec, Marielle Boge, Jamal Ayour, Catherine Renard, Guy Clauzel, Alain Blanc, Jean Marc Audergon
article
Journées de Restitution du projet ANR-ILLIAD, Jan 2016, Montpellier, France
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titre
Identification des principaux facteurs biochimiques impliqués dans la réponse différentielle des variétés d’abricot au traitement thermique
auteur
Albert Ribas-Agusti, Barbara Gouble, Sylvie Bureau, Jean Francois Maingonnat, Jean Marc Audergon, Mohamed El Maataoui, Catherine Renard
article
Journées de Restitution du projet ANR-ILLIAD, Jan 2016, Montpellier, France
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titre
Des étiquettes gustatives pour les abricots? Une expérimentation économique
auteur
Sandrine Costa, Zouhair Bouhsina, Danièle Scandella, Maxime Sebbane, Jean Marc Audergon, Barbara Gouble
article
Colloque restitution ILLIAD, Jan 2016, Montpellier, France
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titre
La mécanisation de la récolte d’abricots : faisabilité technique, conduite des vergers et comportements des variétés
auteur
Barbara Gouble, Jean Michel Broquaire, Christophe Chamet, Eric Hostanou, Patrice Reling, Sylvie Bureau, Marielle Boge, Adrienne Samper, Jamal Ayour, Catherine Renard, Jean Marc Audergon
article
Journées de Restitution du projet ANR-ILLIAD, Jan 2016, Montpellier, France
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titre
Deciphering the genetic control of tomato fruit composition in flavonoids in the resequencing Era
auteur
Mathilde Causse, Laura Pascual, Christopher Sauvage, Elise Albert, Jean-Paul Bouchet, Dominique Brunel, Marie-Christine Le Paslier
article
24. International Plant and Animal Genome Conference, Jan 2016, San Diego, United States
resume
Identifying the genes controlling the variation of quantitative traits is a key goal for breeders. Genetic variations underlying quantitative traits (QTL) have been mapped by linkage mapping for years and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of genetic background on QTL effect has been underlined. Multi-allelic Advanced Generation Inter-Cross (MAGIC) populations allow a wide range of variability to be analyzed. We have constructed a MAGIC population by crossing 8 tomato lines, representing a wide range of genetic diversity within the species. The large range of phenotypic variability represented by these lines was then characterized at different scales, metabolomic, proteomic and transcriptomic. The whole genomes of the 8 founder lines were resequenced identifying more than 4 millions SNPs when mapped onto the reference genome. A set of 1536 SNPs markers was then selected to genotype the MAGIC population and used to construct a linkage map. A large increase in recombination frequencies compared to bi-parental populations was shown. QTLs for fruit composition traits were mapped and related to the variations detected at the genome sequence and expression levels in the parental lines. QTL for flavonoid compounds were mapped and candidate genes identified will be presented
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titre
A draft assembly of the almond genome
auteur
Tyler S. Alioto, Fernando Cruz, Jessica Gómez-Garrido, Leonor Frias, Paolo Ribeca, Marta Gut, Konstantinos Alexiou, Werner Howad, Jordi Morata, Josep Casacuberta, Maria J. Rubio-Cabetas, Beatriz Galán, José Luis García, Amit Dhingra, Henri Duval, Angel Fernandez I Marti, Michelle Wirthensohn, Ivo G. Gut, Pere Arús
article
24. International Plant and Animal Genome Conference, Jan 2016, San Diego, United States
resume
Almond is one of the oldest cultivated nut crops with its origin in central and western Asia. The selection of the sweet type [i](Prunus dulcis[/i]) distinguishes the domesticated almond from its bitter wild relatives. It is economically important, especially in California with the highest worldwide production, followed by Australia and Spain. The almond belongs to the same subgenus as the peach, for which there already exists a reference genome. However, to fully understand the genetic underpinnings marking the key phenotypic differences between almond and peach, we have sequenced the genome of the ‘Texas’ almond, one of the traditional cultivars producing a sweet nut. Whole-genome shotgun sequencing of Illumina paired-end libraries gave an initial low-contiguity assembly of 512 Mbp, nearly double the estimated genome size. Counting of k-mers indicates a 275 Mbp genome with substantial heterozygosity as well as repetitive sequence. In order to tackle both problems, we constructed a fosmid library and sequenced 68 pools of ~500 clones per pool. We then assembled the pools, merged them and finished the assembly by scaffolding with paired end and mate pair libraries, which resulted in a 240 Mbp assembly with a scaffold N50 of 500 kbp, a contig N50 of 33.5 kbp and CEGMA completeness of 99%. Two thirds of the assembly was anchored to the peach-almond genetic map, and using re-sequencing data of peach-almond hybrids and their parents we inferred the two haplotypes of the sequenced almond tree. We performed additional validation of the assembly using Oxford Nanopore MinION sequencing.
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https://hal.archives-ouvertes.fr/hal-01344926/file/Duval%20Plant%20and%20Animal%20Genome%202016%201-5_1.pdf https://hal.archives-ouvertes.fr/hal-01344926/file/Duval%20Plant%20and%20Animal%20Genome%20XXIV%20Conference%202016_2.htm BibTex

Lectures

titre
Prenez-en de la graine ! Les légumes secs du jardin à l’assiette
auteur
Marie Josephe Amiot-Carlin, Michel Pitrat, Pascal Coquin
article
2016
resume
Consommées depuis plusieurs millénaires, les légumineuses seraient parmi les premières plantes à avoir été cultivées, avec les céréales. Présentes dans de nombreuses recettes traditionnelles à travers le monde, elles ont aujourd’hui toute leur place dans notre alimentation grâce à leurs vertus nutritionnelles et écologiques.
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Lectures
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https://hal.inrae.fr/hal-02798501/file/2016_Expo%20itin%C3%A9rante%20STC_LEGIMINEUSES_1.pdf BibTex

Other publications

titre
Méthodes et dispositifs innovants pour l'évaluation du matériel végétal fruitier, MEDIEVAL
auteur
Sylvie Colleu, Marine Guadagnini-Palau, Jean Marc Audergon, Daniel Plénet, Jean-Luc Regnard, Benoit Jeannequin, Sandrine Codarin, Christian Hilaire, Vincent Mathieu, Julien Ruesch, Yann Bintein
article
2016, pp.33
resume
Ce rapport, rédigé par un groupe de travail du Groupement d'Intérêt Scientifique, GIS Fruits a eu deux objectifs. D'une part dresser un état des lieux et réaliser une analyse critique des dispositifs actuels d’évaluation du matériel végétal fruitier. D'autre part, identifier les nouveaux outils, méthodes et dispositifs qui pourraient être mobilisés pour améliorer l'évaluation du matériel végétal fruitier et faciliter la connaissance et le transfert des informations, ainsi que repérer les pistes de recherches complémentaires pour développer de nouveaux outils et méthodes.
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https://hal.archives-ouvertes.fr/hal-01603980/file/Rapport%20de%20Synth%C3%A8se%20M%C3%A9di%C3%A9val_VF-VF_1.pdf BibTex
titre
Des espèces légumières venues du monde entier
auteur
Michel Pitrat
article
2016, pp.1-4
resume
Quelques légumes font encore localement l’objet de cueillette des formes sauvages : la mâche, le pissenlit et d’autres « salades » récoltés dans les prés, les jeunes pousses d’asperge sauvage ([i]Asparagus acutifolius[/i]) ou de tamier dans les haies et les sous-bois, sans oublier tous les champignons sylvestres. Cependant la plupart des légumes que nous consommons sont des formes domestiquées et cultivées. Quelle est l’origine des légumes consommés régulièrement en France et en Europe ? Depuis les travaux de de Candolle, Vavilov, Harlan, nous avons beaucoup d’éléments de réponse à cette question, même s’il subsiste des incertitudes, en particulier à cause de la grande diversité des espèces légumières.
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https://hal.archives-ouvertes.fr/hal-01312108/file/2016_Pitrat%20_Jardins%20de%20France%20640_1.pdf BibTex
titre
Data from :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
2016
resume
Data from :Insight into the durability of plant resistance to aphids from a demo-genetic study of Aphis gossypii in melon crops
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Poster communications

titre
Improving modern breeding in tomato: the crucial role of genetic resources
auteur
Christopher Sauvage, Mathilde Causse
article
13. Japan Solanaceae Consortium (JSOL2016), Nov 2016, Tokyo, Japan. 2016
resume
The tomato is one of the most produced vegetable in the world and this species is also a model in science to the study of fruit development. Over the past 60 years, many sampling campaigns in Central and South America (source area) helped preserving more than 80,000 accessions of this species, including most of its crop wild relatives. In parallel, the contribution of molecular biology through the development of molecular markers was used to map many QTLs for traits of agronomic interest such as fruit quality and resistance to biotic and abiotic stresses. Since 2012, date of publication of the tomato genome, the combination of the rich genetic resources and high-throughput genomic was used to extend the work to a genome-wide scale to better understand its dynamic, to identify large amount of polymorphic sites but also revisiting scientific questions, such as the evolutionary history (i.e. domestication) of this species and the study of the genetic architecture of quantitative traits through new approaches such as genome-wide association study (GWAS) or genomic selection genomics. The genetic resources of this species are essential for fundamental scientific research but also for the genetic improvement of this species.
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Poster communications
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https://hal.archives-ouvertes.fr/hal-01604959/file/Sauvage%20JSOL%202016_1.pdf https://hal.archives-ouvertes.fr/hal-01604959/file/Sauvage%20JSOL%202016_2.docx BibTex
titre
Genetic and genomic control of tomato adaptation to water stress
auteur
Elise Albert, Laura Pascual-Banuls, Christopher Sauvage, Jean-Paul Bouchet, Frederique Bitton, Isidore Diouf, Matthieu Beukers, Yolande Carretero, Mathilde Causse
article
Argentina Plant Physiology meeting, Nov 2016, Corrientes, Argentina. 2016
resume
Genetic and genomic control of tomato adaptation to water stress. Argentina Plant Physiology meeting
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titre
Genetic dissection of tomato fruit quality in the genome era: new tools for in depth QTL characterization
auteur
Elise Albert, Laura Pascual-Banuls, Christopher Sauvage, Janejira Duangjit, Jean-Paul Bouchet, Frederique Bitton, Isidore Diouf, Yolande Carretero, Mathilde Causse
article
3. International Symposium on Horticulture in Europe, SHE2016, Oct 2016, Chania, Greece. 2016
resume
Tomato fruit quality is characterized by a large number of components influenced by the genotypes and the environment. To better understand t~e genetic control of these components, quantitative trait loci (QTL) have been mapped for years. Today the genome sequence availability changes the paradigm of genetic approaches. QTL have been first identified using linkage mapping populations and positional cloning identified a few QTLs. However Iinkage mapping is Iimited to the analysis of traits differing between two parentallines. Genome-wide association (GWA) has then been proposed to assess a large range ofvariability. ln tomato, we have shown that GWAstudy is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure. Nevertheless, GWAsuccess is limited in sorne regions due to the low decay of linkage disequilibrium, which varies along the genome. Rare alleles are also difficult to detect with GWA studies. Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditionallinkage and GWAs by increasing the precision of QTLmapping but with equilibrated allelic frequencies. We have developed a MAGICpopulation by crossing eight tomato lines whose genomes were resequenced. We showed the potential of the MAGIC population when coupled with whole genome sequèncing to detect candidate single nuc\eotide polymorphisms (SNP) underlying the QTLs. QTLs for fruit quality traits were mapped and related to the variations detected at the genome sequence and expression levels. The advantages and limitations of the three types of population, in the context of the available genome sequence and resequencing facilities, will be discussed.
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https://hal.archives-ouvertes.fr/hal-01604736/file/Albert_Sauvage_Causse%20SHE%202016%2045_1.pdf BibTex
titre
PICLÉG': a "research, development and stakeholders" all-together initiative for integrated production of field vegetables in France
auteur
Mathilde Causse, Vincent Faloya, Benoit Jeannequin
article
3. International Symposium on Horticulture in Europe, SHE2016, Oct 2016, Chania, Greece. 2016
resume
PICLÉG': a "research, development and stakeholders" all-together initiative for integrated production of field vegetables in France. 3. International Symposium on Horticulture in Europe, SHE2016
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https://hal.archives-ouvertes.fr/hal-01602854/file/Causse%20SHE%202016%20195%20poster_1.pdf BibTex
titre
Effect on water deficit on tomato fruit quality - Genetic variability of the fruit response
auteur
Nadia Bertin, Beatrice Brunel, Julien Bonnefoi, Ivana Petrović, Mathilde Causse
article
3. International Symposium on Horticulture in Europe, SHE2016, Oct 2016, Chania, Greece. 2016
resume
Water deficit is known to improve fleshy fruit quality at the expense of yield. However in tornato, recent studies showed that such effects are highly dependent on genotypes. Thus, breeding tomato plants adapted to grow under limited water supply requires a better understanding of the effects of WD on fruit quality and their genetic variability. ln the present work, four experiments have been performed under greenhouse conditions on the 8 parents of the Multi-Parent Advanced Generation Inter-Cross population which offers the largest allelic variability observed in tomato. Moderate and intensive WDs have been applied during the whole period of fruit development The experiments were performed either in spring or in autumn to analyze the interactions between WD and season. Moreover, interaction between moderate WD and plant fruit load was measured in spring. Fruit quality was assessed through fresh and dry masses, and fruit composition (soluble sugars, organic acids, vitamin C, carotenoids). Results show that fruit fresh mass is reduced p,roportionally to WD intensity, whereas the % dry mass is increased. Big fruit size genotypes are much more sensitive to WD than small fruit size genotypes. The improvement of fruit taste, based on the increase of the sugar:acid ratio, resulted more from concentration effects than from metabolic trigger effects. Trade-offs between fruit size decrease and quality improvement allowed discriminating the 8 accessions for their genetic interest under water limited conditions.
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titre
Transcriptomic regulation in pepper during the interaction with Phytophthora capsici.
auteur
Gaëtan Maillot, Emmanuel Szadkowski, Anne Massire, Jean-Paul Bouchet, Veronique Brunaud, Martin-Magniette Marie-Laure, Sandrine Balzergue, Guillem Rigaill, Kurt Lamour, Véronique Lefebvre
article
16th Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary
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titre
Transcriptomic regulation in pepper during the interaction with Phytophthora capsici
auteur
Gaëtan Maillot, Emmanuel Szadkowski, Anne Massire, Jean-Paul Bouchet, Veronique Brunaud, Marie-Laure Martin-Magniette, Sandrine Balzergue, Guillem Rigaill, Kurt Lamour, Véronique Lefebvre
article
16. Eucarpia Capsicum and Eggplant Meeting, Sep 2016, Kecskemét, Hungary. 2016
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https://hal.inrae.fr/hal-02799453/file/Maillot%20Eucarpia%20Hungary%202016%20poster_1.pdf BibTex
titre
GWAS of tomato response to water deficit: focus on major fruit quality traits
auteur
Elise Albert, Vincent Segura, Justine Gricourt, Romain Novaretti, Yolande Carretero, Esther Pelpoir, Julien Bonnefoi, Laurent Derivot, Mathilde Causse
article
13. Solanaceae Conference, Sep 2016, Davis, United States. 2016
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https://hal.inrae.fr/hal-02799533/file/Albert_Causse%202016%20Poster_1.pdf BibTex
titre
Influence of iron availability on tomato fruit quality
auteur
Ester Izquierdo Alegre, Pierre Fourcroy, Jossia Boucherez, Geneviève Conejero, Nicolas Tissot, Christophe Rothan, Cécile Bres, Jean-Philippe Mauxion, Mathilde Causse, Patricia Siso Terreza, M Alvarez-Ferandez, Javier Abadia, Jean-Francois Briat, Frédéric Gaymard, Christian Dubos
article
11e Colloque National de la Société Française de Biologie Végétale SFBV, Jul 2016, Angers, France. 2016
resume
Influence of iron availability on tomato fruit quality. 11e Colloque National de la Société Française de Biologie Végétale SFBV
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titre
The type III effector RipAX2 confers avirulence of #Ralstonia solanacearum# to the eggplant AG91-25, carrying the resistance gene Ers1
auteur
Jérémy Guinard, Keke Wang, Fabien Lonjon, Lakshmi Sujeeun, Marco E. Mechan Llontop, Anne-Claire Cazalé, Patrick Barberis, Stéphane Genin, Marie-Christine Daunay, Jacques Dintinger, Stéphane Poussier, Boris A. Vinatzer, Nemo Peeters, Emmanuel Wicker
article
6th IBWS, Jul 2016, Toulouse, France. 2016
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no abstract
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De la ferme à la fourchette : TRADITOM Un nouveau projet de recherche de l'UE sur la valorisation des variétés traditionnelles de tomate
auteur
Brigitte Navez, Valentine Cottet, Raphael Tisiot, Mathilde Causse, Lilian Fontanet
article
Journées Portes Ouvertes du CTIFL, Jun 2016, Balandran, France. 2016
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https://hal.inrae.fr/hal-02794688/file/Causse%202016%20Poster_1.pptx https://hal.inrae.fr/hal-02794688/file/Causse%202016%20Poster_2.pptx BibTex
titre
Resistance sources against a new an old world begomoviruses associated with epidemic diseases in curcubit crops
auteur
Gustavo Romay, Cecile Desbiez, Catherine Wipf-Scheibel, Pauline Millot, Michel Pitrat, Hervé Lecoq
article
13. International plant virus epidemiology symposium, Jun 2016, Avignon, France. 165 p., 2016, “Building bridges between disciplines for sustainable management of plant virus diseases”. IPVE 2016. Programme and abstracts
resume
The cucurbits include several important vegetables to human consumption which are threatened for epidemic diseases such as those caused by begomoviruses. The Old World begomovirus Tomato leet curl New Delhi virus (ToLCNDV) was first described in India and is currently spreading in some Mediterranean countries. Meanwhile, the New World begomovirus Melon chlorotic mosaic virus (MeCMV) has been only described in Venezuela. This work aims to evaluate melon lines in order to look for resistance sources against these viruses.
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https://hal.inrae.fr/hal-02740930/file/Pitrat%202016%20poster%2074_1.pdf BibTex
titre
Exploring plant tolerance to viruses as a sustainable means of disease control
auteur
Judith Hirsch, Gregory Girardot, Alain Palloix, Benoît Moury
article
13. International plant virus epidemiology symposium, Jun 2016, Avignon, France. 165 p., 2016, “Building bridges between disciplines for sustainable management of plant virus diseases”. IPVE 2016. Programme and abstracts
resume
The use of resistant plant cultivars is an efficient, cost-effective and environmentally-friendly method of disease control, particularly against viral pathogens. However, resistance is subject to breakdown, through the often rapid adaptation of viral populations to newly deployed resistant genotypes. As it exerts a weaker selection pressure on parasite populations, plant tolerance to parasites - the mechanisms that reduce the negative impact of infection on host fitness or yield, despite relatively elevated parasite concentrations - appears as an interesting alternative to resistance sensu stricto - mechanisms that reduce pathogen accumulation (1). However, the durability of tolerance has seldom been experimentally tested, and counter-examples exist (2). Moreover, littie is known about the genetic determinants controlling tolerance to pathogens. We have chosen the interaction between pepper and Cucumber mosaic virus (CMV) as a model to study plant tolerance to viral pathogens and evaluate the durability of tolerance.
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https://hal.inrae.fr/hal-02744161/file/Palloix%202016%20poster%2034_1.pdf BibTex
titre
The resistance to virus triggered by aphid inoculation in Vat melon is not systemic
auteur
Pascale Mistral, Nathalie Boissot
article
13. International Plant Virus Epidemiology Symposium, Jun 2016, Avignon, France. 177 p., 2016
resume
Host plant resistance is an essential mean of controlling virus epidemies in crops. Resistance to viruses in plant belongs to three major families, either recessive or dominant resistance genes, as weil as the antiviral defense system based on RNA silencing. Most NBS-LRR antiviral resistances are triggered by the recognition of the NBS-LRR protein and a virus protein, playing the raie of avirulence factor. The Vat resistance gene in melon is unique among the dominant resistance to virus genes. It is a CC-NBS-LRR gene, it is triggered by the recognition between an aphid avirulence factor, delivered in plant cells by Aphis gossypii puncturing, and the CC-NBS-LRR pratein produced by Vat plants. This resistance is efficient against unrelated viruses transmitted on the non persistent mode (Boualem et al., 2016). We investigated if the resistance to virus triggered by A. gossypii in Vat plants is systemic.
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https://hal.inrae.fr/hal-02739588/file/Mistral_Boissot%202016%20poster%2054_1.pdf BibTex
titre
Impact of iron availability on tomato fruit quality
auteur
Ester Izquierdo Alegre, Pierre Fourcroy, Jossia Boucherez, Geneviève Conejero, Nicolas Tissot, Christophe Rothan, Cécile Bres, Jean-Philippe Mauxion, Mathilde Causse, Patricia Siso Terreza, M Alvarez-Ferandez, Javier Abadia, Jean-Francois Briat, Frédéric Gaymard, Christian Dubos
article
XVIII International Symposium on Iron Nutrition and Interactions in Plants, May 2016, Madrid, Spain. 2016
resume
Impact of iron availability on tomato fruit quality. XVIII International Symposium on Iron Nutrition and Interactions in Plants
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titre
Impact of cooking and storage on apricots fruit microconstituents.
auteur
Carine Le Bourvellec, Sylvie Bureau, Patrice Reling, Romain Bott, Albert Ribas, Jean Marc Audergon, Catherine Renard, Barbara Gouble
article
2nd Euro-Mediterranean Symposium on Fruit and Vegetable Processing, Apr 2016, Avignon, France. 2016
resume
Apricots are a rich source of phenolics and carotenoids that may contribute to reduced risks of chronic diseases. However, because of the seasonal availability, apricots are commonly consumed after processing and storage. The different thermal processing methods have been shown to reduce polyphenolic and carotenoid levels in fruit. However information is lacking on how different methods and storage influence the phenolic and carotenoid composition and their content in processed apricots. Four apricot cultivars were processed in two different ways: home cooking (85°C) and industrial processing (95°C). Cans from industrial processing were analyzed immediately and after storage of 2 months at ambient temperature. Phenolics and carotenoids were quantified by HPLC with diode array detection. Industrial processing caused a significantly higher loss of total phenolics compared to domestic cooking. Upon cooking, procyanidins were retained in apricot tissues while flavan-3-ol monomers and hydroxycinnamic acids were partially leached into the syrup. Due to leaching of flavan-3-ol monomer procyanidin’s DPn significantly increased from fruit to canned products. Anthocyanins were not significantly altered by heat treatment. Total carotenoids exhibited no significant change after heat processing. However among carotenoids, a cis-β-carotene isomer was significantly increased after industrial processing, but with lower amounts after domestic cooking. No significant losses were observed for total phenolic compounds after two months in cans at ambient temperature, this was mainly due to procyanidins which were stable over time. However, flavan-3-ol monomers, hydroxycinnamic acids and anthocyanins were significantly lower in the fruit after storage. Total carotenoids compounds significantly decreased over the storage period. Based on HPLC data, carotenoids were more stable than phenolics after heat treatment. Carotenoids and phenolics in fruit decreased with storage time. More interestingly, this study indicates that apricots are a rich source of procyanidins, having profiles similar to those found in apples. Processing changed not only the content of procyanidins in apricot products but also the relative ratio of the different molecular weights.
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titre
Apricot texture: variability as a function of cultivar, influence of maturity and impact of cooking
auteur
Jamal Ayour, Barbara Gouble, Patrice Reling, Albert Ribas, Jean Marc Audergon, Mohamed Benichou, Catherine Renard
article
2nd Euro-Mediterranean Symposium on Fruit and Vegetable Processing, Apr 2016, Avignon, France. 2016
resume
Apricot (Prunus armeniaca L.) is a fleshy fruit of real economic and nutritional interest. The rapid loss of fruit firmness is a decisive factor for quality and to decide apricot use (fresh or processed) and commercialization ways (short or storage). To better understand the texture heterogeneity in apricot, we studied the impact of the harvest stage and the effect of a heat treatment on a large range of cultivars.
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https://hal.inrae.fr/hal-02742833/file/FVP16_Ayour_apricot%20texture_poster_1.pdf BibTex
titre
Microstructural changes in cooked apricots related to the loss of texture
auteur
Albert Ribas-Agusti, Barbara Gouble, Jean Marc Audergon, Mohamed El Maataoui, Catherine Renard
article
2nd Euro-Mediterranean Symposium on Fruit and Vegetable Processing, Apr 2016, Avignon, France. 2016
resume
Introduction. The quality of the apricot products is largely defined by their texture, which is significantly lost upon processing. The pectin properties of apricots may play an important role in this loss of texture, even more than the initial firmness, but this is not yet well understood. This study aims to identify a varietal differentiation in the texture-loss properties and to link them with microstructural changes, with a final goal of understanding the mechanisms that influence the texture loss in apricot. Materials and Methods. Fruits were selected from four varieties at similar ripening stages, which were determined by their firmness using a compression test]. The apricot halves were cooked at 85°C in sugar syrup and their texture was measured by the maximum force in the penetrometry test. Microstructure changes were revealed by ruthenium red staining (pectin) and LM19 immunolabelling (unmethylated and low-methylated pectin). Results and Discusson. Variety largely influenced the loss of texture. Orangered was the variety with higher resistance to the texture loss (67% of the initial firmness), followed by Hargrand (74%), Iranien (75%) and Goldrich (86%). The tissues did not show severe damaging after cooking, however, some microstructural changes could be observed. The cells lost turgor as demonstrated by the higher sinuosity of the cell walls. Some intercellular spaces swelled, creating round-shaped microstructures filled with unmethylated pectin, as showed by LM19. Their presence across the varieties showed to be in line with their resistance to the loss of texture. Varietal differences in the biochemical properties must have prompted the ease of pectin to be leached from the tissue or to be retained within the intercellular spaces. Conclusions. We identified a link between the creation of intercellular microstructures and the loss of texture. This study opens the possibility of understanding the creation of these microstructures and the biochemical properties that are implied, which is in the interest of the food industry for the elaboration of higher quality apricot products.
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https://hal.inrae.fr/hal-02738899/file/FVP16_Ribas_microstrutural%20changes_poster_1.pdf BibTex

2015

Conference papers

titre
Recherche de résistance aux nématodes à galles chez la laitue
auteur
Brigitte Maisonneuve
article
Rencontres du GIS PIClég, Groupement d'Intérêt Scientifique pour la Production Intégrée en Cultures légumières (Gis Piclég). FRA., Nov 2015, Paris, France
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A la recherche de méthodes alternatives aux tests biologiques classiques pour la détermination de la date de sortie d'endodormance, la quête du haut débit par le Groupe de Travail Dormance de Perpheclim et d'ODS.
auteur
Marc Bonhomme, Jean-Paul Charpentier, Vincent Segura, Luc Pâques, Jean Marc Audergon, José Quero-Garcia, Elisabeth Dirlewanger, Rémi Beauvieux, Bénédicte Wenden, Jean-Michel Legave, Isabelle Farrera, Hendrik Davi, Frederic Jean, Isabelle Chuine
article
Colloque francophone PHENOLOGIE, Nov 2015, Clermont-Ferrand, France. 135 p
resume
Pour améliorer les modélisations de la phénologie, nous avons besoin de dates de débourrement et de floraison mais aussi de dates de levée de dormance, sur un grand nombre d’espèces. On est à la recherche de méthodes alternatives aux tests classiques, peu onéreuses et permettant de s’approcher du haut débit. Une approche en spectrométrie proche infrarouge montre une bonne corrélation entre NIRS et paramètre classique de dormance (DMD) sur poudre de bourgeons végétatifs et floraux. Une autre approche concernant la visualisation de callose au niveau de la zone méristématique, considérée comme un marqueur d’état dormant, a été entreprise.
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https://hal.archives-ouvertes.fr/hal-01580642/file/2015_Bonhomme_Orale_Ph%C3%A9no_%7BF8DC2941-1275-420D-B6C7-3EC6F8507BC5%7D.pdf BibTex
titre
TALEN and CRISPR strategies for targeted editing of the plant genome
auteur
Marianne Mazier, Fabien Nogué
article
CORESTA AP2015, Oct 2015, Izmir, Turkey
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https://hal.inrae.fr/hal-02801029/file/Mazier%202015%20Coresta%20AP_1.pdf https://hal.inrae.fr/hal-02801029/file/Mazier%202015%20Coresta%20AP_2.docx BibTex
titre
Vitamin C and cell wall metabolisms in tomato: GDP-D-mannose epimerase (GME) a key actor of these interrelated pathways
auteur
Louise Gilbert, Marie Dumont, Carine Ferrand, Celine Bournonville, Antoine Monier, Joana Jorly, Isabelle Atienza, Michel Hernould, Rebecca Stevens, Arnaud Lehner, Jean-Claude Mollet, Christophe Rothan, Patrice Lerouge, Pierre Baldet
article
The 12th Solanaceae Conference SOL 2015, Oct 2015, Bordeaux, France
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https://hal.inrae.fr/hal-02739180/file/Stevens%202015%2012th%20Solanaceae%20Conference%2050_1.pdf BibTex
titre
Toward a characterization of the pepper host resistance effect on the gene expression of the pathogenic Phytophthora capsici
auteur
Gaëtan Maillot, Anne Massire, Jean-Paul Bouchet, Véronique Brunaud, Marie-Laure Martin-Magniette, Sandrine Balzergue, Kurt Lamour, Véronique Lefebvre
article
12. Solanaceae Conference, Oct 2015, Bordeaux, France
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https://hal.inrae.fr/hal-02795452/file/Maillot_Lefebvre%202015%2012th%20Solanaceae%20Conference%2062_1.pdf BibTex
titre
Genotype by watering regime interaction in cultivated tomato: from phenotypes to genes
auteur
Elise Albert, Yolande Carretero, Justine Gricourt, Esther Pelpoir, Romain Novaretti, Claire Duffes, Julien Bonnefoi, Nadia Bertin, Frederique Bitton, Stephanie Pateyron, Jean-Philippe Tamby, Mathilde Causse
article
12. Solanaceae Conference, Oct 2015, Bordeaux, France
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https://hal.inrae.fr/hal-02743885/file/Albert_Causse%202015%2012th%20Solanaceae%20Conference%2084_1.pdf BibTex
titre
Assessment of factors affecting genomic selection in populations of tomato
auteur
Coralie Picard, Janejira Duangjit, Mathilde Causse, Christopher Sauvage
article
12. Solanaceae Conference, Oct 2015, Bordeaux, France
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https://hal.inrae.fr/hal-02795275/file/Causse_Sauvage%2012th%20Solanaceae%20Conference%2030_1.pdf BibTex
titre
Modelling the population history using population genomics : the tomato domestication as a case of study
auteur
Christopher Sauvage, Charlotte Aichholz, Gautier Sarah, Manuel Ruiz, Mathilde Causse, Jacques David, Sylvain Glemin
article
12. Solanaceae Conference, Université de Bordeaux (UB). FRA., Oct 2015, Bordeaux, France
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absent
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https://hal.archives-ouvertes.fr/hal-01269378/file/Sauvage_Causse%202015%2012th%20Solanaceae%20Conference%2097_1.pdf BibTex
titre
Genomic variation in tomato, from wild to cultivated
auteur
José Blanca, Javier Montero-Pau, Christopher Sauvage, Guillaume Bauchet, Eudald Illa, Maria José Diez Niclos, David Francis, Mathilde Causse, Esther van der Knaap, Joaquîn Cafiizares
article
12. Solanaceae Conference, Oct 2015, Bordeaux, France
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https://hal.inrae.fr/hal-02800701/file/Causse%202015%2012th%20Solanaceae%20conference%2027_1.pdf BibTex
titre
Metabolic genome-wide-association unravels trait architecture and natural variation in tomato primary and secondary metabolisms
auteur
Guillaume Bauchet, Stéphane Grenier, Nicolas Samson, Vincent Segura, Aniko Kende, Jules Beekwilder, Katarina Cankar, Arnaud G. Bovy, Jean-Luc Gallois, Julien Bonnet, Laurent Grivet, Elek Segura, Charles Segura, Mathilde Causse
article
12. Solanaceae Conference, Oct 2015, Bordeaux, France
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absent
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https://hal.archives-ouvertes.fr/hal-01269376/file/Bauchet_Causse%202015%2012th%20Solanaceae%20Conference%2041_1.pdf BibTex
titre
Pectinmethylesterase activity heterogeneity in apricot fruit
auteur
Albert Ribas-Agusti, Barbara Gouble, Jean Marc Audergon, Catherine Renard
article
EuroFoodChem XVIII, Oct 2015, Madrid, Spain
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titre
Yield prediction based on QTLs for yield components using crop eco-physiological models
auteur
M. Wubs, Egbert Heuvelink, J. J. Magan, Alain Palloix, Fredericus van Eeuwijk
article
MODEL-IT, Symposium on modelling for Horticulture, Oct 2015, Wageningen, Netherlands
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https://hal.inrae.fr/hal-02796656/file/Palloix%202015%20Symp.%20model.%20Hort._1.pdf https://hal.inrae.fr/hal-02796656/file/Palloix%202015%20Symp.%20model.%20Hort._2.docx BibTex
titre
Identification de géniteurs de résistance à des nématodes à galles du genre Meloidogyne chez la laitue
auteur
Brigitte Maisonneuve
article
Journée nationale Salade, Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL). FRA., Oct 2015, Bellegarde, France
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titre
RNA-Seq study of host resistance and isolate aggressiveness on gene expression in [i]Phytophthora capsici[/i]
auteur
Gaëtan Maillot, Anne Massire, Jean-Paul Bouchet, Veronique Brunaud, Marie-Laure Magniette, Sandrine Balzergue, Kurt Lamour, Véronique Lefebvre
article
8. Effectome Meeting, Sep 2015, Lauret, France
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absent
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https://hal.archives-ouvertes.fr/hal-01210021/file/Maillot%202015%20effectome%20abstract_1.pdf https://hal.archives-ouvertes.fr/hal-01210021/file/Maillot%202015%20effectome%20abstract_2.docx BibTex
titre
Effect of shrinkage on prediction accuracy of methionine and proline fruit contentsin a broad-based tomato population
auteur
Janejira Duangjit, Mathilde Causse, Christopher Sauvage
article
Genomics, Bioinformatics and System Biology Conference (GBSBC 2015), Sep 2015, Bangkok, Thailand
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https://hal.inrae.fr/hal-02739886/file/Causse_Sauvage%202015%20GBSBC%201-6_1.pdf BibTex
titre
Spatial pattern of Eurasian woolly mammoth extinctions during the Late Pleistocene based on statistical inference from fossil records
auteur
Frédérik Saltré, Joel Chadoeuf, B.W. Brook, Damien A. Fordham, Marta Rodriguez-Rey, Corey J.A. Bradshaw
article
9. IALE World Congress, International Association of Landscape Ecology (IALE). USA., Jul 2015, Portland Oregon, U.S. Virgin Islands
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https://hal.inrae.fr/hal-02793379/file/Chadoeuf%202015%20abstract_1.pdf https://hal.inrae.fr/hal-02793379/file/Chadoeuf%202015%20abstract_2.docx BibTex
titre
Mechanical harvest: a realistic challenge for the processed apricot market?
auteur
Barbara Gouble, Patrice Reling, Catherine Renard, J. M. Broquaire, C. Chamet, Jean Marc Audergon
article
16. International Symposium on Apricot Breeding and Culture, International Society for Horticultural Science (ISHS). INT., Jun 2015, Shenyang, China. pp.5, ⟨10.17660/ActaHortic.2018.1214.9⟩
resume
ILLIAD is a French national project in which food-chain sustainability is being evaluated on four products ( wheat, rice, peach and apricot). For apricot, two difficulties for French production have been identified: i) the high cost of manpower in this culture and ii) fruit processors' dependence on surplus fruits from fresh consumption. This leads to very high variability in supply, price and quality from year to year. In this context, one solution might be dedicated orchards for processing industries. At first, cultivars well adapted to processing and with a low demand for inputs were screened for their behavior in mechanical harvest. Mechanical harvest was carried out using tree shaking ( at 40 cm from the ground) and collection on a fabric screen. Results obtained over 2 years on more than 15 cultivars and in two production areas are presented. The low mechanical damage observed just after harvesting or after 7 days of storage for a few cultivars and the possibility of optimizing shaking parameters according to agronomic and physiologic criteria ( fruit falling, maturity heterogeneity, etc.) confirm the suitability of mechanical harvesting and the opportunity to create dedicated orchards.
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Selections issued from CEP Innovation, Centrex and INRA: the apricot breeding program in France
auteur
G. Fremondiere, Alain Blanc, Florent Gilles, Guy Clauzel, J. M. Broquaire, Guillaume Roch, Barbara Gouble, Sylvie Bureau, C. Pitiot, Jean Marc Audergon
article
16. International Symposium on Apricot Breeding and Culture, International Society for Horticultural Science (ISHS). INT., Jun 2015, Shenyang, China. pp.3, ⟨10.17660/ActaHortic.2018.1214.36⟩
resume
French apricot production is located in the south-eastern part of the country, with a focused zone in the Rhone valley and close to the Mediterranean Sea. The north of the Rhone valley is characterized by a continental climate, while the southern region ( Rhone valley and Mediterranean area) is under a warm, typically Mediterranean climate. Obviously, apricot fruit production depends on the development of a specific panel of cultivars in each area of cultivation because of economic and adaptation constraints. In order to enlarge the panel of cultivars for growers of each region, an integrated breeding program has been developed at a national level in France with the participation of INRA, Centrex and CEP Innovation. The main goals of the breeding program are: the elaboration of cultivars suitable for 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 transport). The evaluation phase is organized in the three main French areas of production ( Perpignan, Nimes and Valence) with three complementary evaluation stages: ( i) observation of hybrids on their own roots ( ii) evaluation of pre-selections after grafting in the three main areas, and ( iii) 'elite' agronomic and commercial assessments in small orchards. A tough diagnosis, that includes biological, serological and molecular analysis, is conducted in parallel for assessing resistance to Plum pox virus ( PPV). The main results issued from this program are presented here, with 10 cultivars, including PPV-resistant Aramis (R) cultivars.
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Infrared spectroscopy as a rapid tool to assess apricot fruit quality
auteur
Sylvie Bureau, Catherine Renard, Jean Marc Audergon
article
16. International Symposium on Apricot Breeding and Culture, Jun 2015, Shenyang, China
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https://hal.inrae.fr/hal-02742207/file/Audergon%202015%2016.%20Int.%20Symp.%20Apricot%20Chine%2013_1.pdf BibTex
titre
Aramis®" strategy: a durable manner to develop a sharka resistant apricot cultivar
auteur
Guillaume Roch, Jean Marc Audergon, Thierry Candresse, Véronique Decroocq, David Tricon, Sylvie Dallot, Magaly Lamberet, Guy Clauzel
article
16. International Symposium on Apricot Breeding and Culture, International Society for Horticultural Science (ISHS). INT., Jun 2015, Shenyang, China. 298 p
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https://hal.inrae.fr/hal-02744190/file/Roch_Audergon%202015%2016.%20Int.%20Symp.%20Apricot%20Chine%2026-27_1.pdf BibTex
titre
Genetic structure of a worldwide germplasm collection of Prunus armeniaca L. species
auteur
Hedia Bourguiba, Jean Marc Audergon, Boris Krška, Tatyana Zhebentyayeva, Arnaud Remay, Claudio d'Onofrio, Craig A. Ledbetter, Hiroyuki Iketani, Danilo Christen, Weisheng Liu, Guillaume Roch
article
16. International Symposium on Apricot Breeding and Culture, Jun 2015, Shenyang, China. ⟨10.17660/ActaHortic.2018.1214.35⟩
resume
Analyses of genetic diversity and phylogenetic relationships illuminate the origin and domestication of crop species and have important implications for plant breeding programs and the conservation of genetic resources. Apricot ( Prunus armeniaca L.) genetic resources in collections that are widely dispersed around the world were assessed using 25 simple sequence repeat ( SSR) markers. Analysis of allelic diversity among SSR data revealed at least a double pattern of diffusion from Central Asia to eastern and western countries with a clear east-west loss of genetic diversity related to the genetic bottleneck during apricot domestication. Structure and phylogenetic analysis indicated that accessions from Central Asia and China were genetically most diverse, suggesting that this large region constitutes the apricot center of origin.
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https://hal.inrae.fr/hal-02736957/file/Audergon_Bourguiba%202015%2016.%20Int.%20Symp.%20Apricot%20Chine%2020-21_1.pdf BibTex
titre
Solanaceae pollen tubes and vegetative organs have structurally divergent cell wall xyloglucan
auteur
Flavien Dardelle, François Le Mauff, Corinne Loutelier-Bourhis, Muriel Bardor, Christophe Rihouey, Mathilde Causse, Patrice Lerouge, Azeddine Driouich, Jean-Claude Mollet, Arnaud Lehner
article
International Symposium on Plant Signaling and Behavior (PSB, 3, 2015), Jun 2015, Paris, France
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Functional analysis of Mlo genes in powdery mildew resistance in melon
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Sonia Elbelt, Nathalie Giovinazzo, Verane Sarnette, Marc Bardin, Christelle Troadec, Abdelhafid Bendahmane, Catherine Dogimont
article
5. ISHS International Symposium, Curcubits 2015, Jun 2015, Murcia, Spain
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https://hal.inrae.fr/hal-02744309/file/Elbert_Dogimont%202015%205.%20ISHS%20Int.%20Sympo.%20Cucurbits%2043_1.pdf BibTex
titre
Discovery of peach QTLs by using pedigree-based analysis
auteur
José Ramon Hernandez, Diego Micheletti, Marco Bink, Eric van de Weg, Daniele Bassi, Nelson Nazzicari, Andrea Caprera, Maria Teresa Dettori, Sabrina Micali, Elisabeth Dirlewanger, Patrick Lambert, Thierry Pascal, Elisa Bianchi, Laura Rossini, Ignazio Verde, Bénédicte Quilot-Turion, Francois Laurens, Pere Arús, Maria Jose Aranzana
article
14. Eucapia Fruit breeding and genetics symposium, Jun 2015, Bologne, Italy. 2 p
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absent
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Assessing brown rot resistance in peach fruit
auteur
I. Pacheco, Leandro de Oliveira-Lino, A. Ciacciulli, M. Lama, S. Foschi, F. Faoro, Veronique Signoret, D. Bassi, Bénédicte Quilot-Turion
article
XIV Eucarpia Symposium on Fruit Breeding and Genetics, Jun 2015, Bologne, Italy
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https://hal.inrae.fr/hal-02740286/file/Quilot_%20Bologna_2015_1.pdf BibTex
titre
A pyramiding strategy for resistance to rootknot nematodes meloidogyne spp. in prunus rootstock material
auteur
Henri Duval
article
Innovation in Integrated & Organic Horticulture, INNOHORT 2015, International Society for Horticultural Science (ISHS). INT., Jun 2015, Avignon, France
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https://hal.inrae.fr/hal-02738895/file/Duval%202015%20ISHS%20Avignon_1.pdf BibTex
titre
Screening tomato germplasm for resistance to late blight
auteur
Bernard Caromel, Coralie Hamers, Nasradin Touhami, Alexandre Renaudineau, Alexandre Bachellez, Anne Massire, Rene Damidaux, Véronique Lefebvre
article
Innovation in Integrated & Organic Horticulture, INNOHORT 2015, Jun 2015, Avignon, France
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https://hal.inrae.fr/hal-02744090/file/Caromel_Bachellez%202015%20ISHS%20Avignon_1.pdf BibTex
titre
Physical host factors for brown rot resistance in peach fruit
auteur
Leandro de Oliveira-Lino, Michel Génard, Véronique Signoret, Bénédicte Quilot-Turion
article
Innovation in Integrated & Organic Horticulture, INNOHORT 2015, International Society for Horticultural Science (ISHS). INT., Jun 2015, Avignon, France. ⟨10.17660/ActaHortic.2016.1137.15⟩
resume
Brown rot in peach fruits caused by the fungi Monilinia sp. is a common disease that can provoke as much as 30 to 40% of crop losses. Little is known about the fruit resistance factors and the infection process. The aim of this study was to investigate the physical factors of resistance of the fruit and their genetic control. This would provide a tool to rationalize genotype x cultural practice combinations in order to reduce brown rot incidence. Mechanical characteristics of fruit skin (conductance, stomatal density, microcracks) potentially linked to Monilinia (M.) resistance were investigated in 27 cultivars. Two cultivars and a segregating population were phenotyped for fruit cuticular conductance and sensitivity was assessed by two independent infection tests. In the microscopy analyses, high diversity of germination and penetration of fungi through stomata and microcracks were observed. Preliminary results show significant differences in the number of stomata among genotypes. However, no obvious relationship was found between stomata number, cuticular conductance and infection at the early stage of fruit development. At maturity, the population displayed high variability in the resistance to M. laxa, giving hope for breeding programs, despite the low stability of results among tests and years. The knowledge gained from these experiments will be integrated into an existing ecophysiological model in order to concurrently optimize fruit characteristics and cultural practices to reduce infection risks.
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Assessment of diseases susceptibility of peach cultivars in experimental plots and on-farm for organic and low-input systems. Baseline of french case studies
auteur
Claude Eric Parveaud, Johanna Brenner, Sophie-Joy Ondet, Christelle Gomez, Gilles Libourel, François Warlop, Laurent Brun, Vincent Mercier, Guy Clauzel, Jean Marc Audergon
article
Innovation in Integrated & Organic Horticulture, INNOHORT 2015, International Society for Horticultural Science (ISHS). INT., Jun 2015, Avignon, France
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https://hal.inrae.fr/hal-02738751/file/Audergon_Clauzel%202015%20ISHS%20Avignon_1.pdf BibTex
titre
Host factors for brown rot resistance in peach fruit
auteur
Leandro de Oliveira-Lino, Michel Génard, Bénédicte Quilot-Turion
article
Innovation in Integrated & Organic Horticulture, INNOHORT 2015, International Society for Horticultural Science (ISHS). INT., Jun 2015, Avignon, France. 56 p
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https://hal.inrae.fr/hal-02738605/file/DeOliveiraLino_Quilot_Avignon_2015_1.pdf BibTex
titre
Genetic and genomic control of response to water deficit in cultivated tomato
auteur
Elise Albert, Yolande Carretero, Justine Gricourt, Esther Pelpoir, Romain Novaretti, Claire Duffes, Julien Bonnefoi, Mathilde Causse
article
Innovation in Integrated & Organic Horticulture, INNOHORT 2015, International Society for Horticultural Science (ISHS). INT., Jun 2015, Avignon, France
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https://hal.inrae.fr/hal-02744107/file/Albert_Causse%202015%20ISHS%20Avignon_1.pdf BibTex
titre
Combinations of varietal and technical innovations for the sustainable and integrated management or root-knot nematodes: the gedumen project
auteur
Caroline Djian-Caporalino, Ariane Fazari, Nathalie Marteu, Mireille Navarrete, Arnaud Dufils, Marc Tchamitchian, Claudine Furnion, Amélie Lefevre, Laure Pares, Thierry Mateille, Johannes Tavoillot, Alain Palloix, Anne-Marie Sage-Palloix, Hélène Védie, Claire Goillon, Philippe Castagnone-Sereno
article
Innovation in Integrated & Organic Horticulture, INNOHORT 2015, International Society for Horticultural Science (ISHS). INT., Jun 2015, Avignon, France
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https://hal.inrae.fr/hal-02739482/file/Palloix_Sage-Palloix%202015%20ISHS%20Avignon_1.pdf BibTex
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A kinetic model of sugar metabolism allows the simulation of sugar concentrations and its genetic variability during peach fruit growth
auteur
Elsa Desnoues, Michel Génard, Bénédicte Quilot-Turion, Valentina Baldazzi
article
10. International Symposium on Modelling in Fruit Research and Orchard Management, International Society for Horticultural Science (ISHS). INT., Jun 2015, Montpellier, France
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https://hal.inrae.fr/hal-02744196/file/Desnoues_Quilot%20Montpellier_2015_1.pdf BibTex
titre
Joint estimation of effective population sizes and selection coefficients from time-sampled data: a case study on virus populations submitted to plant resistance
auteur
Elsa Rousseau, Frédéric Fabre, Jérôme Coville, Ludovic Mailleret, Alain Palloix, Rachid Senoussi, Frédéric Grognard, Benoît Moury
article
9. colloque de la Société Française de Phytopathologie, Societe Francaise de Phytopathologie (SFP). FRA., Jun 2015, Colmar, France
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https://hal.inrae.fr/hal-02738575/file/2015_Rousseau_SFP_1.pdf BibTex
titre
Epidemic reconstruction for the inference of vector dispersal in fragmented landscapes
auteur
David Pleydell, Samuel Soubeyrand, Sylvie Dallot, Gerard Labonne, Joel Chadoeuf, Gael Thébaud
article
Risques et modèles en épidémiologie humaine, animale & végétale, Université des Antilles et de la Guyane (UAG). Pointe-à-Pitre, FRA., May 2015, Point-à-Pitre, France
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https://hal.inrae.fr/hal-02799006/file/sharka_short_1.pdf BibTex
titre
Estimation of genetic drift and selection from next generation sequencing time-sampled data
auteur
Elsa Rousseau, Frédéric Fabre, Jérôme Coville, Ludovic Mailleret, Alain Palloix, Rachid Senoussi, Frédéric Grognard, Benoît Moury
article
Modelling biological evolution 2015: linking mathematical theories with empirical realities, Apr 2015, Leicester, United Kingdom
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no abstract
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Effect of the lettuce genotype on the protective efficacy of plant defence stimulators against Bremia
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Brigitte Maisonneuve, Caroline Allen-Aubouard
article
Eucarpia Leafy Vegetable 2015, Apr 2015, Murcia, Spain
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https://hal.inrae.fr/hal-02739598/file/Maisonneuve%20Eucarpia%202015_1.pdf https://hal.inrae.fr/hal-02739598/file/Maisonneuve%20Eucarpia%202015_2.docx BibTex
titre
PERPHECLIM ACCAF Project perennial fruit crops and forest phenology evolution facing climatic changes.
auteur
Inaki Garcia de Cortazar Atauri, Jean Marc Audergon, Patrick Bertuzzi, Christel Anger, Marc Bonhomme, Isabelle Chuine, Hendrik Davi, Sylvain Delzon, Eric Duchêne, Jean-Michel Legave, Helene Raynal, Christian Pichot, Cornelis van Leeuwen, . Perpheclim Team
article
General Assembly of the European Geosciences Union (EGU), Apr 2015, Vienne, Austria. pp.EGU2015-9846
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https://hal.inrae.fr/hal-02739606/file/2015_GarciadeCortazar_EGU_Abstract_1.pdf BibTex
titre
Déterminants génétiques du contournement de la résistance des solanacées maraîchères au virus Y de la pomme de terre : vers la compréhension et la gestion de la durabilité des résistances
auteur
Benoît Moury, Frédéric Fabre, Mekki Ben Khalifa, Hatem Fakhfakh, Alain Palloix
article
26. Forum International des Sciences Biologiques et de Biotechnologie, Association Tunisienne des Sciences Biologiques (ATSB). TUN., Mar 2015, Monastir, Tunisie
resume
De nombreux gènes de résistance sont utilisés chez les solanacées maraîchères (piment et tomate) pour lutter contre le virus Y de la pomme de terre (PVY). Ces résistances ont montré des durabilités très contrastées : certaines résistances sont efficaces depuis plus de 50 ans sans qu’il y ait émergence de souches adaptées (virulentes) de PVY alors que pour d’autres résistances, des souches virulentes sont déjà présentes dans les cultures avant même l’utilisation de variétés porteuses de ces résistances par les agriculteurs. L’identification des mutations du PVY responsables du contournement de ces différentes résistances et de leur impact sur le pouvoir pathogène du virus ont permis de comprendre les raisons de ces disparités. Par ailleurs, une approche de modélisation mathématique des événements biologiques en jeu dans le contournement des résistances a permis de définir des stratégies optimales d’utilisation des variétés cultivées dans un paysage agricole. Ces résultats soulignent l’importance de la connaissance du déterminisme génétique du pouvoir pathogène chez les virus pour lutter efficacement et durablement contre les maladies qu’ils induisent.
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Le projet GEDUNEM : Innovations techniques et variétales pour une gestion durable & intégrée des nématodes à galles dans les systèmes maraîchers sous abris
auteur
Caroline Djian-Caporalino, Ariane Fazari, Nathalie Marteu, Mireille Navarrete, Arnaud Dufils, Marc Tchamitchian, Claudine Furnion, Amélie Lefevre, Laure Pares, Thierry Mateille, Johannes Tavoillot, Alain Palloix, Anne-Marie Sage-Palloix, Hélène Védie, Claire Goillon, I. Forest, Philippe Castagnone-Sereno
article
5. Conférence Internationale sur les Méthodes Alternatives de Protection des Plantes AFPP, Mar 2015, Lille, France
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https://hal.inrae.fr/hal-02743394/file/Palloix_Sage-Palloix%202015%205.%20Conf.%20Lille_1.pdf https://hal.inrae.fr/hal-02743394/file/Palloix_Sage-Palloix%202015%205.%20Conf.%20Lille_2.doc BibTex
titre
GENIUS project. Genome ENgineering Improvement for Useful plants of a Sustainable agriculture
auteur
Fabien Nogué, Philippe Vergne, Anne-Marie Chèvre, Jean-Eric Chauvin, Oumaya Bouchabke-Coussa, Annabelle Dejardin, Elisabeth Chevreau, Laurence Hibrand-Saint Oyant, Marianne Mazier, Pierre Barret, Emmanuel Guiderdoni, Luc Mathis, Christophe Sallaud, Mireille Matt, Jean-Philippe Pierron, Eric Bonnel, Séverine Foucrier, Alain Toppan, Laure Trannoy, Peter Rogowsky
article
15. Rencontres de Virologie Végétale (RVV), Jan 2015, Aussois, France
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https://hal.archives-ouvertes.fr/hal-01204208/file/Mazier%202015%20Aussois%20R%C3%A9sum%C3%A9%20du%20poster_2.pdf https://hal.archives-ouvertes.fr/hal-01204208/file/Mazier%202015%20Aussois%20poster_1.pdf https://hal.archives-ouvertes.fr/hal-01204208/file/Mazier%202015%20Aussois%20R%C3%A9sum%C3%A9%20du%20poster_3.docx BibTex
titre
The tomato-potyvirus system, a comparative system for natural and induced resistances associated with the initiation factors 4E
auteur
Camille Gauffier, Caroline Lebaron, André Moretti, C. Constant, F. Moquet, G. Bonnet, Carole Caranta, Jean-Luc Gallois
article
15. Rencontres de Virologie Végétale, Jan 2015, Aussois, France
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https://hal.inrae.fr/hal-02794002/file/OK%28prod%29%20Gauffier%20T017%20Eucarpia%20tomato%202014_1.pdf BibTex
titre
Joint estimation of effective population sizes and selection coefficients from time-sampled data: a case study on virus populations exposed to plant resistance
auteur
Elsa Rousseau, Frédéric Fabre, Jérôme Coville, Ludovic Mailleret, Alain Palloix, Rachid Senoussi, Frédéric Grognard, Benoît Moury
article
15. Rencontres de Virologie Végétale (RVV), Jan 2015, Aussois, France
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https://hal.inrae.fr/hal-02738942/file/2015_Rousseau_RVV_1.pdf BibTex
titre
Évaluer l’acceptabilité par les agriculteurs d’innovations variétales et agronomiques pour maîtriser les nématodes à galles en maraîchage sous abri (le projet GEDUNEM)
auteur
Mireille Navarrete, Claudine Furnion, Caroline Djian-Caporalino, Arnaud Dufils, Philippe Castagnone, Alain Palloix, Marc Tchamitchian, Ariane Fazari, Nathalie Marteu, Anne-Marie Sage-Palloix, Amélie Lefevre, Laure Pares, Thierry Mateille, Johannes Tavoillot, Hélène Védie, Claire Goillon, Isabelle Forest
article
Les Rencontres du Végétal, AGROCAMPUS OUEST. FRA., Jan 2015, Angers, France. 10 p
resume
La gestion des nématodes à galles (Meloidogyne spp.) est un problème majeur en maraîchage sous abri, notamment dans le Sud-Est de la France où plus de 40 % des exploitations sont touchées par ce ravageur (enquête 2007-2010). Suite aux restrictions d’utilisation des nématicides chimiques et afin de conforter la durabilité des moyens de lutte alternatifs, il est nécessaire d’élaborer de nouvelles stratégies de gestion des cultures et des populations de nématodes. Des prototypes de systèmes de culture ont été construits en partenariat avec des conseillers techniques. Ils intègrent des résistances génétiques, des rotations de cultures alternant plantes hôtes et non-hôtes et l’utilisation d'engrais verts à action nématicides pendant l’interculture. Le projet Gedunem vise à évaluer ces stratégies du point de vue de leur efficacité agronomique, de la durabilité de la protection des cultures et d’un point de vue sociotechnique. Cette communication porte sur l’évaluation de l’acceptabilité des stratégies par les agriculteurs. L’étude repose sur une comparaison des systèmes de culture actuels des agriculteurs et des prototypes en cours de test. Il s’agit de recueillir les avis des agriculteurs sur la faisabilité en exploitation pour chacun des 3 prototypes élaborés (Furnion 2014). Les principaux problèmes déjà identifiés dans la mise en œuvre de ces prototypes sont le coût et le temps nécessaire à la mise en place de certaines pratiques (engrais verts nématicides) ainsi que la disponibilité des parcelles suivant les successions de cultures. Il s’agit aussi d’analyser dans quelle mesure l’importance des différentes contraintes varie suivant les types d’exploitation. Cette étude permettra de repérer les adaptations de ces prototypes de systèmes de culture à prévoir pour les rendre plus faciles à mettre en œuvre dans les exploitations sur le plan agronomique, économique et social.
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Conception et évaluation d’innovations variétales et agronomiques pour maîtriser les nématodes à galles en maraîchage sous abri (le projet GEDUNEM)
auteur
Caroline Djian-Caporalino, Philippe Castagnone-Sereno, Ariane Fazari, Nathalie Marteu, Mireille Navarrete, Arnaud Dufils, Marc Tchamitchian, Claudine Furnion, Alain Palloix, Anne-Marie Sage-Palloix, Amélie Lefevre, Laure Pares, Thierry Mateille, Johannes Tavoillot, Hélène Védie, Claire Goillon, Forest Isbell
article
8. Rencontres du végétal, Jan 2015, Angers, France
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https://hal.inrae.fr/hal-02801729/file/Palloix_Sage-Palloix%202015%20Renc.%20du%20V%C3%A9g%C3%A9tal_1.pdf BibTex
titre
GnpIS-Asso : A Generic Database for Managing and Exploiting Plant Genetic Association Studies Results Using High Throughput Genotyping and Phenotyping Data
auteur
Delphine Steinbach, Guillaume Merceron, Célia Michotey, Raphaël-Gauthier Flores, Nacer Mohellibi, Cyril Pommier, Christopher Sauvage, Stephane Nicolas, Pierre Dubreuil, Jacques Le Gouis
article
23. Plant and Animal Genome, Jan 2015, San Diego, United States
resume
We will present a new functionality developed in GnpIS information system to manage association studies data (GWAS). A query form is available on http://urgi.versailles.inra.fr/gnpis portal and directly at this URL https://urgi.versailles.inra.fr/association/association/viewer.do#form. The tool allows plant scientists or breeders to get associations values between traits and markers obtained in several association studies. Several filters are available to refine the query, such as the species, trait (s), or marker (s) or panel of germplasms. The tool gives also the possibility in a second round of analysis, to add a new set of filters, i) on statistical values, or ii) on treatment done in the study, or iii) on the location and iv) year of the phenotyping trial or according to the v) statistical model chosen to do the analysis. It allows to view graphically the results with dedicated plots (QQPlot, Manhattan Plot), generated dynamically and to extract data in files to continue the analysis with external tools. After selecting the best markersassociated to trait of interest, the tool allows also to automatically jump on the genome to find where this marker is located on chromosomes and to identify in a very simpler way which genes or other markers or features of interest are near it. This tool is already now used for dealing GWAS studies (association, genotyping and phenotyping data) for 2 species: tomato and maize, data that are already referenced in two 2 publications and will also manage wheat data in 2015.
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Spatial pattern of Eurasian woolly mammoth extinctions during the Late Pleistocene based on statistical inference from fossil records
auteur
Frédérik Saltré, B.W. Brook, Joel Chadoeuf, Damien A. Fordham, Marta Rodriguez-Rey, Corey J.A. Bradshaw
article
International Biogeography Society (IBS 2015), Jan 2015, Bayreuth, Germany
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https://hal.inrae.fr/hal-02792581/file/Chadoeuf%202015%20poster_1.pdf BibTex
titre
Estimation du niveau de dormance des bourgeons avec la NIRS, résultats préliminaires
auteur
Marc Bonhomme, Jean-Paul Charpentier, Vincent Segura, Luc Pâques, Jean Marc Audergon, José Quero-Garcia, Jean-Michel Legave, Isabelle Farrera, Hendrik Davi, Frédéric Jean
article
2. rencontres scientifiques du réseau NIRS INRA, 2015, Orléans, France. 2 p
resume
Pour améliorer les modélisations de la phénologie, nous avons besoin de dates de débourrement et de floraison mais aussi de dates de levée de dormance, sur un grand nombre d’espèces. On est à la recherche de méthodes alternatives aux tests classiques, peu onéreuses et permettant de s’approcher du haut débit. La NIRS était potentiellement un bon candidat. Les essais préliminaires montrent une bonne corrélation entre NIRS et paramètre classique de dormance (DMD) sur poudre de bourgeons végétatifs et floraux. La corrélation est moins bonne sur poudre de tige mais pourrait cependant constituer une alternative dans le cas de screening haut débit.
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https://hal.inrae.fr/hal-02800715/file/2015_Bonhomme_NIRS_1.pdf BibTex

Master thesis

titre
Mise au point du ciblage génique chez la tomate
auteur
Célia Casset
article
Sciences du Vivant [q-bio]. 2015
typdoc
Master thesis
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02798194/file/Celia%20Caset%202015%20rapport_1.pdf BibTex
titre
Evaluation d'une stratégie de sélection génomique dans 3 dispositifs expérimentaux chez la tomate
auteur
Coralie Picard
article
Agricultural sciences. 2015
resume
La sélection pour améliorer les caractères d’intérêts agronomiques est réalisée à l’aide de la SAM ou de la GWA qui capturent difficilement les loci à effets mineurs, et grâce à des étapes de phénotypage souvent longues et couteuses. La sélection génomique (SG) est une méthode de prédiction de la performance des caractères via des modèles statistiques pour sélectionner des plantes élites dans un schéma de sélection, en estimant l’effet de tous les marqueurs qui sous-tendent l’architecture génétique des caractères étudiés. Nous avons évalué l’utilisation de la SG chez la tomate en estimant la précision de la prédiction pour 25 caractères liés à la qualité du fruit pour trois types de populations différentes (GWA, MAGIC et RIL). Une démarche de validation croisée a été menée en estimant le poids de paramètres (taille des populations d’entrainement (PE) et de validation (PV), interactions GxE, modèles statistiques prédictifs, densité de marquage, héritabilité des caractères, type de population) sur la précision de la prédiction. Nos résultats démontrent que l’approche SG semble puissante pour prédire les valeurs phénotypiques (avec des précisions allant de 0.32 à 0.93 lorsque la PE est optimisée, par exemple). Nous observons que (1) plus la PE est grande et plus elle contient des individus proches génétiquement et ayant été phénotypés dans des environnements similaires par rapport à la PV, plus la précision de la prédiction est élevée (2) la précision de la prédiction est plus élevée avec l’optimisation de la PE avec une grande diversité génétique (+ 9% en moyenne) (3) plus l’héritabilité du caractère est élevée, meilleure est la prédiction (4) les différents modèles statistiques conduisent à des prédictions très similaires (5) la densité de marqueurs optimale dépend du DL de la population. Pour conclure, bien que la SG soit une pratique qui n’en est qu’à ses débuts en ce qui concerne le monde du végétal l’application de la SG chez la tomate semble très prometteuse et pourrait être utilisée dans les programmes de sélection
typdoc
Master thesis
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02800021/file/2015_Picard_Coralie_Selection_genomique_tomate-6_1.pdf BibTex

Other publications

titre
Maladies et ravageurs émergents: stabilité pour la tomate
auteur
Michel Pitrat, Yannie Trottin-Caudal
article
2015, pp.21-22
resume
Les cultures de tomate peuvent être attaquées par de nombreux agents pathogènes et ravageurs, aussi bien aériens que telluriques. Suivant le type de culture (en plein champ, sous abris froids ou chauffés), l’importance relative de ces maladies et ravageurs est très différente.
typdoc
Other publications
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01312107/file/2015_Pitrat_Jardins%20de%20France%20633_1.pdf BibTex

Poster communications

titre
Stratégie de résistance durable aux nématodes à galles chez les porte-greffe de Prunus 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
Restitution des projets CTPS, Dec 2015, Paris, France. 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02797924/file/Duval%202015%20Poster%20CTPS%20Pyredune_1.pdf BibTex
titre
Texture deterioration in cooked apricot: characterization of the loss of firmness and visualization of the unmethylated pectin in two varieties with very different patterns
auteur
Albert Ribas, Barbara Gouble, Jean Francois Maingonnat, Jean Marc Audergon, Mohamed El Maataoui, Catherine Renard
article
Fruit Structure, Nov 2015, Angers, France. 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02796049/file/2015_Poster%20fruit%20structure%20Albert%20Ribas_1.pdf BibTex
titre
Mise en place d'un réseau national d'observations harmonisées de la phénologie chez les espèces fruitières
auteur
Marc Bonhomme, Pascale Guillermin, Jean-Michel Legave, José Quero-Garcia, Teresa Barreneche, Gilles Orain, Jean-Marc Ebel, V. Mathieu, Jean Marc Audergon
article
Colloque francophone PHENOLOGIE, Nov 2015, Clermont-Ferrand, France. INRA UMR PIAF, 135 p., 2015, Colloque francophone Phénologie 2015
resume
Dans le cadre du projet ACCAF PerPheClim, la phénologie a été étudiée en tant qu’indicateur de l’impact des changements climatiques. Pour appréhender son évolution, la mise en place d’observatoires implantés en des sites contrastés et suivis sur le long terme est apparue particulièrement utile. De tels observatoires, existaient pour la vigne et les espèces forestières mais pas pour les espèces fruitières (Domergues et al.,2004). Il a donc été décidé de mettre en place un dispositif national en réseau adapté à révéler les interactions génotype x environnement chez les espèces fruitières (Legave, 2009) et d’accompagner le dispositif par la mise en oeuvre de protocoles de suivis harmonisés.
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02743106/file/2015_Bonhomme_Poster1_Ph%C3%A9no_1.pdf BibTex
titre
Are patterns of Populus nigra geographical differentiation for resistance to Melampsora larici-populina dependent of genetic variation of the pathogen populations?
auteur
Catherine Bastien, Arnaud Dowkiw, Patricia Faivre-Rampant, Elise Albert, Marc Villar, Patrick Poursat, Jose-Luis Almeida Falcon, Celine Ridel, Vanina Guérin, Brigitte Viguier, Marijke Steenackers, Véronique Jorge
article
5. International Workshop on the Genetics of Tree-Parasite Interactions, Aug 2015, Orléans, France. 2015, 5th International Workshop on the Genetics of Tree-Parasite Interactions. Book of abstracts
resume
absent
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01269242/file/2015_Bastien_GTPI_comorale_1.pdf BibTex
titre
Back to the wild: identification and genetic mapping of resistance factors to Melampsora larici-populina in Populus nigra
auteur
Véronique Jorge, Arnaud Dowkiw, Redouane El Malki, Elise Albert, Marie Pégard, Vincent Segura, Vanina Guérin, Celine Ridel, Patrick Poursat, Jose-Luis Almeida Falcon, Patricia Faivre-Rampant, Catherine Bastien
article
5. International Workshop on the Genetics of Tree-Parasite Interactions, Aug 2015, Orléans, France. 2015, 5th International Workshop on the Genetics of Tree-Parasite Interactions. Book of abstracts
resume
absent
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01269239/file/2015_Jorge_GTPI_comorale_1.pdf BibTex
titre
ILLIAD project: Sustainable, local or localised, innovative food chains – application to apricot production
auteur
Sylvie Bureau, Barbara Gouble, Jean Marc Audergon, Sandrine Costa, Selma Tozanli
article
16. International Symposium on Apricot Breeding and Culture, Jun 2015, Shenyang, China. 2018, ⟨10.17660/ActaHortic.2018.1214.7⟩
resume
ILLIAD (a French national project, 2012 - 2015) proposes a method to analyze the system sustainability of food chains. The sustainability of food systems has been defined in terms of their effects on environment, economics and society, until now. ILLIAD aims to propose a method that allow to take into account the ability of these food systems to perdure or develop, in the long run, and aims to access their ability to increase their positive effects on environment, economics and society.
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02736932/file/Bureau_Illiad%20project_China%202015_poster_1.pdf BibTex
titre
Selections issued from CEP INNOVATION-CENTREX and INRA apricot breeding program in France
auteur
G. Femondière, C. Pitiot, Alain Blanc, Frederic Gilles, Jean Marc Audergon, Guy Clauzel, J.M. Broquaire, Barbara Gouble, Sylvie Bureau
article
16. International Symposium on Apricot Breeding and Culture, Jun 2015, Shenyang, China. 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02800714/file/Audergon%202015%2016.%20Int.%20Symp.%20Apricot%20Chine%2071_1.pdf BibTex
titre
Mechanical harvest: a realistic challenge for processed apricot market?
auteur
Barbara Gouble, Patrice Reling, Catherine Renard, Jean-Marc Broquaire, Christophe Chamet, Jean Marc Audergon
article
16. International Symposium on Apricot Breeding and Culture, Jun 2015, Shenyang, China. p. 38, 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02794857/file/Audergon%202015%2016.%20Int.%20Symp.%20Apricot%20Chine%2038_1.pdf BibTex
titre
ILLIAD project: sustainable, local or localised, innovative food chains
auteur
Sandrine Costa, Sylvie Bureau, Selma Tozanli, Jean Marc Audergon
article
16. International Symposium on Apricot Breeding and Culture, Jun 2015, Shenyang, China. p. 44, 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02740015/file/Audergon%202015%2016.%20Int.%20Symp.%20Apricot%20Chine%2044_1.pdf BibTex
titre
PERPHECLIM ACCAF Project - Perennial fruit crops and forest phenology evolution facing climatic changes
auteur
Iñaki García de Cortázar-Atauri, Jean Marc Audergon, Patrick Bertuzzi, Christel Anger, Marc Bonhomme, Isabelle Chuine, Hendrik Davi, Sylvain Delzon, Eric Duchêne, Jean-Michel Legave, Christian Pichot, Helene Raynal, Cornelis van Leeuwen, . Perpheclim Team
article
16. International Symposium on Apricot Breeding and Culture, Jun 2015, Shenyang, China. 298 p., 2015
resume
Phenology is a bio-indicator of climate evolutions. Measurements of phenological stages on perennial species provide actually significant illustrations and assessments of the impact of climate change. Phenology is also one of the main key characteristics of the capacity of adaptation of perennial species, generating questions about their consequences on plant growth and development or on fruit quality. Predicting phenology evolution and adaptative capacities of perennial species needs to override three main methodological limitations: 1) existing observations and associated databases are scattered and sometimes incomplete, rendering difficult the implementation of multi-site study of genotype-environment interaction analyses; 2) there are no common protocols to observe phenological stages; 3) access to generic phenological models platforms is still very limited. In this context, the PERPHECLIM project, which is funded by the Adapting Agriculture and Forestry to Climate Change Meta-Program (ACCAF) from INRA, has the objective to develop the necessary infrastructure at INRA level (observatories, information system, modeling tools) to enable partners to study the phenology of various perennial species (grapevine, fruit trees and forest trees). Currently the PERPHECLIM project involves 27 research units in France. The main activities currently developed are: defining protocols and observation forms to observe phenology for various species of interest for the project; organizing observation training; developing generic modeling solutions to simulate phenology; supporting the building of research projects at national and international level; developing environment/genotype observation networks for fruit trees species; developing an information system managing data and documentation concerning phenology. Finally, PERPHECLIM aims to build strong collaborations with public (Observatoire des Saisons) and private sector partners (technical institutes) in order to allow a more direct transfer of knowledge.
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02743994/file/Audergon%202015%2016.%20Int.%20Symp.%20Apricot%20Chine%2041-42_%7B7ABB10B0-A482-4B0F-A381-27F8090AEF89%7D_1.pdf BibTex
titre
Exploring and exploiting phenotypic and genetic diversity in peach: identification of major genes and QTLs by GWAS
auteur
Maria Jose Aranzana Civit, Jose Ramon Hernandez Mora, D. Micheletti, S. Micali, N. Nazzicari, I. Pacheco, S. Foschi, Teresa Barreneche, Bénédicte Quilot-Turion, L. Wang, R. Ma, Xiaojian Li, I. Iglesias, J. Carbó, M. Troggio, E. Banchi, V. Aramini, M.T. Dettori, A. Caprera, C. da Silva Linge, Thierry Pascal, Patrick Lambert, Z. Gao, I. Verde, D. Bassi, L. Rossini, Francois Laurens, P. Arus
article
14. EUCARPIA Symposium on Fruit Breeding and Genetics, Jun 2015, Bologne, Italy. Acta Horticulturae, 2017, ⟨10.17660/ActaHortic.2017.1172.79⟩
resume
Genetic variability is a key requirement for breeding. Although new peach cultivars are released yearly to the market, the genetic pool of cultivated peaches is very limited. To evaluate the variability available in commercial but also in old local peach accessions we selected a panel of 1,580 accessions maintained and evaluated in four European and one Chinese germplasm collections. Phenotypic data collected over years following common protocols have been integrated in a database, generating a useful tool for breeders and researchers. These accessions were genotyped with the peach 9K SNP array v1. T. Genotypic data distributed the accessions in three main subpopulations (Occidental obtained in breeding programs, Occidental old local varieties and Chinese cultivars). Linkage disequilibrium (LD) was in agreement with previous studies reporting long extension. Phenotypic and genotypic data have been combined in a GWAS study allowing the design of markers for marker assisted selection (MAS). Preliminary analyses on quantitative traits are promising, while further analysis will be required to integrate all data in a single genome-wide association analysis.
typdoc
Poster communications
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titre
GIS fruits - medieval working group an initiative dedicated to the prospective evaluation of fruit species
auteur
Benoit Jeannequin, Marine Guadagnini-Palau, Daniel Plénet, Yann Bintein, Jean Marc Audergon
article
Innovation in Integrated & Organic Horticulture, INNOHORT 2015, Jun 2015, Avignon, France. 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02792488/file/Audergon%202015%20ISHS%20Avignon_1.pdf BibTex
titre
Genome ENgineering Improvement for Useful plants of a Sustainable agriculture
auteur
Fabien Nogué, Philippe Vergne, Anne-Marie Chèvre, Jean-Eric Chauvin, Oumaya Bouchabke, Annabelle Dejardin, Elisabeth Chevreau, Laurence Hibrand-Saint Oyant, Marianne Mazier, Pierre Barret, Emmanuel Guiderdoni, Luc Mathis, Christophe Sallaud, Mireille Matt, Jean-Philippe Pierron, Eric Bonnel, Séverine Foucrier, Alain Toppan, Laure Trannoy, Peter Rogowsky
article
IUFRO Tree Biotechnology Conference 2015; Treebiotech2015, Jun 2015, Florence, France. 2015, Tree Biotechnology 2015 Conference "Forests: the importance to the planet and society"
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02743151/file/2015_Nogue_TB_S4P1_1.pdf https://hal.inrae.fr/hal-02743151/file/2015_IUFRO_Tree%20Biotechnology_program_2.pdf BibTex
titre
Joint estimation of the strength of genetic drift and selection from next generation sequencing time-sampled data : a case study on the adaptation of virus populations to host plant resistance
auteur
Elsa Rousseau, Frédéric Fabre, Jérôme Coville, Ludovic Mailleret, Alain Palloix, Rachid Senoussi, Benoît Moury, Frédéric Grognard
article
SMBE Satellite meeting SMBEBA 2015 "Investigating biological adaptation with NGS: data and models", May 2015, St Martin de Londres, France. 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02797375/file/Abstract_1 BibTex
titre
Genetic diversity of almond rootstocks. The INRA Prunus rootstock breeding program
auteur
Henri Duval
article
16. Grempa Meeting on Almonds and Pistachios, May 2015, Meknès, Morocco. 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02801445/file/Duval%202015%20XVI%20grempa%20meeting_1.pdf BibTex
titre
Estimation of genetic drift and selection from next generation sequencing time-sampled data
auteur
Elsa Rousseau, Frédéric Fabre, Jérôme Coville, Ludovic Mailleret, Alain Palloix, Rachid Senoussi, Frédéric Grognard, Benoît Moury
article
Modelling biological evolution 2015: linking mathematical theories with empirical realities, Apr 2015, Leicester, United Kingdom. 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02738798/file/PosterFabre_1.pdf BibTex
titre
PERPHECLIM ACCAF Project - Perennial fruit crops and forest phenology evolution facing climatic changes
auteur
Iñaki García de Cortázar-Atauri, Jean Marc Audergon, Patrick Bertuzzi, Christel Anger, Marc Bonhomme, Isabelle Chuine, Hendrik Davi, Sylvain Delzon, Eric Duchêne, Jean-Michel Legave, Christian Pichot, Helene Raynal, Cornelis van Leeuwen, . Perpheclim Team
article
3. Climate Smart Agriculture, Mar 2015, Montpellier, France. 298 p., 2015, CSA15 : Parallel Session L2 Climate Smart Strategies
resume
Phenology is a bio-indicator of climate evolutions. Measurements of phenological stages on perennial species provide actually significant illustrations and assessments of the impact of climate change. Phenology is also one of the main key characteristics of the capacity of adaptation of perennial species, generating questions about their consequences on plant growth and development or on fruit quality. Predicting phenology evolution and adaptative capacities of perennial species needs to override three main methodological limitations: 1) existing observations and associated databases are scattered and sometimes incomplete, rendering difficult the implementation of multi-site study of genotype-environment interaction analyses; 2) there are no common protocols to observe phenological stages; 3) access to generic phenological models platforms is still very limited. In this context, the PERPHECLIM project, which is funded by the Adapting Agriculture and Forestry to Climate Change Meta-Program (ACCAF) from INRA, has the objective to develop the necessary infrastructure at INRA level (observatories, information system, modeling tools) to enable partners to study the phenology of various perennial species (grapevine, fruit trees and forest trees). Currently the PERPHECLIM project involves 27 research units in France. The main activities currently developed are: defining protocols and observation forms to observe phenology for various species of interest for the project; organizing observation training; developing generic modeling solutions to simulate phenology; supporting the building of research projects at national and international level; developing environment/genotype observation networks for fruit trees species; developing an information system managing data and documentation concerning phenology. Finally, PERPHECLIM aims to build strong collaborations with public (Observatoire des Saisons) and private sector partners (technical institutes) in order to allow a more direct transfer of knowledge.
typdoc
Poster communications
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titre
Genetic determinants of response to water deficit in cultivated tomato fruits – QTL x E analysis
auteur
Elise Albert, Claire Duffes, Julien Bonnefoi, Justine Gricourt, Yolande Carretero, Esther Pelpoir, Mathilde Causse
article
The Genome Analysis Centre, Jan 2015, Norwich, United Kingdom. 2015
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02799805/file/Albert%202015%20TGAC%20poster_1.pdf BibTex
titre
Role of the genetic background on elF4E-based resistance to a PVY strain in tomato
auteur
Camille Gauffier, Caroline Lebaron, André Moretti, C. Constant, F. Moquet, G. Bonnet, Carole Caranta, Jean-Luc Gallois
article
15. Rencontres de Virologie Végétale, Jan 2015, Aussois, France. 1 p., 2014
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Poster communications
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titre
A new elF4E allele characterized by RNAseq in tomato is associated with resistance to potyviruses
auteur
Caroline Lebaron, Christopher Sauvage, Camille Gauffier, Benoît Moury, Jean-Luc Gallois
article
15. Rencontres de Virologie Végétale, Jan 2015, Aussois, France. 2015
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Poster communications
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Reports

titre
Amélioration et homogénéisation des procédures touchant aux bases de données, à l'assurance qualité et la conservation de graines dans le CRB Légumes
auteur
Marie-Christine Daunay, Jérémy Salinier
article
[Contrat] 2015
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Reports
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titre
Création de tomates de qualité pour le frais et l’industrie : F1 GARANCE et F1 TERRADOU
auteur
Rene Damidaux, . Département Bap, . Asirpa (analyse Socio‐économique Des Impacts de la Recherche Publique Agronomique)
article
[Rapport Technique] 2015
resume
Les recherches en génétique et pathologie menées par l’INRA en collaboration étroite avec la filière depuis les années 1970 ont conduit à la création de deux variétés emblématiques : La tomate F1 GARANCE a été conçue à l’origine pour explorer d’autres manières de produire des fruits de très bonne qualité organoleptique tout en répondant aux exigences de la filière (moins de traitements, bonne tenue à la manipulation). Deux points innovants maximisent le potentiel gustatif de F1 GARANCE : la récolte à pleine maturité et la conservation à température ambiante. L’inscription de la tomate F1 TERRADOU, très riche en matières sèches solubles et multi résistantes aux maladies, a ouvert la voie à la mise en place d’une grille de paiement des producteurs à la qualité. L’impact sur le bilan énergétique de cette filière est très significatif. Les qualités de ces deux tomates sont des indicateurs forts pour les pistes futures à explorer par les sélectionneurs et les producteurs.
typdoc
Reports
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02794423/file/2015_Damidaux_Projet%20ASIRPA_1.pdf https://hal.inrae.fr/hal-02794423/file/2015_Damidaux_Projet%20ASIRPA_ENG_2.pdf BibTex
titre
Projet ANR VirAphid. Comment utiliser les résistances des plantes pour gérer durablement l'évolution des virus et des pucerons
auteur
Nathalie Boissot, Benoît Moury, Flavie Vanlerberghe-Masutti
article
[Contrat] Institut National de la Recherche Agronomique (INRA). 2015
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Reports
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titre
Conception d’idéotypes culturaux adaptés à la contrainte hydrique et améliorés sur des critères de qualité gustative et nutritionnelle – Cas d’étude: la tomate
auteur
Mathilde Causse, Nadia Bertin
article
[Contrat] Vilmorin; Gautier semences. 2015
typdoc
Reports
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02793458/file/OK%20CR%20ctps%20mars2016-final_1.pdf https://hal.inrae.fr/hal-02793458/file/OK%20CR%20ctps%20mars2016-final_2.docx BibTex

Preprints, Working Papers, ...

titre
Joint estimation of the strength of genetic drift and selection from next generation sequencing time-sampled data : a case study on the adaptation of virus populations to host plant resistance
auteur
Elsa Rousseau, Frédéric Fabre, Jérôme Coville, Ludovic Mailleret, Alain Palloix, Rachid Senoussi, Benoît Moury, Frédéric Grognard
article
2015
resume
no abstract
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Preprints, Working Papers, ...
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2014

Conference papers

titre
Comment utiliser les résistances des plantes pour gérer durablement l'évolution des virus et des pucerons ?
auteur
Nathalie Boissot
article
Programme ANR SYSTERRA: "Agricultures et écosystèmes : du développement durable aux changements globaux - Des programmes thématiques pour impulser des recherches nouvelles ?, Agence Nationale de la Recherche (ANR). FRA., Dec 2014, Paris, France
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titre
Les acides dicaféoylquiniques comme molécules aphicides de biocontrôle
auteur
Marie-Hélène Sauge, Yvan Rahbé, Gérard Febvay, Jean-Luc Poessel
article
7. Rencontres du réseau Biologie Adaptative des Pucerons et Organismes Associés (BAPOA), Réseau Biologie Adaptative des Pucerons et des Organismes Associés (BAPOA). Le Rheu, FRA., Nov 2014, Avignon, France
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titre
Profil de résistance aux pucerons conféré par le gène Vat: apport des plantes transgéniques
auteur
Veronique Chovelon, Nathalie Boissot, Catherine Dogimont
article
7. journées du réseau Biologie et Adaptation des Pucerons et Organismes Associés, Réseau Biologie Adaptative des Pucerons et des Organismes Associés (BAPOA). FRA., Nov 2014, Avignon, France
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Conference papers
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titre
Conception d'associations en maraîchage de plein champ : exemple de production de melons associés à des bandes fleuries pour lutter contre les pucerons et les virus
auteur
Alexandra Schoeny, Nathalie Boissot, Jérôme Lambion, Catherine Wipf-Scheibel, Pascale Mistral, Patrick Gognalons, Karine Nozeran, Hervé Lecoq
article
CIAG 2014 : Carrefours de l'Innovation Agronomique "Associations Végétales", Nov 2014, Angers, France
typdoc
Conference papers
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02744024/file/2014%2011%2020%20CIAg%20Schoeny_1.pdf BibTex
titre
Des bandes fleuries pour lutter contre les pucerons et les virus en culture de melons : retour d’expérience(s)
auteur
Alexandra Schoeny, Nathalie Boissot, Jérôme Lambion, Catherine Wipf-Scheibel, Pascale Mistral, Patrick Gognalons, Karine Nozeran, Hervé Lecoq
article
Journées du réseau Biologie et Adaptation des Pucerons et Organismes Associés (BAPOA), Nov 2014, Avignon, France
typdoc
Conference papers
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titre
Approaches of the genetic control of tomato fruit composition in the resequencing era
auteur
Laura Pascual, Christopher Sauvage, Guillaume Bauchet, Nelly Desplat, Jean-Paul Bouchet, Dominique Brunel, Marie-Christine Le Paslier, Mathilde Causse
article
11. Solanaceae conference SOL 2014, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA). BRA., Nov 2014, Bahia, Brazil
resume
Identifying the genes controlling the variation of quantitative traits is a key goal for geneticists. Genetic loci underlying quantitative trait variation (QTL) have been mapped by traditional linkage mapping for years and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of genetic background on QTL effect has been underlined.Thanks to the increase in molecular markers, genome-wide association studies were then proposed to circumvent QTL limitations. ln tomato, a self-pollinated crop, we have shown that association studies are possible, using the admixed nature of cherry tomato genomes that limits the impact of population structure in such an approach. Nevertheless, the results might be restricted by linkage disequilibrium and allele frequency, which vary greatly along the genome. Multi-allelic Advanced Generation Inter-Cross (MAGIC) populations allow a wide range of variability to be analyzed and avoid dealing with population structure.
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https://hal.inrae.fr/hal-02741967/file/Sauvage_Causse%202014%20SOL2014%2032_1.pdf BibTex
titre
Overview of INRA researches on peach brown rot. First results, current works and prospects
auteur
Bénédicte Quilot-Turion
article
COST FA 1104 "4th Management Committee and all Working Group Meeting"_"Sustainable production of high-quality cherries for the Europe market", Oct 2014, Bordeaux, France
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titre
Un modèle intégré écophysiologique-génétique pour l'exploration d'idéotypes: réflexions à partir du cas des monilioses chez la pêche
auteur
Bénédicte Quilot-Turion, Michel Génard, Mohamed Ould Sidi
article
Séminaire-Table ronde AGAP, Oct 2014, Montpellier, France
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titre
Deciphering the genetic control of tomato fruit quality in the resequencing era
auteur
Laura Pascual, Christopher Sauvage, Guillaume Bauchet, Nelly Desplat, Jean-Paul Bouchet, Dominique Brunel, Marie-Christine Le Paslier, Mathilde Causse
article
3. annual conference of the COST ACTION FA 1106, Mediterranean Agronomic Institute. GRC., Sep 2014, Chania, Greece
resume
Identifying the genes controlling the variation of quantitative traits is a key goal for breeders. Genetic variations underlying quantitative traits (QTL) have been mapped by traditional linkage mapping for years and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of genetic background on QTL effect has been underlined. Thanks to the increase in molecular markers, genome-wide association studies were then proposed to circumvent QTL limitations. ln tomato, a self-pollinated crop, we have shown that association studies are possible, using the admixed nature of cherry tomato genomes that limits the impact of population structure in such an approach. Nevertheless, the results might be limited by linkage disequilibrium, which varies greatly along the genome. Multi-allelic Advanced Generation Inter-Cross (MAGIC) populations allow a wide range of variability to be analyzed and avoid dealing with population structure.
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https://hal.inrae.fr/hal-02744187/file/Sauvage_Causse%202014%20Cost%20Action%2044_1.pdf BibTex
titre
Snapmelon (Cucumis melo L. Momordica Group), an indigenous cucurbit from India with immense value for breeding
auteur
N.P.S. Dhillon, H. Singh, Michel Pitrat, Antonio J. Monforte, James D. Mccreight
article
congrès ISHS 2014 « Sustaining Lives, Livelihoods and Landscapes », International Society for Horticultural Science (ISHS). INT., Aug 2014, Brisbane, Australia
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https://hal.inrae.fr/hal-02741451/file/Pitrat%202014%20ISHS_1.pdf BibTex
titre
An ecological multi-level theory of competition for resources used to analyze density-dependence effects in fruit production
auteur
Michel Génard, Zhanwu Dai, Marion Prudent, Bénédicte Quilot-Turion, Francoise Lescourret
article
29. International Horticultural Congress (IHC2014), International Society for Horticultural Science (ISHS). INT., Aug 2014, Brisbane, Australia
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titre
An ecological multi-Level theory of competition for resources used to analyse density-dependence effects in fruit production
auteur
Michel Génard, Francoise Lescourret, Zhanwu Dai, Bénédicte Quilot-Turion, Marion Prudent
article
29. International Horticultural Congress on Horticulture - Sustaining Lives, Livelihoods and Landscapes (IHC) / Int Symposia on the Physiology of Perennial Fruit Crops and Production Systems and Mechanisation, Precision Horticulture and Robotics, Aug 2014, Brisbane, Australia. ⟨10.17660/ActaHortic.2016.1130.6⟩
resume
Lescourret and Génard (2003) developed a multi-level theory of competition for resources applied to fruit production, considering that any collection of unit parts (cells or seeds in a fruit, fruits in an infructescence or in a tree...) can form a population and the population is subject to competition, whatever the level of organization. The principles of the theory are that the mass of each unit decreases when the number of units in the population increases and that the total mass of the population increases as the number of units increases until it reaches a maximum, after which it decreases. A three-parameter model based on that theory was used to analyse the level of density-dependence, i.e., the effect of the population size on its mass. Comparing the number of cells and the mean cell volume in mesocarp of fruits from peach genotypes showed a strong and undercompensating density-dependence that revealed competition between cells. Similarly, when comparing populations for different fruit species, similar results or exact compensation were observed for several levels (fruit, infructescence, tree…). Because undercompensating or exact density-dependence were found in most of the cases, a simpler two parameter model was proposed by Prudent et al. (2013). This two parameter model was used to analyse the genetic control of competition between seeds in multi-seeded fruits.
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titre
The control of soil borne vascular diseases: Limits of genetic resistance of cultivars and rootstocks for controlling Fusarium oxysporum f. sp. melonis (melon) and Verticillium sp. (eggplant)
auteur
F. Villeneuve, F. Latour, T. Thery, Christian Steinberg, Veronique Edel-Hermann, Michel Pitrat, M-Christin Daunay
article
8. International Symposium on Chemical and Non-Chemical Soil and Substrate Disinfestation, Jul 2014, Turin, Italy
resume
After using resistant cultivars or resistant rootstocks for many years to control soil-borne pathogenic fungi causing wilt disease, growers observe more and more frequently wilt like symptoms in their melon and eggplant cultures. Ctifl, in close collaboration with INRA, regional extension services, and seed companies, set up a study designed to investigate the causative pathological agents. The results show the prevalence of Fusarium oxysporum f. sp. melonis race 1-2 yellowing on melon and of Verticillium dahlia on eggplant. Both pathogens are often found together with other pathogenic soil fungi, which act as aggravating factors. The isolates of F. oxysporum f. sp. melonis collected from infected plants appear to be more aggressive than the reference strains currently used for screening resistant material in breeding programmes. In the case of Verticillium wilt, the taxonomic and race status of the isolates sampled, remain unclear
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Quantification de l’intensité de l’activité biologique dans les sols par l’analyse d’images de lames minces de sol : mise au point méthodologique et quantification de l’impact de 250 ans de mise en culture
auteur
Manon Bajard, David Montagne, Jean-Marc Gilliot, Ophélie Sauzet, Mathieu Cammas
article
12ème Journées Nationales d’Etude des Sols. Le sol en héritage, Jun 2014, Bourget du Lac, France
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https://hal.archives-ouvertes.fr/hal-01820570/file/Actes-JES-2014-Session4.pdf BibTex
titre
lnsights into the genetic control of resistance to Aphis gossypii in melon: what we learned from the diversity of aphids
auteur
Nathalie Boissot, Sophie Thomas, Pascale Mistral, Virginie Chareyron, Vincent Rittener
article
2.congrès International Hemipteran-Plant Interactions Symposium. HPIS 2014, Jun 2014, Riverside, United States
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https://hal.inrae.fr/hal-02739307/file/Boissot_Thomas%202014%20HPIS%2027_1.pdf BibTex
titre
Variability of the genetic response of tomato during soil drying and repeated cycles of water deficit and recovery
auteur
Julie Ripoll, Laurent Urban, Béatrice Brunel, Alain Goujon, Jean-Claude l'Hôtel, Mathilde Causse, Nadia Bertin
article
Plant Biology Europe FESPB/EPSO Congress 2014, Jun 2014, Dublin, Ireland
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https://hal.inrae.fr/hal-02795616/file/Poster%20Ripoll%20Julie%201_1.pdf BibTex
titre
Protection of the durability of major resistance genes to plant viruses through quantitative resistance, a modeling approach
auteur
Elsa Rousseau, Jérôme Coville, Frédéric Fabre, Ludovic Mailleret, Alain Palloix, Benoît Moury, Frédéric Grognard
article
ECMTB14 - 9. European Conference on Mathematical and Theoretical Biology, Jun 2014, Goteborg, Sweden
resume
The deployment of virus-resistant crops often leads to the emergence of resistance-breaking (RB) pathogens that suppress the yield benefit provided by the resistance [1]. Although break- downs are well known for plant genes conferring total, i.e. qualitative resistance to the virus, they are still poorly understood for plant genetic factors conferring partial, i.e. quantitative resistance. Furthermore, it has been proved for several pathosystems that combining qualita- tive and quantitative resistances can increase the durability of the qualitative resistance [2, 3]. Two mechanisms can explain this result : either (i) an increase of genetic drift in the virus population, or (ii) a decrease of the selection advantage of the RB mutant. Here, we aim at disentangling the role of these two mechanisms on the durability of plant qualitative resistances to viruses.
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https://hal.inrae.fr/hal-02739537/file/2014_Rousseau_ECMTB14_1.pdf BibTex
titre
Metabolic profiling of transgenic lines silenced for an MDHAR gene and impact on ascorbate redox state and carbon metabolism
auteur
Vincent Truffault, Guy Costagliola, Hélène Gautier, Rebecca Stevens
article
18. EUCARPIA Meeting of the Tomato Working Group, Apr 2014, Avignon, France. 1 p
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https://hal.inrae.fr/hal-02799822/file/Stevens%20Rebecca%20_%20T009_Eucarpia%20tomato%202014_1.pdf BibTex
titre
Deciphering ascorbic acid regulation in tomato fruit ripening
auteur
Celine Bournonville, Carine Ferrand, Daniel Just, Virginie Garcia, Daniel Jacob, Rebecca Stevens, Hélène Gautier, Christophe Rothan, Pierre Baldet
article
18. EUCARPIA Meeting of the Tomato Working Group, Apr 2014, Avignon, France. 1 p
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https://hal.inrae.fr/hal-02800985/file/Stevens%20Rebecca_%20T021_Eucarpia%20tomato%202014_1.pdf BibTex
titre
The Tomato-Potyvirus system, a comparative system for natural and induced resistances associated with the initiation factors 4E
auteur
Camille Gauffier, Caroline Lebaron, André Moretti, C. Constant, F. Moquet, G. Bonnet, Carole Caranta, Jean-Luc Gallois
article
XVIIIth Eucarpia Meeting, Vegetable section, Tomato Working group, Apr 2014, Avignon, France. 1 p
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https://hal.inrae.fr/hal-02798800/file/Gauffier%20Camille%20_%20T017_Eucarpia%20tomato%202014_1.pdf BibTex
titre
The study of domestication reveals a loss of diversity, signature of selection and transcriptional modifications in tomato (Solanum lycopersicum)
auteur
Christopher Sauvage, Benoit Nabholz, S. Gautier, M. Ruiz, Mathilde Causse, J. David, S. Glemin
article
XVIIIth Eucarpia Meeting, Vegetable section, Tomato Working group, Apr 2014, Avignon, France. 1 p
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https://hal.inrae.fr/hal-02794508/file/Sauvage%20Christopher%20_%20T004_Eucarpia%20tomato%202014_1.pdf BibTex
titre
Tomato variation, origin and domestication
auteur
Jose Miguel Blanca, J. Monterau-Pau, Christopher Sauvage, Guillaume Bauchet, E. Illa, Monique Diez, Mathilde Causse, D. Francis, Joaquin Canizares, E. van der Knaap
article
XVIII. Eucarpia Meeting, Vegetable section, Tomato Working group, Apr 2014, Avignon, France. 1 p
resume
A collection of 949 accessions composed by S. lycopersicum var. lycopersicum (SLL; 514), S. l. var. cerasiforme (SLC; 291), S. pimpinellifolium (SP; 128), S. galapagense (SG;3), S. neorickii (SN; 1), S. chmielewski (Schm; 1) and 11 crosses between SP, SLC, SLL and S. pennellii was analyzed. The genotyping was carried out using the 7720 markers of the SolCAP genotyping platform and some key genes involved in the domestication process (CNR/FW2.2, SlKLUH/FW3.2, LC, FAS, OVATE and SUN). Using Principal Component Analyses (PCAs) based on the genetic data a new genetic-based classification divided the accessions in SP (121), SLC (236), SLL (492) and mixture (100). Within SP and Andean SLC a complex geographical structure correlated with the climate was found. Ecuadorian SP was remarkably differentiated from the rest of SP. In non-Andean SLC the structure found was not as marked. In a neighbor phylogenetic network SLC appeared intermediate between SP and SLC. Thus SLC was found to be a semi-domesticate with a key role in the tomato domestication. Andean SLC had a diversity comparable to SP while the non-Andean SLC had a lower diversity comparable to vintage SLL, indicating that the main bottleneck in the tomato domestication happened in the migration from the Andean region to Mesoamerica. Most SLC accessions were reported to have cherry-sized fruit, but interestingly some South American SLC were collected in markets as full-sized vintage tomatoes. Thus the vintage tomato in South America included SLC as well as SLL materials.
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https://hal.inrae.fr/hal-02796249/file/Blanca%20Jose_%20T001_Eucarpia%20tomato%202014_1.pdf BibTex
titre
A multilocus mixed model for GWAS reveals associations for metabolic traits in the tomato, [i]Solanum lycopersicum[/i]
auteur
Christopher Sauvage, Vincent Segura, Guillaume Bauchet, Rebecca Stevens, P.T. Do, A. Fernie, Mathilde Causse
article
XVIIIth Eucarpia Meeting, Vegetable section, Tomato Working group, Apr 2014, Avignon, France. 1 p
resume
absent
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https://hal.archives-ouvertes.fr/hal-01268525/file/Sauvage%20Christopher_P015_Eucarpia%20tomato%202014_1.pdf BibTex
titre
Protecting the durability of major resistance genes to plant viruses with quantitative resistance
auteur
Elsa Rousseau, Frédéric Fabre, Ludovic Mailleret, Alain Palloix, Vincent Simon, Sophie Valière, Benoît Moury, Frédéric Grognard
article
Conférence Jacques Monod, Apr 2014, Roscoff, France
resume
The deployment of virus-resistant crops often leads to the emergence of resistance-breaking (RB) pathogens that suppress the yield benefit provided by the resistance (Fabre et al,2012). Although breakdowns are well known for qualitative resistances conferring total resistance to the virus, they are still poorly understood for quantitative resistances conferring partial resistance. Furthermore, it has been proved for several pathosystems that combining qualitative and quantitative resistances can increase the durability of the qualitative resistance (Palloix et al, 2009, Quenouille et al, 2013). Two mechanisms can explain this result : either (i) an increase of genetic drift in the virus population, or (ii) a decrease of the selection advantage of the RB mutant. The purpose of the ongoing work presented here is to disentangle the role of these two mechanisms on the durability of plant qualitative resistances to viruses.To investigate this, we concentrated on a pepper Potato virus Y (PVY) pathosystem on which we report consistent variability in bottlenecks undergone by viral populations at inoculation and in viral accumulation, both determined by the host genotype. We follow by high-throughput sequencing the within-host demo-genetic dynamics of several virus variants in contrasted plant genotypes, carrying a qualitative resistance and different combinations of quantitative resistances. The respective effects of genetic drift and selection are evaluated by fitting models to these data (Fabre, 2012). We further aim at predicting the potential of combining qualitative and quantitative plant resistances to achieve sustainable plant resistance management at the epidemic scale.
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titre
From genetics to marketing (and through hidden connexions and interdependencies): an integrative approach of the ecologisation of fruit production
auteur
Claire Lamine, Jean Marc Audergon, Servane Penvern, Sylvaine Simon, Jean Pluvinage
article
11. European IFSA Symposium: Farming systems facing global challenges: Capacities and strategies., Apr 2014, Berlin, Germany. 143 p
resume
This paper discusses a systemic analysis of the changes in the peach and apricot industry since the 1960s, based on a sociological framework anchored in transition and actor network theories, with a specific focus on the place of genetics and breeding strategies in this trajectory, an aspect which indeed is often neglected in the literature. We show how, a long with a process of specialization and intensification of the fruit production at the farm and regional levels, breeding strategies mainly focus on improving yield and technological fruit quality and on extending the production period (from 3 to nearly 6 months for peach production) to offer retailers a continuity in each product type over this entire extended season through “varietal series”. These objectives are thus market-driven and neglect the environmental aspects (even though substantial work has been done for decades on resistant cultivars) and the fruit production constraints, and they lead to create and then market fruits that are easy to store and transport, but often disappointing in terms of taste and quality. These changes are due to the constraints which affect all the socio-technical system up to the breeding process criteria and to a deep reconfiguration of the network of institutions and actors dealing with fruit production in general (research institutes, breeders, producers’ organizations, retailers, etc.). In this paper, we also try to adopt a reflexive perspective about the way we discuss with the projects’ members and partners (researchers from various disciplinary backgrounds, producers’ organizations, marketers and advisors) some key issues that are central to the construction of more ecological and resilient transition pathways at the scale of the agrifood system.
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titre
Conservation and use of natural genetic variation of eggplant in the genomics Era
auteur
J. Prohens, Marie-Christine Daunay, S. Knapp, R. Meyer, S. Vilanova
article
Applied Vegetable Genomics, Feb 2014, Vienne, Austria. 1 p
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https://hal.inrae.fr/hal-02794179/file/Daunay%202014%20Applied%20vegetable%20genomics%2011_1.pdf BibTex
titre
Variation and origin of the tomato
auteur
J. Blanca, J. Montero-Pau, Christopher Sauvage, Guillaume Bauchet, E. Illa, M. Diez, D. Francis, Mathilde Causse, E. van der Knaap, Joaquin Canizares
article
Applied Vegetable Genomics, Vienna Institute for Nature Conservation and Analyses (VINCA). AUT., Feb 2014, Vienne, Austria. pp.12
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https://hal.inrae.fr/hal-02739830/file/Sauvage_Bauchet%202014%20Applied%20vegetable%20genomics%2012_1.pdf BibTex
titre
Valorisation of the natural variation available in tomato accessions to decipher the genetic control of fruit quality traits
auteur
Laura Pascual-Banuls, Jiaxin Xu, Christopher Sauvage, Guillaume Bauchet, Nelly Desplat, Jean-Paul Bouchet, Dominique Brunel, Mathilde Causse
article
Applied Vegetable Genomics, Feb 2014, Vienne, Austria
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https://hal.inrae.fr/hal-02741808/file/OK%20Sauvage_Bauchet%202014%20Applied%20vegetable%20genomics%2020_1.pdf BibTex
titre
Reconstruction bayésienne d’arbres de transmission à partir de données épidémiologiques et génétiques
auteur
Gael Thébaud, M. J. Morelli, Joel Chadoeuf, Donald Peter King, Daniel T. Haydon, Samuel Soubeyrand
article
Réunion du Réseau Ecologie des Interactions Durables, Feb 2014, Montpellier, France
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titre
Effet des génotypes des plantes sur l’efficacité des Stimulateurs de Défenses des Plantes (SDP) : exemples des couples oïdium/melon et mildiou/laitue
auteur
Brigitte Maisonneuve, Caroline Allen-Aubouard, Michel Pitrat
article
SIVAL, Jan 2014, Angers, France
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titre
Control of chilling requirement and flowering time in trees; linking genetics and genomics to understand these complex phenological traits in deciduous fruit and forest trees
auteur
Albert G. Abbott, Stéphanie Mariette, Lucia Andreini, Tatyana Zhebentyayeva, Zongrang Liu, Guillaume Roch, David Tricon, Patrick Lambert, Jean Marc Audergon, Macha Nicholski, Alexis Groppi, Aurélien Barré, Catherine Bodénès, Grégoire Le Provost, Christophe Plomion, Antoine Kremer, Christopher Dardick, Ralph Scorza, Fred Hebard, C. Dana Nelson, Scott Merkle, Campbell J. Nairn, Véronique Decroocq
article
Plant and Animal Genome XXII Conference, Jan 2014, San Diego, United States
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https://hal.inrae.fr/hal-02798021/file/Roch_Lambert%202014%20Plant_1 BibTex
titre
Genome wide sequence-based association studies for dissection of important agronomie traits in apricot
auteur
Véronique Decroocq, Stéphanie Mariette, Fabienne Wong Jun Tai, Stephane Decroocq, David Tricon, Patrick Lambert, Guillaume Roch, Jean Marc Audergon, Macha Nicholski, Alexis Groppi, Aurélien Barré, Filippo Geuna, Daniele Bassi, Stefano Tartarini, Luca Dondini, Tatyana Zhebentyayeva, Albert Abbott
article
Plant and Animal Genome XXII Conference, Jan 2014, San Diego, United States
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https://hal.inrae.fr/hal-02796089/file/Lambert_Roch%202014%20Plant_1 BibTex

Other publications

titre
Légumes : l’innovation pour tous
auteur
Michel Pitrat
article
2014, pp.53-55
resume
Résistance aux bio-agresseurs, diversification, qualité, rusticité, agriculture biologique sont les principales innovations marquantes de ces dernières années en matière d’espèces légumières. L’amateur, qui n’a pas les mêmes exigences que le professionnel, n’est pas oublié...
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https://hal.archives-ouvertes.fr/hal-01312110/file/2014_Pitrat_Jardins%20de%20France%20629_1.pdf BibTex
titre
Le melon, toute une histoire !
auteur
Michel Pitrat
article
2014
resume
Membre de la famille des cucurbitacées, le melon ([i]Cucumis melo[/i]) est proche parent du concombre ([i]Cucumis sativus[/i]) et plus éloigné de la pastèque ([i]Citrullus lanatus[/i]). Il est relativement facile de différencier sur les étalages en France ces trois espèces, en particulier la pastèque avec les graines réparties dans la chair et non regroupées dans une cavité centrale. Cependant, au cours de voyages à l’étranger, on peut avoir quelques difficultés à s’y reconnaître. Par ailleurs, les documents anciens ne permettent pas toujours de distinguer ces trois espèces. C’est dans un petit voyage dans le temps et dans l’espace que nous vous convions autour de la diversité biologique du melon.
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https://hal.archives-ouvertes.fr/hal-01312109/file/2014_Pitrat_Jardins%20de%20France%20627_1.pdf BibTex
titre
Vers une meilleure résistance des variétés de melon aux pucerons
auteur
Nathalie Boissot, Patricia Le Crenn, Pascale Mistral, Virginie Chareyron
article
2014
resume
Le melon, culture d’importance économique à l’échelle mondiale, est sujet aux attaques de pucerons, devenus résistants à la plupart des insecticides. En explorant divers fonds génétiques, les chercheurs Inra d’Avignon ont révélé de nouvelles sources de résistance chez le melon qui pourraient déboucher sur des variétés plus performantes.
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Poster communications

titre
Evaluation of Turkish melon accessions for resistance to Fusarium wilt, downy mildew, powdery mildew, Cucumber mosaic virus and Zucchini yellow mosaic virus
auteur
Ilkour Solmaz, N. Sari, Catherine Dogimont, Michel Pitrat
article
29. International Horticultural Congress on Horticulture - Sustaining Lives, Livelihoods and Landscapes (IHC) / International Symposium on Plant Breeding in Horticulture, Aug 2014, Brisbane, Australia. Acta Horticulturae, 1127, 2016, Acta Horticulturae. ⟨10.17660/ActaHortic.2016.1127.22⟩
resume
The aim of this study was to detect disease resistance in melon genetic resources collected from different regions (south-eastern Anatolia, middle Anatolia, Aegean, Marmara-Thrace and eastern Anatolia) of Turkey. A total of 85 melon and 15 snake melon genotypes were tested against Fusarium wilt (races 1 and 2), downy mildew and powdery mildew (race 3) as fungal diseases, and Cucumber mosaic virus (CMV) and Zucchini yellow mosaic virus (ZYMV) as virus diseases. In the case of Fusarium wilt race 1, eight genotypes were found resistant, 86 genotypes were susceptible and one genotype was segregating. Fifty-four percent of the genotypes were found to be resistant, 28% were susceptible and 18% were segregating for Fusarium wilt race 2. In the case of downy mildew, four genotypes (‘Kav 28’, ‘Kav 71’, ‘Kav 237’ and ‘Kav 255’) were resistant, while 78 genotypes were susceptible and 16 genotypes were segregating. Among all the genotypes tested, only two genotypes (‘Kav 60’ and ‘Kav 277’) were resistant to powdery mildew. While two genotypes (‘Kav 281’ and ‘Ac 33’) were found to be resistant to CMV, none of the genotypes were resistant to ZYMV.
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Poster communications
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https://hal.archives-ouvertes.fr/hal-01604952/file/Dogimont_Pitrat%20Acta%20Horticulturae%202016%20133-140_1.pdf BibTex
titre
New advances on the flesh's red pigmentation in peach
auteur
Thierry Pascal, Sylvie Bureau, Laure Heurtevin, Jehan-Baptiste Mauroux, Carole Confolent, Patrick Lambert, Virginie Diévart, Christophe Tuero, Jean-Luc Poessel, Zhijun Shen
article
7. International Rosaceae Genomics Conference, Jun 2014, Seattle, United States. 2014
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Poster communications
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https://hal.inrae.fr/hal-02743461/file/Pascal%202014%20RGC7%2087_1.pdf BibTex
titre
Identification and characterization of QTLs for peach fruit quality by pedigree-based analyses (PBA) in the FruitBreedomics project
auteur
Jose Ramon Hernandez, Diego Mlcheletti, Pere Arús, Teresa Barreneche, Daniele Bassi, Marco Bink, Maria Teresa Dettori, Elisabeth Dirlewanger, Patrick Lambert, Francois Laurens, Sabrina Micali, Thierry Pascal, Bénédicte Quilot-Turion, Laura Rossini, Michela Troggio, Verde Lgnazio, Eric van de Weg, Maria José Aranzana
article
7. International Rosaceae Genomics Conference, Jun 2014, Seattle, United States. 2014
resume
absent
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https://hal.archives-ouvertes.fr/hal-01209974/file/OK%20Lambert_Pascal%202014%20RGC7%20101_1.pdf BibTex
titre
Identification by a RNAseq approach of virulence gene candidates in the non-model species Aphis Gossypii
auteur
Leslie Dutartre-Fricaux, Jean-Paul Bouchet, Coralie Beucher, Nathalie Boissot, Catherine Dogimont
article
2. International Hemipteran-Plant Interactions Symposium. HPIS 2014, Jun 2014, Riverside, United States. 2014
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Poster communications
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https://hal.inrae.fr/hal-02801072/file/Boissot_Dogimont%202014%20HPIS%2056_1.pdf BibTex
titre
Differential effect of resistance inducers on the susceptibility of lettuce varieties to Sclerotinia sclerotiorum and Botrytis cinerea
auteur
Asti Irawanti Azis, Magali Duffaud, Claire Troulet, Brigitte Maisonneuve, Efi Toding Tondok, Suryo Wiyono, Marc Bardin, Philippe C. Nicot
article
13. IOBC-WPRS Meeting of the working group "Biological control of fungal and bacterial plant pathogens". Biocontrol of plant diseases: "from the field to the laboratory and back again", Jun 2014, Uppsala, Sweden. 2014
resume
The preventive use of resistance inducers has been shown to be an interesting method to reduce dependency on pesticides for plant protection. However, little is known on possible differences in the protective effects of such methods for different varieties of a given crop. In the present study, we assessed the effect of three compounds (acibenzolar-S-méthyl, a calcium-based mineral compound and a yeast extract) for the protection of six varieties of lettuce against two major pathogens, Sclerotinia sclerotiorum and Botrytis cinerea. The compounds were sprayed on the plants three days before inoculation. A water spray was used as a control. The protective effect of the compounds was then assessed by comparing the size of lesions developing on inoculated leaves. For both pathogens, none of the compounds fully inhibited disease development. However, reduction in lesion size was observed on some of the leaves. The effect of the three compounds was different for the two pathogens. For tests with B. cinerea, effects of plant treatment were not statistically significant. In contrast, significant effects were found for five of the varieties inoculated with S. sclerotiorum. Overall, the yeast extract provided the highest level of protection against that pathogen. However, for all compounds, the extent of the protective effect depended on the variety. Furthermore, in some cases the effect of the compound was opposite to that desired and disease was more severe on treated plants than on the water control. Possible consequences for field application of such methods will be discussed.
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Poster communications
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https://hal.inrae.fr/hal-02740639/file/2014-Azis_IOBC_1.pdf BibTex
titre
Regulation of tomato ascorbate levels: a candidate gene involved in fruit nutritional value and stress tolerance
auteur
Noé Gest, Vincent Truffault, Hicham El Airaj, Cecile Garchery, Gisèle Riqueau, Mathilde Causse, Hélène Gautier, A. Jimenez, Rebecca Stevens
article
XVIIIth Eucarpia Meeting, Vegetable section, Tomato Working group, Apr 2014, Avignon, France. 1 p., 2014
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Poster communications
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https://hal.inrae.fr/hal-02796653/file/Stevens%20Rebecca_P007_Eucarpia%20tomato%202014_1.pdf BibTex
titre
Deciphering the genetic control of quantitative traits with magic
auteur
Laura Pascual-Banuls, Nelly Desplat, Jean-Paul Bouchet, Aurore Desgroux, Laure Bruguier, B. Chauchard, P. Verschave, Mathilde Causse
article
XVIIIth Eucarpia Meeting, Vegetable section, Tomato Working group, Apr 2014, Avignon, France. 2014
resume
absent
typdoc
Poster communications
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https://hal.archives-ouvertes.fr/hal-01208696/file/Causse%20Mathilde_%20T028_Eucarpia%20tomato%202014_1.pdf BibTex
titre
GWAS reveals candidate regions for metabolic traits in tomato, Solanum lycopersicum
auteur
Guillaume Bauchet, S. Grenier, N. Samson, J. Bonnet, L. Grivet, E. Bolygo, C. Baxter, Mathilde Causse
article
XVIIIth Eucarpia Meeting, Vegetable section, Tomato Working group, Apr 2014, Avignon, France. 1 p., 2014
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Poster communications
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https://hal.inrae.fr/hal-02800694/file/Bauchet%20Guillaume_%20T024_Eucarpia%20tomato%202014_1.pdf BibTex
titre
Promote adaptation to drought and fruit quality by alternating increased intensity of deficit irrigation and recovery period
auteur
Julie Ripoll, Laurent Urban, Béatrice Brunel, Alain Goujon, Jean-Claude l'Hôtel, Mathilde Causse, Nadia Bertin
article
XVIII. Eucarpia Meeting, Vegetable section, Tomato Working group, Apr 2014, Avignon, France. 2014
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02743661/file/OK%20Causse%20Mathilde_P006_Eucarpia%20tomato%202014_1.pdf BibTex
titre
Combining deficit irrigation and recovery periods can save water and maintain yield and fruit quality in tomato
auteur
Julie Ripoll, Laurent Urban, Béatrice Brunel, Alain Goujon, Jean-Claude l'Hôtel, Mathilde Causse, Nadia Bertin
article
18. EUCARPIA Meeting of the Tomato Working Group, Apr 2014, Avignon, France. 2014
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Poster communications
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https://hal.inrae.fr/hal-02743459/file/PosterEucarpia2014_1.pdf BibTex
titre
Protecting the durability of major resistance genes to plant viruses with quantitative resistance
auteur
Elsa Rousseau, Frédéric Fabre, Ludovic Mailleret, Alain Palloix, Vincent Simon, Sophie Valière, Benoît Moury, Frédéric Grognard
article
Conférences Jacques Monod : “From emerging to pandemic viruses: interplay between host ecology and viral evolution”, Apr 2014, Roscoff, France. 2014
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Poster communications
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https://hal.inrae.fr/hal-02738827/file/2014_Rousseau_Conf%20Monod_poster_1.pdf https://hal.inrae.fr/hal-02738827/file/2014_Rousseau_Conf%20Monod_2.pdf BibTex
titre
Genome wide associations for metabolic traits in tomato
auteur
Guillaume Bauchet, S. Grenier, N. Samson, J. Bonnet, L. Grivet, E. Bolygo, C. Baxter, Mathilde Causse
article
Applied Vegetable Genomics, Feb 2014, Vienne, Austria. pp.28, 2014
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Poster communications
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https://hal.inrae.fr/hal-02740557/file/Bauchet_Causse%20Applied%20vegetable%20genomics%2028_1.pdf BibTex
titre
Étude du rôle des gènes Mlo dans la résistance aux oïdiums du melon
auteur
Sonia Elbelt, Nathalie Giovinazzo, Verane Sarnette, Christelle Troadec, Abdelhafid Bendahmane, Catherine Dogimont
article
10. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Journées Jean Chevaugeon 2014, Jan 2014, Aussois, France. 2014
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Poster communications
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https://hal.inrae.fr/hal-02800948/file/Elbert_Dogimont%202014%2010.%20renc.%20phyto-myco%20Poster_1.pdf BibTex

Reports

titre
Clonage des gènes effecteurs de phytophtora capsici pour guider le développement de variétés résistantes de poivrons
auteur
Véronique Lefebvre
article
[Contrat] Association Provençale de Recherche et d'Expérimentation Légumière (APREL); University of Tennessee; The James Hutton Institute. 2014
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titre
Valorisation des ressources génétiques et génomiques de la tomate pour l'amélioration de la qualité des fruits
auteur
Mathilde Causse
article
[Contrat] Institut National de la Recherche Agronomique (INRA); Vilmorin. 2014
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2013

Conference papers

titre
Point sur les projets labellisés. DEFILeg (2010-2013) : Alternatives aux pesticides dans une gestion durable de la protection des cultures,
auteur
Brigitte Maisonneuve
article
6. Rencontres du GIS PIClég, Groupement d'Intérêt Scientifique pour la Production Intégrée en Cultures légumières (Gis Piclèg). FRA., Dec 2013, Paris, France
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titre
LactuMel (2014-2016) : Recherche de résistance aux nématodes à galles chez la laitue
auteur
Brigitte Maisonneuve
article
6. Rencontres du GIS PIClég, Groupement d'Intérêt Scientifique pour la Production Intégrée en Cultures légumières (Gis Piclèg). FRA., Dec 2013, Paris, France
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titre
Iconographie du Moyen Age à la renaissance: Contribution à l'histoire des plantes (Solanacées, curcubitacées)
auteur
Marie-Christine Daunay, Jules Janick, Harry S. Harris
article
Journées d'étude de l'Inst. Nat. d'Hist.de l'Art (Paris) et du Potager du Roi (Versailles), Entre jardin et table: regards sur la nature morte des fruits et légumes, nouvelles approches du vivant, Nov 2013, Paris, France
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titre
How a species becomes polyploid – The Brassica model
auteur
Anne-Marie Chèvre, Frederique Eber, Maryse Lodé-Taburel, Gwenn Trotoux, Virginie Huteau, Olivier Coriton, Cyril Falentin, Gilles Lassalle, Emmanuel Szadkowski, Maria Loreto Suay Llopis, Maria Manzanares-Dauleux, Régine Delourme, Sophie Paillard, Eric Jenczewski, Karine Alix-Jenczewski
article
Colloque de Génomique Environnementale : Diversité, Evolution et Fonctionnement du Vivant à l’Ere des Nouvelles Technologies de Séquençage, Nov 2013, Rennes, France
resume
How a species becomes polyploid – The Brassica model. Colloque de Génomique Environnementale : Diversité, Evolution et Fonctionnement du Vivant à l’Ere des Nouvelles Technologies de Séquençage
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titre
New resistance-genes deployment strategies as non chemical alternatives for the durable management of root-knot nematodes in vegetable crops rotation
auteur
Caroline Djian-Caporalino, Alain Palloix, Ariane Fazari, Nathalie Marteu, Arnaud Barbary, Anne-Marie Sage-Palloix, Sabine Risso, Roger Lanza, Catherine Taussig, Philippe Castagnone-Sereno
article
2nd international symposium on organic greenhouse horticulture, International Society for Horticultural Science (ISHS). INT., Oct 2013, Avignon, France. 310 p
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https://hal.inrae.fr/hal-02744854/file/Palloix%20_2013_%20ISHS-1_1.pdf https://hal.inrae.fr/hal-02744854/file/Palloix%20_2013_%20ISHS-1_2.doc BibTex
titre
The GEDUNEM project: Varietal and technical innovations for the sustainable and integrated management of root-knot nematodes in protected vegetable cropping systems
auteur
Mireille Navarrete, Caroline Djian-Caporalino, Mathilde Chapuis, Marc Tchamitchian, Arnaud Dufils, Amélie Lefevre, Laure Pares, Thierry Mateille, Alain Palloix, Hélène Védie, Claire Goillon, Ariane Fazari, Nathalie Marteu, Philippe Castagnone
article
2. International Symposium on Organic Greenhouse Horticulture, International Society for Horticultural Science (ISHS). Leuven, INT., Oct 2013, Avignon, France. 6 p
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titre
Combining systems biology, genome resequencing and MAGIC population to decipher the genetic variation of tomato fruit quality
auteur
Laura Pascual, Jiaxin Xu, Nelly Desplat, Yves Gibon, Annick Moing, Mickael Maucourt, Stéphane Bernillon, Catherine Deborde, Jean-Paul Bouchet, Dominique Brunel, Marie-Christine Le Paslier, Mathilde Causse
article
10. Solanaceae conference (SOL 2013), Oct 2013, Beijing, China
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https://hal.inrae.fr/hal-02750138/file/SOL2013_combinig-systems-biology_1.pdf BibTex
titre
Early history and iconography of the Solanaceae: 3. Tomato
auteur
Marie-Christine Daunay, Jules Janick
article
10. Solanaceae Conference: “geno versus pheno", Oct 2013, Beijing, China
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Conference papers
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https://hal.inrae.fr/hal-02806135/file/Daunay%202012%20SOL%20newsletter%201-16_1.pdf BibTex
titre
Towards a better interaction between european Solanaceae germplasm holders and Solanaceae omics researchers
auteur
Marie-Christine Daunay, Willem van Dooijeweert, Roel Hoekstra, Lukas A. Mueller
article
10. Solanaceae Conference: “geno versus pheno”, Oct 2013, Beijing, China
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Conference papers
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https://hal.inrae.fr/hal-02804268/file/Daunay%202012%20SOL%20newsletter%201-16_1.pdf BibTex
titre
Collaborative work on effectors in Phytophthora capsici
auteur
Véronique Lefebvre, Kurt Lamour
article
6. Effectome meeting, Sep 2013, Lauret, France
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titre
Which strategies to search for avirulence factor in resistance plant/aphid interaction
auteur
Leslie Dutartre, Nathalie Boissot
article
6. Effectome meeting, Sep 2013, Lauret, France
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titre
Influence of ascorbate-recycling, light and temperature during tomato fruit ripening on ascorbate pool and ascorbate-degradation
auteur
Vincent Truffault, Hélène Gautier, Rebecca Stevens
article
11. International POG Conference Reactive Oxygen and Nitrogen Species in Plants, Sep 2013, Varsovie, Poland
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Conference papers
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https://hal.inrae.fr/hal-02745080/file/Truffault_Stevens%202013%20BioTechnologia%20199_1.pdf https://hal.inrae.fr/hal-02745080/file/Truffault_Stevens%202013%20BioTechnologia%20199_2.docx BibTex
titre
Valorization of the natural variation available in tomato accessions to decipher the genetic control of quantitative traits
auteur
Laura Pascual-Banuls, J. Xu, Christopher Sauvage, Guillaume Bauchet, Nelly Desplat, Jean-Paul Bouchet, D. Bruner, Marie-Christine Le Paslier, Mathilde Causse
article
57. Annual Congress SIGA, Sep 2013, Foggia, Italy
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titre
Preserving the efficiency of resistance genes against viruses from the individual host plant to agricultural landscapes
auteur
Benoît Moury, Frédéric Fabre, Alain Palloix
article
EMBO Workshop : Green viruses, from gene to landscape, Sep 2013, Hyères-les-Palmiers, France. 129 p
resume
The emergence of virus variants able to circumvent the resistance mechanisms of host plants, i.e. resistance- ‐breaking variants, is a complex phenomenon that involves different evolutionary forces operating at different spatial scales. Resistance breakdown can be decomposed into three major steps: appearance of resistance- ‐breaking virus variants by mutation, accumulation of these variants in plants in competition with wild- ‐type viruses and spread from plant to plant. Resistance breakdown occurs when these three steps are achieved efficiently. If not, the resistance is said durable. Reverse genetics analyses allowed the identification of the mutational pathways responsible for resistance breakdown and the measure of fitness costs associated to these mutations in a number of resistance gene- ‐virus species pairs. However, predicting the consequences of these genetic parameters at higher scales (crop fields, heterogeneous agricultural landscapes) is far beyond our experimental capacities because of the high number of plant- ‐virus combinations to analyze and because of the high number of factors at play during virus emergences. For this purpose, we developed different mathematical models. An analytical model showed that the evolutionary constraint exerted on virus pathogenicity factors (the factors that are recognized by the plant resistance genes) was a good predictor of the durability of the corresponding plant resistance gene. In another approach, simulation models allowed quantifying the respective roles of genetic, demographic and epidemiological factors affecting viral populations during resistance breakdown and estimating what effects on resistance durability could be expected from different leverages available to plant breeders and growers (choice of resistance genes, distribution of resistant and susceptible cultivars among fields, additional control methods acting on epidemics).
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titre
Origin and diversity of the sources of resistance to PPV in apricot: implications and use in marker-assisted resistance to sharka
auteur
Véronique Decroocq, David Tricon, Stephane Decroocq, Stéphanie Mariette, Sevda Babayeva, Patrick Lambert, Guillaume Roch, Jean Marc Audergon, F. Geuna, Daniele Bassi, Luca Dondini, Stefano Tartarini, Jaroslav Salava, Tatyana Zhebentyayeva, Albert Abbott
article
2. International Symposium on Plum Plox Virus, Sep 2013, Olomouc, Czech Republic
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Conference papers
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https://hal.inrae.fr/hal-02806628/file/Lambert_Roch%202013%20Int.%20Sym.%20Plum%20Pox%20Virus_1.pdf BibTex
titre
Analysis of a complex QTL region controlling the broad-spectrum resistance to Phytophthora capsici root rot by comparative mapping and association study in pepper germplasm
auteur
Véronique Lefebvre, Melissa Cantet, Céline Vandecasteele, Sonia Vautrin, Jean-Paul Bouchet, Anne Massire, Alexandre Bachellez, Nasradin Touhami, Stéphanie Mallard, Marie-Christine Le Paslier, Anne-Marie Sage-Palloix, Abdelhafid Bendahmane, Alain Palloix, Helene Berges, Dominique Brunel
article
15. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2013, Torino, Italy
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Conference papers
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https://hal.inrae.fr/hal-02750004/file/Lefebvre_Cantet%202013%20Eucarpia%20139-146_1.pdf BibTex
titre
Peppers and Potyviruses, a pathosystem teaches how to breed for durable resistance in plants
auteur
Alain Palloix, Julie Quenouille, Estelle Paulhiac, Benoît Moury
article
15. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2013, Torino, Italy
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 three 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 pvr23 and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h2=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr23 breakdown frequency. Three of the four QTLs controlling pvr23 breakdown frequency were also involved in quantitative resistance, strongly suggesting that QTLs controlling quantitative resistance have a pleiotropic effect on the durability ofthe 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 pvr23 and the spectrum of the resistance against different potyviruses. This trade-off seemed to have been resolved by the accumulation of minor-effect durability QTLs under field selection
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Conference papers
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02747945/file/Palloix%202013%20Eucarpia%20323-331_1.pdf BibTex
titre
Potentialities of wild relatives for eggplants and eggplants rootstocks breeding
auteur
Marie-Christine Daunay, F. Bletsos, J.W. Hennart, J.P.W. Haanstra, G. van der Weerden
article
15. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2013, Torino, Italy
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Conference papers
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02748311/file/Daunay%202012%20Eucarpia%20231_1.pdf BibTex
titre
Multivariate QTL analyses and predictions of yield related traits in pepper
auteur
Nurudeen Adeniyi Alimi, M.C.A.M. Blink, Alain Palloix, F.A. van Eeuwijk
article
15. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2013, Torino, Italy
resume
Yield is a key trait in pepper and is often measured simultaneously with other traits over several environments. The understanding and genetic improvement of yield may benefit from the joint analysis of yield with its related traits simultaneously. Linear mixed models have emerged as a flexible approach that correctly model underlying variance-covariance structures among the traits and between environments simultaneously. ln this study, we applied four different QTL approaches based on linear mixed model on five yield related pepper traits measured across four environments. We evaluated the performance of the approaches in terms of the number of QTLs detected for each trait and their explained variance. The QTL models are a single-trait single-environment approach (STSE), a multi-trait approach (MT), a multi-environment approach (ME), and a multi-trait multienvironment approach (MTME). We further compared prediction accuracies between STSE and MT models. The predictions were subjected to a five-fold cross validation. Our results showed that multi-trait and/or multi-environment QTL analyses are more powerful and effective to map pleiotropic QTL and QTL by environment interactions th an performing STSE analysis. The multivariate models further showed improvement over STSE in terms of both number of QTLs and the explained variance. MTME clearly outperformed ail the other methods. With MTME, nine QTLs explaining 51% of genetic variation were identified for yield in the autumn trial in Spain as against three, three and six QTLs explaining 37%,29% and 43% from STSE, ME and MT analyses, respectively. The MT model for yield in SP2 had prediction accuracy of 0.53, against 0.42 from the STSE model. These results confirmed that multivariate analyses of traits have better capabilities to unravel complex traits than single trait approach. Our result showed that trait's prediction accuracy depends not only on prediction model of choice and traits genetic architecture but also on the environmen
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Conference papers
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02748944/file/Palloix%202013%20Eucarpia%20273-280_1.pdf BibTex
titre
Genetic structure of the INRA Capsicum spp. collection using SSR loci: refining the wild origin of cultivated C. annuum and impact of human selection on the structuration of genetic diversity in cultivar types
auteur
Anne-Marie Sage-Palloix, Maryse Nicolaï, Melissa Cantet, Véronique Lefebvre, Alain Palloix
article
15. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2013, Torino, Italy
resume
Germplasm collections of cultivated plants constitute the source for further genetic progress and gained interest with approaches for tracking allelic variants associated to phenotypic variations within core collections. ln 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 Il 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 botanic 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 refined. The 3 C. annuum clusters were significantly distinct for plant and fruit descriptors corresponding to cultivar types, showing that the genetic structuration of this cultivated species was strongly impacted by the long term hurnan selection of landraces in prirnary as weil 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 through put genotyping assays. By compiling phenotypic and genotypic data, a larger core-collection of332 accessions was established, capturing 97% of the C. annuum genetic and phenotypic diversity for further genetic association studies
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Conference papers
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https://hal.inrae.fr/hal-02746221/file/Sage-palloix%202013%20Eucarpia%20243-251_1.pdf BibTex
titre
Evaluation of new resistance-genes deployment strategies in the pepper Capsicum annuum for the durable management of root-knot nematodes
auteur
Caroline Djian-Caporalino, Alain Palloix, Ariane Fazari, Nathalie Marteu, Arnaud Barbary, Anne-Marie Sage-Palloix, S. Risso, R. Lanza, C. Taussig, P. Castagnone-Sereno
article
15. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2013, Torino, Italy
resume
The current restrictions on the use of chemical nematicides have contributed to increase rootknot nematode problems in horticultural crops. ln this context, plant resistance appears as the most effective method of control, but the possible occurrence of virulent nematodes able to reproduce on R-plants may constitute a severe threat to this control strategy. ln Capsicum annuum, resistance to RKN is controlled by several dominant genes - the N and Me genes. To implement a rational management of the R-lines increasing the durability of the R-genes, we tested several R-gene deployment strategies. Experiments were conducted in climate-controlled roorns, in greenhouses, and under 3-years-field agronomie conditions to compare i) the succession of the same R-genes every year, when introgressed in a partially resistant vs. a susceptible genetic background, ii) the alternance, ii) the mixed cultivation and iv) the pyramiding of two R-genes with different modes of action in a single genotype. At the plant level, we previously showed that the choice of the R-genes and the genetic backgrounds in which they are introgressed can lower the frequency of resistance breakdown, and that the pyramiding of two different R-genes in one genotype totally suppressed the emergence of virulent isolates. Here, at the field and rotation level, we confirmed these results and showed that i) alternating different R-genes in rotation is efficient to reduce the selection pressure of R-genes on the pathogens and allows to recycle broken R-genes, and ii) optimal cultivation practices of R-plants increase their "trap" effect and may decrease the amount of pathogens in the soil, below their damage threshold. These results are in good agreement with concepts recently developed from the analysis of other plant-pathogen interactions. The root-knot nematode model could thus contribute to generalize strategies for the breeding and management of R-cultivars strengthening and increasing the durability of qualitative resistances
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Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02746488/file/Palloix%202013%20Eucarpia%2037-45_1.pdf BibTex
titre
Towards the deciphering of the genetic factors involved in durability of plant major resistance genes to root knot nematodes in pepper
auteur
Arnaud Barbary, Alain Palloix, Ariane Fazari, Nathalie Marteu, Philippe Castagnone-Sereno, Caroline Djian-Caporalino
article
15. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2013, Torino, Italy
resume
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, few resistance genes (Rgenes) are available and some nematode populations may become able to overcome them with time. Sustainable management of these valuable resources is thus a key point of R-gene durability. ln pepper (Capsicum annuum), Me3 is a dominant major R-gene, currently used in breeding programs, that controls M. arenaria, M. incognita and M. javanica, the three main RKNs species. It was introgressed in either a susceptible or a partially resistant (i.e., that shows reduced symptoms) genetic background in either homozygous or heterozygous allelic status. Doux Long des Landes (DLL) was used as susceptible recipient pepper line and Yolo Wonder (YW) as a partially resistant one. Challenging all these genotypes with a high inoculation pressure of an avirulent M. incognita isolate demonstrated that i) the efficiency of the R-gene in reducing the reproductive potential of RKNs is strongly affected by the plant genetic background, ii) 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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https://hal.inrae.fr/hal-02749808/file/Palloix%202013%20Eucarpia%20281-288_1.pdf BibTex
titre
How a species becomes polyploid? The Brassica model
auteur
Anne-Marie Chèvre, Frederique Eber, Maryse Lodé-Taburel, Gwenn Trotoux, Virginie Huteau, Olivier Coriton, Cyril Falentin, Gilles Lassalle, Emmanuel Szadkowski, Maria Loreto Suay Llopis, Maria Manzanares-Dauleux, Régine Delourme, Sophie Paillard, Eric Jenczewski, Karine Alix-Jenczewski
article
7.European Plant Science Organisation (EPSO) Conference, Sep 2013, Porto Heli, Greece
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How a species becomes polyploid? The Brassica model. 7.European Plant Science Organisation (EPSO) Conference
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titre
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
4. Breeding for inducible resistance, Aug 2013, Avignon, France
resume
Four stimulators of plant defences (SPD) were tested on two pathosystems: powdery mildew (PM) due to Podosphaera xanthii on melon and downy mildew (DM) due to Bremia lactucae on lettuce. More than 450 accessions of melon were screened for the stimulation of their defence reactions by a formulation with laminarin, BION® 50WG and CalFlux and more than 400 accessions of lettuce with BION, Calflux and a formulation with yeast extract (ABE IT 56). In the PM/melon pathosystem, only BION was able to induce resistance; in the majority of the accessions resistance was not activated but some accessions fully susceptible to PM in the control sprayed with water were very well protected by BION. In the DM/lettuce pathosystem, the three tested SPD could induce resistance, but again BION was the most effective. Close to half accessions of the 300 susceptible to Bl: 25 and a quarter of the 110 accessions tested with Bl: 26 were well protected against the tested strain by BION and some of these were also protected by CalFlux (13% and 14%, respectively) and few by ABE IT 56 (10% and 4%, respectively). In both pathosystems, the induced resistance seems to be strain-specific as some accessions were protected against one strain and not protected against another strain; nevertheless some promising accessions were protected against both strains
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titre
Light and temperature of ripening tomato fruits interact to regulate ascorbate synthesis, oxidation and recycling
auteur
Hélène Gautier, Capucine Massot, Doriane Bancel, Vincent Truffault, Rebecca Stevens
article
11. International POG Conference Reactive Oxygen and Nitrogen Species in Plants, Jul 2013, Varsovie, Poland
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https://hal.inrae.fr/hal-02744410/file/Stevens_Truffault%202013%20BioTechnologia%20174_1.pdf https://hal.inrae.fr/hal-02744410/file/Stevens_Truffault%202013%20BioTechnologia%20174_2.docx BibTex
titre
New insights on blood-flesh determinants in peach
auteur
Thierry Pascal, Carole Confolent, Patrick Lambert, Jean-Luc Poëssel, Bénédicte Quilot-Turion, Z. Shen
article
8. International Peach Symposium, Jun 2013, Matera, Italy
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https://hal.inrae.fr/hal-02744629/file/Pascal%202013%208.%20Int.%20peach%20symp._1.pdf BibTex
titre
Molecular assisted selection (MAS): a promising approach under development in peach breeding
auteur
Patrick Lambert, Elisabeth Dirlewanger, Bénédicte Quilot-Turion, Michela Troggio, Diego Micheletti, Maria Jose Aranzana, Thierry Pascal
article
8. International Peach Symposium, International Society for Horticultural Science (ISHS). INT., Jun 2013, Matera, Italy
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titre
Use of Prunus genetic diversity for peach rootstocks
auteur
Henri Duval
article
8. International Peach Symposium, Jun 2013, Matera, Italy
resume
ln 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 aIlows the breeder to obtain the best performance for aIl traits in order to replace an existing rootstock
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titre
High or low fructose? Consequences for sugar metabolism in peach fruit
auteur
Elsa Desnoues, Yves Gibon, Valentina Baldazzi, Veronique Signoret, Michel Génard, Bénédicte Quilot-Turion
article
8. ISHS International Peach Symposium, Jun 2013, Matera, Italy. 1 p
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https://hal.inrae.fr/hal-02740591/file/Peach_Symposium_V2_1.pdf https://hal.inrae.fr/hal-02740591/file/Peach_Symposium_V2_2.doc BibTex
titre
Biological features, positional cloning and validation of the Ma gene for high-Ievel and complete-spectrum resistance to root-knot-nematodes in Prunus
auteur
Daniel Esmenjaud, Cyril van Ghelder, Joel Polidori, Samira Khallouk, Henri Duval
article
Eighth International Peach Symposium, Jun 2013, Matera, Italy
resume
Stone fruit crops Prunus spp. grown under Mediterranean climates are severely damaged by root-knot nematodes (RKN) Meloidogyne spp. and breeding for RKN-resistant rootstocks is a promising control alternative to nematicide ban. Resistance (R) genes that confer different spectra have been identified and mapped in plums (Ma and Rjap), peach (RMia) and almond (RMja). Thus sustainable resistance in Prunus is based on pyramiding of R genes in interspecific rootstock mate rial to take into account the risk of resistance breaking in the durable plant-nematode interaction for perennials. The Ma gene from Myrabalan plum has been shown to confer a complete-spectrum, high-Ievel and heat-stable resistance to both mitotic (M. arenaria, M. incognito, M. javanico and M. enterolobii) and meiotic (M. f/oridensis) RKN. Ma triggers a hypersensitive-like reaction (HLR) in raot apices and severe nematode attacks induce the development of subterminal lateral rootlets replacing primary terminal apices and providing an acive, resist,ance response to HLR damage (1). Sustainability of resistance conferred by Ma has been challenged in multi-year experiments applying a high and continuous nematode inoculum pressure by co-cultivation of RKN-infested susceptible tomato plants together with Prunus plants carrying Ma or, for comparison, with R tomato plants carrying the Mi-l reference gene. Galling and virulent nematode individuals have been observed in Mi-l resistant tomatoes but not in Ma-carrying Prunus plants. The positional cloning of the Ma locus in accession P.2175 has been performed using high resolution mapping developed in two successive steps totalling over 3000 segregants. The Ma locus interval has been reduced to a 32-kb cluster of three TIR-NB-LRR genes (TNLl to TNL3) including a pseudogene (TNL2) and a truncated gene (TNL3). Using A. rhizogenes transformed hairy raots and composite plants (2), the best candidate gene, TNLl, comprising the genomic sequence and the native promoter region (15.3 kb), has been validated as Ma as it conferred the same complete-spectrum and high-Ievel resistance as in the donor accession P.2175. The full-Iength cDNA (2048 aa) of Ma is the longest of ail R genes cloned tc-date. Its TNL structure is extended by a huge Cvterminal post-LRR (PL) region (1088 aa) comprising five repeated PL exons (3)
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titre
Facteurs biotiques et abiotiques influençant l’efficacité des SDP
auteur
Marie Torres, Brigitte Maisonneuve, Michel Pitrat
article
Colloque Elicitra, Jun 2013, Avignon, France
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titre
Effects of genetic resistance combinations in melon on density and genetic diversity of Aphis gossypii populations in fields
auteur
Sophie Thomas, Flavie Vanlerberghe-Masutti, Nathalie Boissot
article
9. International Symposium on Aphids (9ISA 2013), Jun 2013, Beijing, China
resume
Since the deployment of genetic resistant cultivars, several cases of breakdown have occurred rising the question of durability. Quantitative resistances are considered broad-spectrum and more durable than qualitative resistances but this has been poorly tested. We studied selection pressures exerted by qualitative and quantitative plant resistances in fields in the aim to understand how local adaptation of pest populations cou Id occur in agrosystems and to develop strategies for the management of resistances. Field trials were set up in three areas with different melon resistance combinations in a homogeneous genetic background, associating a major gene (the Vat gene) and quantitative trait loci (QTLs) known to affect plant acceptance in two clones of Aphis gossypii. Effects of the Vat gene and the QTLson the density and the genetic diversity of A. gossypii field populations were analyzed. Among the 138 multilocus genotypes (MLGs) identified in 2772 aphids collected, only 11 developed colonies. The Vat gene reduced density of aphid populations on melon crops in ail areas and resulted in changes of the clonai diversity and the genetic structure of aphid populations; the clonai richness was reduced to 6 MLGs in colonies collected on Vat-plants. Conversely, the QTLs did not affect aphid density and slightly affected genetic diversity. Along with selection, competition and local extinction probably condition emergence of certain MLGs on Vat-plants. Because of their narrow-spectrum, the QTLs tested did not reduce the risk of emergence of MLGs adapted ta the Vat gene when these MLGs were associated ta the Vat gene.
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titre
Comparison of evolutionary and swarm intelligence-based approaches in the improvement of peach fruit quality
auteur
Abdeslam Kadrani, Mohamed Mahmoud Ould Sidi, Bénédicte Quilot-Turion, Michel Génard, Francoise Lescourret
article
International Symposium on Operational Research and Applications, May 2013, Marrakech, Morocco. 9 p
resume
We investigated two major families of algorithms for the multi-objective optimization: evolutionary and swarm intelligence-based optimization approaches. Non-dominated Sorting Genetic Algorithm II (NSGA-II) and multi-objective particle swarm optimization (MOPSO) algorithms are biology inspired and are population-based as use a set of solutions which evolve within the search space. These approaches employ different strategies and computational effort; therefore, a comparison of their performance is needed. This paper presents the application and performance comparison of NSGA-II and one variant of the MOPSO, namely MOPSO-CD which incorporates the crowding distance computation and the constraints handling, to design ideotypes for sustainable fruit production systems. The design of 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, and both NSGA-II and MOPSO-CD are 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.
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https://hal.inrae.fr/hal-02809764/file/paper_Kadrani_isorap13_1.pdf BibTex
titre
Intégration du contrôle génétique dans des modèles
auteur
Bénédicte Quilot-Turion
article
Séminaire "concevoir et évaluer des idéotypes", GIS GC-HP2E, Feb 2013, Paris, France
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titre
Intégration des stimulateurs de défense des plantes dans les stratégies de protection des cultures légumières
auteur
Brigitte Maisonneuve, Michel Pitrat, Marie Torres
article
Piclèg : quand chercheurs, conseillers agricoles et producteurs de légumes renouvellent les pratiques de culture, SIA (Salon de l'agriculture), Groupement d'Intérêt Scientifique pour la Production Intégrée en Cultures légumières (Gis Piclèg). FRA., Feb 2013, Paris, France
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Conference papers
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https://hal.inrae.fr/hal-02805886/file/Maisonneuve_Pitrat%202013%20SIA%20Paris_1.pdf BibTex
titre
Quantitative resistance loci reduce the breakdown frequency of a major resistance gene. A relevant way for durable resistance breeding
auteur
Julie Quenouille, Estelle Paulhiac, Benoît Moury, Alain Palloix
article
12. IPVE Symposium, International Committee on Plant Virus Epidemiology (ISPP). St Paul.; International Institute of Tropical Agriculture, CGIAR (IITA). Ibadan, NGA., Jan 2013, Arusha, Tanzania. 256 p
resume
The combination of major resistance genes with quantitative resistance factors is hypothesized as a promising breeding strategy to preserve the durability of resistant cultivars. In three pathosystems, experimental data demonstrate that the durability of a major resistance gene depends on the plant genetic background but the genetic factors involved are still unknown. Using the pepper (Capsicum annuum)/Potato virus Y (PVY)) pathosystem, we aimed to identify genetic factors directly involved in pvr23 resistance breakdown frequency and to compare them with genetic factors affecting quantitative resistance. For QTL mapping experiments, 156 doubled haploid lines carrying the pvr23 resistance allele were tested for pvr23 resistance breakdown frequency, virus accumulation and symptom intensity. Four loci including additive QTLs and epistatic interactions explained together 70% of the variance of pvr23 breakdown frequency. Comparative mapping of the different traits showed that three of the four QTLs controlling the breakdown frequency of the pvr23 allele were also involved in quantitative resistance, indicating that QTLs for quantitative resistance have a pleiotropic effect on the durability of the major resistance gene. This study provides the first mapping of QTLs directly affecting resistance durability and opens the way for sustainable resistance breeding.
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titre
The chloroplast phosphoglycerate kinase is involved in rwm1-mediated resistance to Water melon mosaic potyvirus in Arabidopsis
auteur
Laurence Ouibrahim, Joan Estevan, Marianne Mazier, Hervé Lecoq, Cecile Desbiez, Gaelle Pagny, Véronique Decroocq, André Moretti, Carole Caranta
article
14. Rencontres de Virologie Végétale, Jan 2013, Aussois, France
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titre
Specificity of eIF4E factors towards resistance to potyviruses in Arabidopsis thaliana
auteur
Aramata Marena, Caroline Callot, André Moretti, Jean-Luc Gallois
article
14. Rencontres de Virologie Végétale (RVV 2013), Jan 2013, Aussois, France
resume
The translational initiation factors eIF4E represent the main resistance to Potyvirus as well as to other families of plant RNA virus. Although those factors are encoded by small multigenic families, it has been shown that each virus can only use specific eIF4E to perfom its cycle in plants. Often, this coincides with the ability of the virus VPg to interact with those host proteins. Using Arabidopsis transgenic approaches, we aimed at better understanding the basis of the virus specificity for eIF4E.
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https://hal.inrae.fr/hal-02745414/file/Gallois%202013%2014.%20RVV_1.pdf BibTex
titre
Genetic variability study in a wide germplasm of domesticated peach through high throughput genotyping
auteur
Diego Micheletti, Valeria Aramini, Pere Arus, Elisa Banchi, Teresa Barreneche, Daniele Bassi, Elisabeth Dirlewanger, Zhongshan Gao, Laura Gazza, Patrick Lambert, Francois Laurens, Xiongwei Li, Thierry Pascal, Bénédicte Quilot-Turion, Laura Rossini, Michela Troggio, Ignazio Verde, Maria Jose Aranzana
article
21. Plant and Animal Genome Conference, Jan 2013, San Diego, United States
resume
Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programs is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium-high degree of multiplexing. To address this limitation, about 1,300 peach cultivars were genotyped with the 9K peach SNP chip (Verde et al. 2012) in the frame of FruitBreedomics project. This germplasm was chosen to be representative of the genetic diversity present in five germplasm collection in Europe and in China. Out of the 8144SNPs present in the chip, about 4300 were positively genotyped and used for the further analysis. The average number of heterozygous loci in the genotyped accessions was 1186 (spanning from 13 to 2775). The preliminary results of the population structure reveal three main subpopulations and the presence of high number of admixed individuals. LD seems to decay at distance longer than ca. 1 Mb. These results will be instrumental for implementing LD-based mapping of QTLs and genes in peach.
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Other publications

titre
Quand le réchauffement climatique perturbe les saisons du vivant
auteur
Patrick Bertuzzi, Jean-Marc Audergon, Inaki Garcia de Cortazar Atauri, Frédéric Jean
article
2013, pp.Web INRA
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Poster communications

titre
Variation for fruit shape morphology and candidate genes in eggplant materials
auteur
M. Hurtado, M. Plazas, P. Gramazio, S. Vilanova, Marie-Christine Daunay, E. van der Knaap, J. Prohens
article
15. Eucarpia Meeting on Genetics and Breeding of Capsicum and Eggplant, Sep 2013, Torino, Italy. 2013, Breakthroughs in the geneties and breeding of capsicum and eggplant
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Poster communications
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https://hal.inrae.fr/hal-02748085/file/Daunay%202013%20Eucarpia%20381_1.pdf BibTex
titre
A MAGIC population to decipher the genetic control of quantitative traits in tomato
auteur
Laura Pascual, Mathilde Causse, Jiaxin Xu, Christopher Sauvage, Guillaume Bauchet, Nelly Desplat, Jean-Paul Bouchet, Aurore Desgroux, Dominique Brunel, Marie-Christine Le Paslier
article
7. EPSO Conference, Sep 2013, Porto Heli, Greece. 2013
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Poster communications
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https://hal.inrae.fr/hal-02748316/file/Pascual_Causse_Sauvage%202013%20Poster_1.pdf BibTex
titre
The cell wall of tobacco and tomato pollen tubes contains fucosylated xyloglucan not found in somatic cells
auteur
Flavien Dardelle, Arnaud Lehner, Muriel Bardor, Christophe Rihouey, Mathilde Causse, Patrice Lerouge, Azeddine Driouich, Jean-Claude Mollet
article
XIIIth Cell Wall Meeting, Jul 2013, Nantes, France
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titre
How gene flow between wild and cultivated lettuce can influence the dynamic of adaptation of Bremia lactucae
auteur
Romain Valade, Brigitte Maisonneuve, Aurore Ducasse, R. Michelmore, Claire Neema
article
1. International Conference Wild Plant Pathosystems, Jul 2013, Olomouc, 2013
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Poster communications
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https://hal.inrae.fr/hal-02746835/file/Valade_Maisonneuve%202013%20Wild%20Plant%20Pathosystems%20poster_1.pdf BibTex
titre
Building high-density peach linkage maps based on the ISPC 9K SNP chip for mapping mendelian traits and QTLs: benefits and drawbacks
auteur
Jehan-Baptiste Mauroux, Bénédicte Quilot-Turion, Thierry Pascal, Elisabeth Dirlewanger, José Antonio Campoy-Corbalan, M. Troggio, I. Verde, D. Micheletti, M.J. Aranzana, Patrick Lambert
article
8. ISHS International Peach Symposium, Jun 2013, Matera, Italy. 1 p., 2013
resume
“FruitBreedomics” European project has been designed by an international consortium including scientists, stakeholders and breeding companies. One of its aims is to increase the efficiency of breeding programs in apple and peach by developing Marker Assisted Breeding (MAB) using novel genomic tools. In the frame of this project, six peach mapping populations (two intraspecific F2, two interspecific F1 derived from P. davidiana, one self pollinated derived from Bolinha and one advanced pseudo-backcross) segregating for mendelian traits and/or Quantitative Trait Loci (QTLs) for pest resistance and fruit quality were genotyped using an Infinium II Illumina bead-chip containing 8144 SNPs derived from the sequencing of the peach genome. Mapping results were contrasted depending on the population considered. Relevancy of using general medium-range SNP bead- chips for breeding purposes is discussed in this study
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Poster communications
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https://hal.inrae.fr/hal-02808695/file/poster_matera_JB_v5_PL_final_1.pdf BibTex
titre
Combination of genetic resistance and management of field borders: towards an effective and sustainable control of Aphis gossypii outbreaks and virus epidemics in cantaloupe melon crops
auteur
Alexandra Schoeny, Patrick Gognalons, Nathalie Boissot, Pascale Mistral, Virginie Chareyron, Catherine Wipf-Scheibel, Hervé Lecoq
article
9. International Symposium on Aphids (9ISA 2013), Jun 2013, Pékin, China. 2013, 9ISA Program & Abstracts book
resume
Aphis gossypii is a major pest of cantaloupe melon crops, causing direct damage (sap uptake) and indirect damage (virus transmission). The cantaloupe gene Vat confers resistance to colonization by A. gossypii and resistance to the non-persistent viruses (CMV, WMV, etc) carried by A. gossypii. lt is however ineffective in blocking the transmission of viruses carried by other aphid species and its use is thus generally coupled with aphicide treatments to limit virus transmission by non-colonizing aphids. Moreover, due to its intraspecific variability, A. gossypii can adapt to various selective pressures (host plants, insecticides); this adaptation ability enhances the risk of resistance breakdown. ln France, cantaloupe protection faces a double challenge: to reinforce the effectiveness of Vat in a context of reducing pesticide use, and ensure the sustainability of Vat in a context of increasing Vat deployment. The hypothesis tested in this project is that an appropriate management of field borders can contribute to regulating the populations of aphids and/or their virus load, thereby reducing the risks of virus epidemies and resistance breakdown. lndeed, literature suggests that flower strips can participate in pest biological control by favoring natural enemies (predators and parasitoids), and strips of non host plants can protect crops from non-persistent viruses by allowing aphids to probe on healthy plants and thus to lose their virus load before reaching the crops. An experimental field approach was initiated to compare three types of field border management (bare soil, grass strip and flower strip) on the effectiveness and sustainability of Vat.
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Poster communications
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https://hal.inrae.fr/hal-02749673/file/2013%20ISA%20Beijing%20abstract%20Schoeny_1 BibTex
titre
Diversification of host targets to promote resistance against Potyvirus and Begomovirus in tomato
auteur
Camille Gauffier, Caroline Lebaron, André Moretti, C. Constant, F. Moquet, G. Bonnet, Carole Caranta, Jean-Luc Gallois
article
14. Rencontres de Virologie Végétale (RVV 2013), Jan 2013, Aussois, France. 2013
resume
Tomato (Solanum lycopersicum) is one of the most cultivated vegetable in the world, but suffers from important yield losses caused by viral diseases. Therefore, the development and use of cultivars that are genetically resistant to viruses has become a critical factor of competitiveness for both breeders and producers and one of the key stakes for sustainable agriculture. In this context, generating new resistance alleles using biotechnological approaches (e.g., TILLING) appears as a powerful tool to diversify host targets to promote resistance against viruses.
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Poster communications
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https://hal.inrae.fr/hal-02745583/file/Gauffier_Gallois%202013%2014.%20RVV%20Poster_1.pdf BibTex
titre
Couplage entre résistance génétique et aménagement parcellaire : vers une gestion efficace et durable du puceron Aphis gossypii et des épidémies virales en cultures de melon
auteur
Alexandra Schoeny, Patrick Gognalons, Nathalie Boissot, Pascale Mistral, Virginie Chareyron, Catherine Wipf-Scheibel, Hervé Lecoq
article
14. Rencontres de Virologie Végétale (RVV 2013), Jan 2013, Aussois, France. 2013
resume
Le gène Vat confère au melon une résistance à la colonisation par le puceron Aphis gossypii ainsi qu'une résistance aux phytovirus non persistants (CMV, WMV,...) transmis par ces pucerons (Lecoq et al., 1979; Pitrat & Lecoq, 1982 ; Boissot et al., 2010). Il est toutefois inefficace pour bloquer la transmission des virus portés par les autres espèces de pucerons. L'utilisation de Vat est donc généralement couplée à des traitements aphicides afin de limiter la transmission virale par les pucerons non colonisateurs du melon. Or, la réduction progressive de l'usage des produits phytosanitaires dans la protection des cultures imposée par l'évolution de la réglementation (plan Eco-Phyto 2018) conduit à rechercher de nouvelles stratégies permettant d'accompagner la lutte génétique pour la gestion des bio-agresseurs. La bibliographie suggère que l'implantation de bandes de plantes non hôtes (enherbées ou fleuries) à la périphérie des cultures pourrait être une option efficace pour diminuer 1) la pression puceron (et donc le risque de contournement de Vat) en favorisant le développement des ennemis naturels (Pfiffner & Wyss, 2004) et 2) la pression virus en constituant notamment un filtre réduisant la charge virale des pucerons avant qu'ils n'atteignent les cultures (Hooks & Fereres, 2006). L'hypothèse testée dans ce projet est qu'un aménagement adéquat de l'environnement parcellaire peut contribuer à réguler les populations de pucerons et/ou leur potentiel virulifère et ainsi à réduire le risque d'épidémies virales. L'effet de trois types d'aménagement (sol nu, bandes enherbées et bandes fleuries) sur l'efficacité de la résistance médiée par le gène Vat est évalué au champ.
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Poster communications
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https://hal.inrae.fr/hal-02749408/file/Schoeny_1 BibTex
titre
Exploring genetic diversity in tomato fruit with a systems biology approach
auteur
Laura Pascual, Jiaxin Xu, Nelly Desplat, Benoit Valot, Jean-Paul Bouchet, Dominique Brunel, Mathilde Causse
article
21. International Plant and Animal Genome, Jan 2013, San Diego, United States. 2013
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Poster communications
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https://hal.inrae.fr/hal-02745690/file/Pascual_Causse_Bouchet%202013%20Poster_1.pdf BibTex

Reports

titre
Adaptation de l’abricotier aux changements climatiques : estimation des risques génétiques et géographiques liés aux avortements floraux et à l’époque de floraison Le réseau agroclimatique de l’INRA et la base associée de données
auteur
Inaki Garcia de Cortazar Atauri, Patrick Bertuzzi, Lucia Andreini, François Madon, Jean Marc Audergon
article
[Contrat] 2013
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Reports
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https://hal.inrae.fr/hal-02809978/file/Raport%20final%20CTPS%20Abricot%202013_1.pdf BibTex

2012

Conference papers

titre
QTL analyses on genotype-specific component traits in a crop simulation model for Capsicum annuum L.
auteur
A. M. Wubs, E. Heuvelink, J. A. Dieleman, J. J. Magan, Alain Palloix, F. A. van Eeuwijk
article
4th International Symposium on Models for Plant Growth, International Society for Horticultural Science (ISHS). INT., Nov 2012, Nanjing, China
resume
QTL for a complex trait like yield tend to be unstable across environments and show QTL by environment interaction. Direct improvement of complex traits by selecting on QTL is therefore difficult. For improvement of complex traits, crop growth models can be useful, as such models can dissect a target trait into a number of component traits. QTL for the component traits are assumed to be more stable across environments. The target trait can be reconstructed from its component traits together with environmental inputs. Instead of observed component traits, QTL fits for component traits may be used when QTL explain a reasonable proportion of the variation in the components. We applied this dissection approach to the target trait total shoot biomass for a population of 149 recombinant inbred lines from the intraspecific cross of Capsicum annuum ‘Yolo Wonder’ and ‘Criollo de Morelos 334’. A simple LINTUL-type simulation model was used, with rate of change of leaf area index and light use efficiency as genotype specific component traits. These two component traits were determined in four phenotyping experiments (spring and autumn cultivations in the Netherlands and Spain), and subjected to QTL analysis. Seven QTL were found for both component traits. For leaf area index development rate 40 to 50% of the observed variance was explained by the QTL, while this was slightly lower for light use efficiency (23-39%). Using the QTL fitted values of the component traits following QTL analysis, the crop simulation model explained 27- 43% of the observed variation in total shoot biomass, which was higher than the variation explained by the QTL for total shoot biomass itself for most experiments. The approach of dissecting a complex trait into its component traits is therefore a promising one. Next step is to extend the model with biomass partitioning
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Fruit size in relation to competition for resources: A common model shared by two species and several genotypes grown under contrasted carbohydrate levels
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Marion Prudent, Zhanwu Dai, Philippe Vivin, Michel Génard, Nadia Bertin, Mathilde Causse
article
4. International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, IEEE., Oct 2012, Shanghai, China
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Fruit size is one important criterion of fruit external quality affecting consumer acceptance. The effects of seed number on fruit size in two fleshy fruits, grape and tomato, of different genotypes and grown under distinct carbohydrate availability levels were analyzed with a model. The two-parameter model described within-fruit resource competition and was able to well represent the commonly observed decrease in fresh weight per seed along with the increase in number of seeds, regardless of species, genotypes, and carbohydrate levels that were evaluated in this study. However, carbohydrate levels largely modified the correlation between seed number and fresh weight per fruit. In grape, lowering carbohydrate level led to a decrease in the parameter reflecting the potential fresh weight per seed, while in tomato, the response to carbohydrate was genotype-dependent and concerned more the parameter reflecting the competition level for resources. The values of the latter parameter suggested an under-compensating competition for resources in domesticated grape and tomato genotypes. Finally, co-localizations among quantitative trait loci for fruit fresh weight and model parameters indicated that plant susceptibility to competition could underlie the fruit fresh weight determination.
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Compromising NSGA-II performances and stopping criteria: case of virtual peach design
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Mohamed Ould Sidi, Abdeslam Kadrani, Bénédicte Quilot-Turion, Francoise Lescourret, Michel Génard
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4. International Conference on Metaheuristics and Nature Inspired Computing, META'2012, Oct 2012, Port El-Kantaoiui, Tunisia
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Protection des laitues contre le mildiou. Diversité génétique de la réactivité aux SDP
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Brigitte Maisonneuve, Caroline Allen-Aubouard, Michel Pitrat
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MIFFEL, salon Méditerranéen Interprofessionnel de la Filière Fruits Et Légumes, Oct 2012, Avignon, France
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https://hal.inrae.fr/hal-02811361/file/Maisonneuve-Pitrat%202012Miffel%20Avignon_1.pdf BibTex
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Intégration du côntrole génétique dans les modèles
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Bénédicte Quilot-Turion
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Ecole-chercheurs "Conception d'idéotypes de plante pour l'agriculture durable", Oct 2012, Seillac, France
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New insights on virulence and evolutionary dynamics of the Ralstonia solanacearum species complex -keys and challenges in the search of durable resistance in solanaceae
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Emmanuel Wicker, Aurore Lebeau, Flora Pensec, Marie-Christine Daunay, Jacques Dintinger
article
Plant resistance sustainability 2012. International conference, Oct 2012, La Colle sur Loup, France
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Bacterial wilt, caused by the soilborne betaproteobacterium Ralstonia solanacearum, is a major disease of solanaceous crops, throughout tropical and subtropical areas, and emerging in temperate regions. If genetic resistance is still considered as the most promising control measure, breeding for resistance to Ralstonia solanacearum (Rsol}, has been hindered for decades by the scarcity of high level resistance sources, strong genotype x environment interactions, and the huge genomic and phenotypic plasticity of the pathogen. Ralstonia solanacearum is a species complex composed of four phylotypes related to geographical origins (1: Africa-Asia, Il: American, III: Africa, IV: Indonesia). Solanaceae-pathogenic strains belong to ail four phylotypes, but most epidemiologically active strains belong to phylotype l, liA, IIB, and III, phylotype 1being the most widespread lineage. Extensive screenings of resistant accessions of tomate, eggplant and pepper towards a worldwide R.sol core-collection, lead to formalize grain Solanaceae-Rsol interactions into six main virulence profiles, and allowed to identify highly resistant accessions, mainly in eggplant and pepper. Among the rn, the eggplant MM960 was demonstrated to carry a phylotype I-resistance major dominant gene (Ersl) and two partial resistance QTLs with strain-specific expression. We identified patterns of strain -specificity, but found no evidence of phvlotvpe-specificltv.'phvlotvpe 1containing four of the six pathopprofiles. Searching for durable resistance implies both the identification of bacterial genes responsible for avirulence and virulence, and assessment of the pathogen evolutionary potential. Considering "immune" accessions (five eggplants, two peppers, one tomato) giving true incompatible interactions (no wilt and no colonization), we then searched for genetic factors associated with bacterial virulence and avirulence using comparative genomics hybridization (CGH) data. We thus identified 61 type III effectors fairly to highly associated to avirulence to eggplants Dingras, SM6, Ceylan, Surya, and MM960, peppers CA8 and Perennial, and tomate HW7996. Interestingly, some of these effectors were elsewhere shown to contribute to bacterial fitness. Focusing on the accessions MM960 and Dingras, less than 10 genes were highly associated with avirulence, among which popP2, avirulence gene interacting with the RRS1-Rresistance gene in Arabidopsis thaliana. We inferred evolutionary dynamics of the R.solanacearum species complex (RSSC) at a global scale, performing multi-Iocus sequence analysis (MLSA) and gene genealogies on a worldwide collection. Although recombination was found ubiquitous within the RSSC, we observed phylotype-specific recombination rates and demographic histories. Phylotype 1 (and, to a lesser extent, phylotype III) is highly recombinogenic, and carries molecular signatures of a recent and rapid demographic expansion. Phylotype Il is actually composed of two evolutionary lineages, one (liA) being moderately recombinogenic and expanding, and the other (IIB) being clonai and poorly expanding. Taken together, these findings strongly suggest that phylotype 1 is the most prone to adapt rapidly to new hosts and varieties, thank to its recombination and mutation rates, capacity to disseminate, and large virulence range. To decipher evolutionary dynamics leading to adaptation at the local, field scale, an experimental evolution trial is in course to monitor the impact of Ersl-carrying eggplant MM960 successive craps on the population structure and putative avirulence genes evolution.
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https://hal.inrae.fr/hal-02745024/file/Daunay%202012%20Plant%20resistance%20sustainability%2068-69_1.pdf BibTex
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Effects of lettuce cultivar mixtures, differing for resistance genes, on Bremia lactucae incidence
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Brigitte Maisonneuve, Eric Martin, Loic Jean, Claude Pope de Vallavieille, Michel Pitrat
article
Plant resistance sustainability 2012. International conference, Oct 2012, La Colle sur Loup, France
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Bremia lactucae, the causal agent of lettucedowny mildew,is still an important problem in lettuce production in spite of many resistance genes used over the last 50 years in Europe. Every new gene introduced into commercial varieties has been overcome in a few years. At INRA, new resistance genes were found in two L. virosa accessions and introgressed into butterhead lettuce (lines named Vi). These resistance genes are not yet introduced in commercial varieties; we would like propose a using strategy of these genes that could increase their durability. Which strategies might be efficient to reduce the evolution of the pathogen and ensure a durable resistance with these genes? A lower selection pressure on B. factucae population could reduce the speed of breakdown of the new resistance. A possibility to have a lower selection pressure on the B. factucae populations could be mixture of two cultivars differing for resistance genes. Therefore Bremia contamination has been studied for several winters in cultures of these resistant Vi lines mixed with a susceptible cultivar. ln the same culture, the progression of Bremia on the susceptible plants has been observed. The disease development has been studied after an artificial contamination with two objectives: (i) does the pathogen overcome the resistance, (ii) is the disease seve rit y on the susceptible cultivar acceptable for commercial use? After eight experimentations under a polythene greenhouse, pure stands were compared to mixture in ratio 1:3 (susceptible:resistant) after focal inoculation with a B. factucae isolate common in the region. No sporulation has been observed on the two Vi lines issued from L. virosa. For the vear with high inoculum pressure, the cultivar mixture did not reduce the disease seve rit y on the susceptible cultivar (for example, in winter 2006-2007, 24 contaminated leaves per susceptible plant in pure stand and in mixture; a disease seve rit y of 53 and 48 on the susceptible variety, respectively in pure stand and in mixture). For intermediate to low inoculum pressure, the disease development was slower on the susceptible cultivar grown in mixtures, with less contaminated plants and less contaminated leaves per plant (1.1 in pure stand vs 0.2 in mixture, in winter 2005-2006) at harvest. The disease severity on susceptible cultivar is lower in mixture than in pure stand for example in winter 2005-2006 (index 1.3 vs 9.5); this seve rit y was similar at the beginning of the epidemics for both treatments, but it became much higher in pure susceptible stand on the last week before harvest. Therefore the mixed culture could be an interesting method to reduce disease level on a cultivar susceptible to the strain that is important in the culture and also possibly increase the durability of new resistance by a lower selection pressure on the virulent strains. Nevertheless this cultural practice must be adapted to the needs of growers economically and technically; it could be difficult to have an efficient design of the mixture in a commercial culture. Some other experiments must be done in connection with the growers and the breeders.
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Constraints on resistance and pathogenicity factors and their consequences on resistance durability
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Benoît Moury, Carole Caranta, Sophie Ewert, Séverine Lacombe, Frederic Fabre, Alain Palloix
article
Plant resistance sustainability 2012 international conference, Oct 2012, La Colle-Sur-Loup, France
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https://hal.inrae.fr/hal-02745963/file/2012-Moury-La%20colle%20sur%20loup_1.pdf BibTex
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Contribution of microbial core-collections and exploitation of polygenic resistances to the development of Phytophthora control strategies in solanaceous crops
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Marie-Line Kuhn, Anne Massire, Melissa Cantet, Rene Damidaux, Elvina Gibowski, Youna Ruellan, Véronique Lefebvre, Franck Panabières
article
Plant Resistance Sustainability 2012 International Conference, Oct 2012, La Colle sur Loup, France
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Oomycetes form a diverse group of fungus-like eukaryotic microorganisms that include saprophytes as weil as pathogens of animais and some of the most devastating pathogens of dicotyledonous plants. Among them, few species of the genus Phytophthora, such as P. capsici and P. infestons cause enormous economic da mage on Solanaceous crops. Major genes have been identified in tomato to confer resistance against P. infestons, but were rapidly overcome by virulent populations: Pepper resistance towards P. capsici is provided by several quantitative trait loci (QTls). Efficient exploitatio-n of such polygenic resistance sources in plant breeding programs requires a good evaluation of their spectrum and durability. This requires a precise knowledge of the diversity of pathogen populations (with a focus on virulence, aggressiveness and host range) and some of their adaptive traits, such as changes in virulence or adaptation to prevalent cultivars. Theoretically, the use of Phytophthora corecollections reflecting the overall intraspecific diversity would help to assess the a priori durability of resistance sources. We initiated a study to evaluate the potential sustainability of polygenic pepper and tomato resistances to Phytophthora. It implied i) to estimate the diversity of P. infestans and P. caps ici collections and their evolution over time; ii) to develop diverse quantitative and qualitative pathogenic assays to identify the various components underlying polygenic resistances. Collections included isolates from various geographic origins. Genetic diversity was investigated using a combination of neutral markers and genes under positive selection. First results on P. capsici reveal significant variations in the structure and dynamics of regional populations, and suggest that P. caps ici core-collections may be of local interest. We also showed that P. infestons populations are diverse but structured. Hence, strains isolated on tomato or potato differ at the genotypic and phenotypic levels. The use of P. infestons core-collections in breeding programs therefore requires gaining knowledge on the structure and epidemiological characteristics of natural pathogen populations collected on tomato.
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https://hal.inrae.fr/hal-02749550/file/Massire_Damidaux%202012%20Plant%20resistance%20sustainability%2072_1.pdf BibTex
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Importance of the genetic background for sustainable resistance: experimental evidence for a major resistance gene to nematodes
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Arnaud Barbary, Alain Palloix, Ariane Fazari, Nathalie Marteu, Philippe Castagnone-Sereno, Caroline Djian-Caporalino
article
Plant resistance sustainability 2012. International conference, Oct 2012, La Colle sur Loup, France
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Root-knot nematodes, 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 ta protect crops against these pests. However, resistance genes (R-genes) are limited and nematode populations are able ta overcome them with time. Good management of these valuable resources is thus a key point of R-gene durability. ln pepper, Me3 is a dominant major resistance gene, currently used in breeding programs, that control M. arenario, M. incognito and M. javanica, the three main root-knot nematodes species. ln this study, it was introgressed in either a susceptible or a partially resistant genetic background in either homozygous or heterozygous allelic status. Confronting these genotypes with a high inoculation pressure of an avirulent M. incognito isolate or a Me3 virulent laboratory-selected population (obtained by successive re-inoculation on a Me3 R-pepper line) demonstrated i) that the genetic background plays an important raie, Me3 being overcome more easily in a susceptible genetic background than in a partially resistant one, ii) that the allelic status has no effect. These results are in good agreement with concepts recently developed from the analysis of very different plant-pathogen interactions: pepper-virus (Palloix et al., 2009) or rapeseed-Leptosphaeria (Brun et al., 2012). Experiments are now underway ta detect and localise genes or loci providing partial resistance (QTLs = Quantitative Trait Loci) ta root-knot nematodes explaining the differences observed between susceptible and partially resistant genetic backgrounds, and ta determine the effectiveness of their « protective » raie on the major R-genes. Ali these results are of main importance for the creation of new varieties by breeders who have to take into account the plant material used and the resistance gene they want ta introgress.
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https://hal.inrae.fr/hal-02745433/file/Palloix%202012%20Plant%20resistance%20sustainability%2081_1.pdf BibTex
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Biological features, positional cloning and validation of the Ma gene for high-Ievel and complete-spectrum resistance to root-knot-nematodes in Prunus
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Cyril van Ghelder, Samira Khallouk, Joel Polidori, Henri Duval, Marc Kleinhentz, Elisabeth Dirlewanger, Daniel Esmenjaud
article
Plant resistance sustainability 2012. International conference, Oct 2012, La Colle sur Loup, France
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Stone fruit crops Prunus spp. grown under Mediterranean climates are severely damaged by root-knot nematodes (RKN) Me/oidogyne spp. and breeding for RKN-resistant rootstocks is a promising control alternative to nematicide ban. Resistance (R) genes that confer different spectra have been identified and mapped in plums (Ma and Rjap), peach (RMia) and almond (RMja). Thus sustainable resistance in Prunus is based on pyramiding of R genes in interspecific rootstock mate rial to take into account the risk of resistance breaking in the durable plant-nematode interaction for perennials. The Ma gene from Myrabalan plum has been shown to confer a complete-spectrum, high-Ievel and heat-stable resistance to both mitotic (M. arenaria, M. incognito, M. javanico and M. entera/obii) and meiotic (M. f/oridensis) RKN. Ma triggers a hypersensitive-like reaction (HLR) in raot apices and severe nematode attacks induce _ the development of subterminal lateral rootlets replacing primary terminal apices and providing an acive, resist,ance response to HLR damage (1). Sustainability of resistance conferred by Ma has been challenged in multi-year experiments applying a high and continuous nematode inoculum pressure by co-cultivation of RKN-infested susceptible tomato plants together with Prunus plants carrying Ma or, for comparison, with R tomato plants carrying the Mi-l reference gene. Galling and virulent nematode individuals have been observed in Mi-l resistant tomatoes but not in Ma-carrying Prunus plants. The positional cloning of the Ma locus in accession P.2175 has been performed using high resolution mapping developed in two successive steps totalling over 3000 segregants. The Ma locus interval has been reduced to a 32-kb cluster of three TIR-NB-LRR genes (TNLl to TNL3) including a pseudogene (TNL2) and a truncated gene (TNL3). Using A. rhizogenes transformed hairy raots and composite plants (2), the best candidate gene, TNLl, comprising the genomic sequence and the native promoter region (15.3 kb), has been validated as Ma as it conferred the same complete-spectrum and high-Ievel resistance as in the donor accession P.2175. The full-Iength cDNA (2048 aa) of Ma is the longest of ail R genes cloned tc-date. Its TNL structure is extended by a huge Cvterminal post-LRR (PL) region (1088 aa) comprising five repeated PL exons (3).
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https://hal.inrae.fr/hal-02745737/file/Duval%202012%20Plant%20resistance%20sustainability%2093_1.pdf BibTex
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The GEDUNEM project: Varietal and technical innovations for the sustainable and integrated management of root-knot nematodes in protected vegetable cropping systems
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Caroline Djian-Caporalino, Alain Palloix, Mireille Navarette, Amélie Lefevre, Thierry Mateille, Hélène Védie, Claire Goillon, Yannie Trottin, P. Boniol, Philippe Castagnone-Sereno
article
Plant resistance sustainability 2012. International conference, Oct 2012, La Colle sur Loup, France
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The recent banning of the most active chemical nematicides raised root-knot nematodes (RKN) as the major problem of vegetable growing in the south-east of France, with over 40% of horticultural farms affected. Resistant (R) cultivars successfully limit nematode attacks of the crop itself and reduce nematode abundance in soil in the short term. But their use in commercial fields faces two major constraints: (1) the limited number of cultivated species with RKN R-genes available (tomate. pepper), which would lead to major changes in crop rotations with socio-economic constraints; (2) the emergence of virulent root-knot nematode populations, able to overcome the resistance conferred by some of the R-genes. Recent research showed that the durability of the resistance per se was possibly increased with an optimal choice of the R-gene or allele combination, and of the genetic background in which the major R-genes where introgressed. However, the requirement for agronomic performance, does not always allow the breeder to fully use the genetic diversity available in R-genes and genetic backgrounds. ln such cases, spatio-temporal deployment strategies of resistant cultivars in the rotation were proposed and provided some success. But combination of genetic resistance with cultivation practices including multicrop rotations, intercultural management and/or prophylactic treatments was poorly tested for its ability to provide complementary selection pressures on the pathogen populations and to increase the durability of the protection. The project aims at identifying innovative strategies across the agrosystem, cornbining varietal resistance in crop rotations with agronomic practices, for a sustainable control of RKN that infect vegetable crops in protected crop systems. This pilot and demonstrative project involves analytical and systemic aspects: il the validation of previous results on the durability of RKN genetic resistance in tomato and pepper by long-term experiments in research stations and in farms, ii/ the impact of agronomic practices on the parasitic pressure in the soil and its contribution in the increase of resistance durability, and iii/ the impact of such innovations on the yield and the economie viability for protected crop systems in a Mediterranean climate. The added value here is to combine together currently dispersed approaches based on synergistic and long-term effects, towards a satisfying level of nematode control over pluri-annual crop sequences. The diversity of partners (research, experimental stations, technical institutes) and associated forces (growers' development structures, 'chambres d'agriculture') brings ail the complementary expertise needed for answering specifie short-term questions as weil as generic mid-long term expectations. 'GEDUNEM' has been launched in the framework of the INRA metaprogramme SMaCH (Sustainable Management of Crop Health).
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https://hal.inrae.fr/hal-02750319/file/Palloix%202012%20Plant%20resistance%20sustainability%2084-85_1.pdf BibTex
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Experimental evidence of the efficiency of two resistance genes deployment strategies - pyramiding or alternating - for sustainable management of root-knot nematodes
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Caroline Djian-Caporalino, Ariane Fazari, Nathalie Marteu, Anne-Marie Sage-Palloix, S. Risso, R. Lanza, Alain Palloix, Philippe Castagnone-Sereno
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Plant resistance sustainability 2012. International conference, Oct 2012, La Colle sur Loup, France
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https://hal.inrae.fr/hal-02744512/file/Sage-Palloix_Palloix%202010%20Plant%20resistance%20sustainability%2042_1.pdf BibTex
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The durability of a major resistance gene is affected by quantitative trait loci which also confer quantitative resistance to virus
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Julie Quenouille-Lederer, Estelle Paulhiac, Pascale Mistral, Ghislaine Nemouchi, Anne-Marie Sage-Palloix, Bruno Savio, Vincent Simon, Benoît Moury, Alain Palloix
article
Plant resistance sustainability 2012. International conference, Oct 2012, La Colle-Sur-Loup, France
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https://hal.inrae.fr/hal-02744632/file/2012-Quenouille-La%20colle%20sur%20loup_1.pdf BibTex
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Effects of resistance combinations in melon on Aphis gossypii field populations
auteur
Sophie Thomas, Flavie Vanlerberghe-Masutti, Virginie Chareyron, Pascale Mistral, Nathalie Boissot
article
Congres international plant resistance sustainability 2012, Oct 2012, La Colle-Sur-Loup, France
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Host-plant resistance has proven its efficiency in controlling pests, including aphids which are one of the major hemipteran pests in crops. Nevertheless, resistance-breaking biotypes have occurred in several plant-aphid systems. The aim of our field study was to investigate the impact of distinct combinations of aphid-resistance Vat gene and QTLs in melons on the density and genetic structure of field populations of the melon aphid species Aphis qossvpii. We set up field trials with melons combining (i) resistance alleles both at the Vat locus and at QTL (Vat/QTL), (ii) resistance allele at the Vat locus and susceptible alleles at QTL (Vat/-) or (iii) susceptible allele at the Vat locus and resistant alleles at QTL (-/QTL). Ali combinations had a homogenous genetic composition except at the Vat locus and QTL (Boissot et al 2010). Twelve trials were conducted in three distant melon producing areas,.: Southeastern France (SE), southwestern France (SW) and French West Indies (FWI), to take into account that aphid populations are geographically structured (Thomas et al 2012). Aphid population densities were significantly lower on Vat/QTL melon plants than on -/QTL plants over trials, revealing a strong effect of the Vat gene in situ. Conversely, no effect of the QTL was observed on aphid density. We also collected about 2800 aphids from these trials that were distributed in two classes whether they were found as isolated apterous individuals on the leaf soon after melon plantation or whether they were collected from a colony later on. Each aphid was genotyped for eight microsatellite loci. Whatever the resistance combination and area, the genetic diversity decreased dramatically during the melon development, from isolated apterous to colonies, which illustrated a strong host plant selective pressure. We also noticed a Vat gene effect in reducing the genetic diversity of both apterous populations in SE and colonies in SE and SW. Furthermore, according to a genetic clustering analysis, the 138 multilocus genotypes identified were separated in two clusters calied the NMl cluster and the Cucurbit luster. Aphids from the NMl cluster were significantly more affected by the Vat gene as apterous individuals were less numerous on Vat/QTL than on -/QTL melons and they did not develop into colonies on Vat/QTL and on Vat/- melons. ln conclusion, this field study did not provide experimental evidence that the combination of qualitative effective major gene and quantitative polygenic resistance to A. qossypii in melon improves control of the aphid populations. QTLs had no effect on demography or on clonai diversity and structure of aphid populations. On the contrary, the effect of the major resistance gene Vat was shown to de pend on the clonai diversity and structure ofthe aphid populations. However, this clonai diversity might substantially vary in time and space according to many ecological factors, which could prevent or at least slow down the spread of a resistance breaking biotype.
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Characterization of adaptation to a resistance gene with a pleiotropic effect, the Vat gene in melon
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Nathalie Boissot, S. Thomas, Virginie Chareyron, Pascale Mistral
article
Congrès international plant Resistance sustainability 2012, Oct 2012, La Colle-Sur-Loup, France. 2 p
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The deployment of resistance genes against aphids, is restricted because few genes have been characterised. The Vat gene, conferring resistance to Aphis gossypii, has been effectively deployed in melon crops since 20 years in South-eastern France. We have studied the adaptation of A. gossypii populations to that Vat gene. Seven clones of A. gossypii were collected in melon producing areas where the Vat gene has been or not deployed. Theses clones were characterized using 8 SSR markers. The phenotypic variability of A. gossypii was shown matching the genetic variability revealed by eight microsatellite markers (Thomas et al, 2012). We phenotyped the seven clones using three resistant melon lines. One line was susceptible to ail clones, the two other lines, Margot and 90625, were known to carry different alleles at the Vat locus. We took advantage of the double phenotype mediated by the Vat gene, the resistance to A. gossypii and the resistance to viruses (CMV, ZYMV...) when inoculated by A. gossypii - melon plants are susceptible to viruses when they are mechanically inoculated or inoculated by other aphids species. Aphid clones triggered three phenotypic responses on Margot or 90625 lines: resistance to aphids and to the virus when inoculated by aphids, susceptibility for both phenotypes, and susceptibility to aphids and resistance to the virus when inoculated by aphids; we did not characterize any clones revealing a melon line resistant to aphids and susceptible to virus when inoculated by aphids. Our results revealed a specifie interaction between plant resistance alleles in melon and aphid clones. The Vat gene belongs to the CC-NBS-LRRresistance gene (Pauquet et al 2004). The avirulence factor in aphid, expected to interact with the Vat protein, is presently unknown, it should be excreted in saliva and introduce in plant tissue during puncturing, and then interacts with the Vat product triggering defence responses (Dogimont et al 2010). These responses are expected to be efficient against aphids and viruses. Our results suggested two adaptation mechanisms of aphids to the Vat mediated resistance: i/ suppression of both phenotypes, i.e. susceptibility to aphids and to virus when inoculated by A. gossypii, what suggests a suppression of the recognition step (non-adapted avirulence product), ii/ susceptibility to aphids associated with resistance to virus when inoculated by aphids, suggested that the recognition step occurs, triggering the defence reponses that are efficient against virus but inefficient against aphids, i.e. aphids are adapted to these defence responses. We only observed adaptations of type i/ when considering the melon line 90625. Because the allele of resistance originating from this line has never been deployed in crops in areas we collected clones, these adaptations, observed in several clones, corresponded to an incomplete spectrum of the resistance efficiency. ln South-eastern France, the resistance that has been deployed is mediated by the allele at the Vat locus present in Margot. ln this area, where A. gossypii diversity is very large (Thomas et al 2012b), two clones, never observed before 2009, exhibited adaptation of type ii/ to that allele of resistance.
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Domestication and diversification of melon
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Michel Pitrat
article
Cucurbitaceae 2012, Proceedings of the Xth Eucarpia Meeting on Genetics and Breeding of Curcubitaceae, European Association for Research on Plant Breeding (EUCARPIA). FRA., Oct 2012, Antalya, Turkey
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https://hal.inrae.fr/hal-02744680/file/Pitrat%202012%20Eucarpia%2031-40_1.pdf BibTex
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How microsatellite diversity helps to understand the domestication history of melon
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Laurana Serres-Giardi, Catherine Dogimont
article
10. EUCARPIA Meeting on Genetics and Breeding of Cucurbitaceae, Oct 2012, Antalya, Turkey. 809 p
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Melon (Cucumis melo L.) population structure remains incomplete because of the sampling weakness in some botanical groups and for wild melons. The purpose of this study was to assess the genetic subdivisions in melon germplasm using a more representative sampling of the worldwide diversity and to investigate the localization of melon domestication and diversification. To reach this objective, a set of 20 microsatellite markers was used to genotype 713 accessions including 635 cultivated and feral melons, 66 wild melons and 12 relative Cucumis sp. A two-level structure in melon was revealed using population genetics statistics, clustering methods with genetic distances and Bayesian assignment method. Accessions split into two groups, fitting very well the subspecie melo and agrestis. Agrestis group was clearly substructured according to geographical origins, with African, Far-Eastern and Indian subgroups. The substructure of melo group was less resolute and the four clusters obtained grouped together several botanical groups originating from Europe, America, Middle East or Central Asia. African and Asian wild Cucumis melo were assigned to two distinct clusters in agrestis group, each with cultivated melons from the same respective geographical origin, suggesting that melon was domesticated twice. The domestication of wild African melon would have had a weak impact on the diversification of cultivated melon producing only Sudanese tibish and seinat types. The domestication of wild Asian melon, probably in india, would have first produced Indian cultivated melons and then be at the origin of Far-Eastern melons. Introduction of Eastern melons in the West and successive breeding activities may have then produced melo ssp. These findings are consistent with recent data on the Cucumis genus structure and origin, and with the high frequency of resistance genes found in melon Indian accessions.
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Resistance of melon to Cucumber Vein Yellowing Virus (CVYV)
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Michel Pitrat, Catherine Wipf-Scheibel, Didier Besombes, Cecile Desbiez, Hervé Lecoq
article
Cucurbitaceae 2012, Proceedings of the Xth Eucarpia Meeting on Genetics and Breeding of Curcubitaceae, European Association for Research on Plant Breeding (EUCARPIA). FRA., Oct 2012, Antalya, Turkey. 8 p
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https://hal.inrae.fr/hal-02748846/file/Pitrat_Besombes%202012%20Eucarpia%20157-164_1.pdf BibTex
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Inheritance of andromonoecy in Tibish
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M.E. Abdelmohsin, A.E. Eljack, E.A. Ahmed, Michel Pitrat
article
Cucurbitaceae 2012, Proceedings of the Xth Eucarpia Meeting on Genetics and Breeding of Curcubitaceae, European Association for Research on Plant Breeding (EUCARPIA). FRA., Oct 2012, Antalya, Turkey
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https://hal.inrae.fr/hal-02748609/file/Pitrat%202012%20Eucarpia%20427-431_1.pdf BibTex
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Functional validation of the double phenotype triggered by the melon Vat gene by complementation experiments
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Veronique Chovelon, Veronique Restier, Nathalie Giovinazzo, Abdelhafid Bendahmane, Catherine Dogimont
article
10. EUCARPIA Meeting on Genetics and Breeding of Cucurbitaceae, Oct 2012, Antalya, Turkey. 809 p
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Aphis gossypii is the only species of aphid colonizing melon, causing stunting and leaf curling and transmitting non-persistent viruses. We demonstrated previously by a map-based cloning strategy that a single CC-NBS-LRR gene, named Vat, confers the double resistance to A. gossypii colonization and to unrelated viruses when transmitted by this vector. We confirm here by complementation experiments, the double function mediated by the Vat gene. Two transgenes carrying the Vat gene under the transcriptional control of its own promoter or under the control of the CaMV-35S promoter respectively were inserted via Agrobacterium tumefaciens into the susceptible melon cultivar 'Védrantais'. Transgenic T2 plants were evaluated for their resistance to A. gossypii colonization and to Cucumber mosaic virus (CMV) transmission by this vector, in comparison with susceptible and resistant melon cultivars. Transgenic plants carrying both transgenes exhibited the Vat phenotype, restricting aphid colonization and CMV infection. The Vat gene under the control of its own promoter induced a high level of resistance, similar to the referent resistant cultivar 'Margot', whereas the gene under control of the CaMV-35S promoter induced a slightly weaker level of resistance.
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Genetic variability description in a wide germplasm of domesticated peach through high throughput genotyping
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Diego Micheletti, Valeria Aramini, Pere Arus, Elisa Banchi, Teresa Barreneche, Daniele Bassi, Elisabeth Dirlewanger, Zhongshan Gao, Laura Gazza, Patrick Lambert, Francois Laurens, Xiongwei Li, Thierry Pascal, Bénédicte Quilot-Turion, Laura Rossini, Michela Troggio, Ignazio Verde, Maria Jose Aranzana
article
6. Rosaceous Genomics Conference, Sep 2012, Mezzocorona, Italy. 1 p
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Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programs is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium‐high degree of multiplexing. To address this limitation, about 1,300 peach cultivars were genotyped with the 9K peach SNP chip (Verde et al. 2012) in the frame of FruitBreedomics project. This germplasm was chosen to be representative of the genetic diversity present in five germplasm collection in Europe and in China. Out of the 8144SNPs present in the chip, about 4300 were positively genotyped and used for the further analysis. The average number of heterozygous loci in the genotyped accessions was 1186 (spanning from 13 to 2775). The preliminary results of the population structure reveal three main subpopulations and the presence of high number of admixed individuals. LD seems to decay at distance longer than ca. 1 Mb. These results will be instrumental for implementing LD‐based mapping of QTLs and genes in peach.
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https://hal.archives-ouvertes.fr/hal-01209951/file/RGC6_Book%20of%20abstracts_FULL_web_1.pdf BibTex
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Domestication bottleneck as a signature of history diffusion of apricot species
auteur
Hedia Bourguiba, Lamia Krichen, Neila Trifi-Farah, Bouchaib Khadari, Ali Mamouni, Samia Trabelsi, Claudio d'Onofrio, José Egea-Caballero, Bayram-Murat Asma, Jean Marc Audergon
article
6. Rosaceae Genomic Conference, Sep 2012, Mezzocorona (Trente), Italy
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Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. The comparison of genetic diversity in Mediterranean areas was assessed. 207 native apricot accessions representatives of the local variability from different Mediterranean countries: Algeria, France, Italy, Morocco, Spain, Tunisia and Turkey in each country were selected excluding those issued from breeding programs. This material was analysed for genetic diversity and structure using a common set of 25 monolocus microsatellites distributed throughout the Prunus genome. According to the geographic origin of the material and using a model‐based clustering method, four main gene pools were revealed, namely ‘Irano‐Caucasian’, ‘North Mediterranean Basin’, ‘South Mediterranean Basin’, and a more transversal one named ‘Adapted Diversity’. A significant gradient of decreasing diversity and allelic richness from the east to the south‐west of the Mediterranean Basin was highlighted. Overall, results suggested that from the Irano‐Caucasian area, apricot was introduced into the Mediterranean Basin through at least two different routes: the first one through the South of Europe and the second one through the North Africa. On the present bases relevant elements have been obtained useful for future management of apricot genetic resources as well as for genetic selection programs related to adaptive traits.
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Diversité génétique de la réactivité des variétés aux stimulateurs de défenses des plantes (SDP), oïdium du melon et mildiou de la laitue.
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Brigitte Maisonneuve, Caroline Allen-Aubouard, Michel Pitrat
article
Rencontre technique Agriculture biologique légumes, Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL). FRA. Institut Technique de l'Agriculture Biologique (ITAB), FRA., Sep 2012, Lanxade, France
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The Ma gene for complete-spectrum resistance to root-knot nematodes in Prunus: biological features, positional cloning and validation
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Daniel Esmenjaud, Cyril van Ghelder, Joel Polidori, Henri Duval, Marc Kleinhentz, Elisabeth Dirlewanger
article
30. Symposium of the European Society of Nematologists, Sep 2012, Adana, Turkey
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Plus fort, plus loin, plus lent : Comment le fond génétique de la plante peut augmenter la durabilité d’un gène majeur de résistance
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Julie Quenouille, Josselin Montarry, Alain Palloix, Benoît Moury
article
34. Réunion annuelle du Groupe d’Etude de Biologie et Génétique des Populations (Petit Pois Déridé 2012), Aug 2012, Avignon, France
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La création et l’utilisation de variétés de plantes hôtes résistantes aux parasites est le moyen de protection des cultures le plus respectueux des ressources naturelles et de l’environnement. Cependant ces résistances perdent parfois leur efficacité du fait de l’adaptation des bioagresseurs ciblés. Il a récemment été montré, pour trois pathosystèmes différents, que les résistances polygéniques combinant un gène majeur de résistance et un fond génétique partiellement résistant sont plus durables que les résistances monogéniques (le même gène majeur dans un fond génétique sensible). En utilisant le pathosystème virus Y de la pomme de terre (PVY)/piment ([i]Capsicum annuum[/i]), nous avons analysé trois mécanismes qui pourraient expliquer la meilleure durabilité des résistances polygéniques : (i) L’effet, sur l’accumulation virale, de la résistance partielle conférée par le fond génétique, (ii) l’augmentation du nombre de mutations nécessaire pour contourner la résistance et (iii) le ralentissement de la sélection des mutants contournant la résistance. Ces trois mécanismes ont été validés expérimentalement. Le premier mécanisme explique environ 75% de la variation de la fréquence de contournement du gène de résistance pvr23 et est, par conséquent, un déterminant majeur de la durabilité de la résistance. Le fond génétique de la plante a également une influence sur le deuxième mécanisme en complexifiant les voies mutationnelles que le virus peut emprunter pour contourner la résistance et sur le troisième mécanisme en ralentissant la sélection des variants viraux les mieux adaptés. Ces travaux fournissent des connaissances sur les mécanismes biologiques responsables de la meilleure durabilité de la résistance polygénique avec comme objectif de préserver la durabilité des gènes majeurs de résistance exploités dans les programmes de sélection.
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https://hal.archives-ouvertes.fr/hal-01208595/file/2012-Quenouille-PPD%20colloque_1.pdf BibTex
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Contribution to phenomics for quantitative disease resistance in a germplasm collection of Capsicum spp.: a multivariate analysis by self-organizing map
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Melissa Cantet, Guillaume Marie, Anne-Marie Sage-Palloix, Anne Massire, Alain Palloix, Véronique Lefebvre
article
9. Solanaceae Conference (SOL2012), Aug 2012, Neuchâtel, Switzerland. 250 p
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Identifying a candidate gene for the broad-spectrum resistance qtl to Phytophthora root rot and blight in pepper
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Véronique Lefebvre, Céline Vandecasteele, Melissa Cantet, Stéphane Mallard, Sonia Vautrin, Abdelhafid Bendahmane, Helene Berges
article
9. Solanaceae Conference (SOL2012), Aug 2012, Neuchâtel, Switzerland
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https://hal.inrae.fr/hal-02746226/file/Lefebvre_Cantet%202012%20SOL2012%2097_1.pdf https://hal.inrae.fr/hal-02746226/file/poster_lefebvre_2.pdf BibTex
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African eggplants and nightshades: an overview of indigenous vegetables
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Marie-Christine Daunay, Anne-Laure Girard
article
9. Solanaceae Conference (SOL2012), Aug 2012, Neuchâtel, Switzerland
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https://hal.inrae.fr/hal-02745546/file/Daunay%202012%20SOL2012%20110_1.pdf BibTex
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Molecular genetic analysis of floral meristem diversity in tomato
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Guillaume Bauchet, Stephane Munos, Christopher Sauvage, Julien Bonnet, Laurent Grivet, Mathilde Causse
article
9. Solanaceae Conference (SOL2012), Aug 2012, Neuchâtel, Switzerland
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https://hal.inrae.fr/hal-02746318/file/Bauchet_Sauvage%202012%20SOL2012%2043_1.pdf BibTex
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Integrative approach of tomato fruit texture using multi-block analysis
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Rémy Aurand, Mireille Faurobert, Mohamed Hanafi, Gérard Mazerolles, Raphaël Tisiot, Laurent Rosso, Brigitte Navez, Nadia Bertin
article
2. Symposium on Horticulture in Europe, Jul 2012, Angers, France
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Integrative approach of tomato fruit texture using multi-block analysis. 2. Symposium on Horticulture in Europe
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https://hal.archives-ouvertes.fr/hal-01595152/file/poster_Aurand.R_SHE2012_1.pdf https://hal.archives-ouvertes.fr/hal-01595152/file/Integrative%20approach%20of%20tomato%20fruit%20texture_doc%20she2012_2.docx BibTex
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Impact of temperature integration under greenhouse on energy use efficiency, plant growth and development and tomato fruit quality (sugars, acids, vitamin C, carotenoids) depending on variety rootstock combination
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Vincent Truffault, Fatiha Fifel, Hélène Gautier, Gilles Vercambre, Serge Le Quillec, Jean Jacques Longuenesse
article
2. Symposium on Horticulture in Europe, Jul 2012, Angers, France. 7 p
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The present study on soil-less tomato crops aims to evaluate and compare on contrasted genotypes the impact of temperature integration (TI) on plant growth and development as well as on fruit yield and quality. TI, taking advantage of plant plasticity regarding temperature, consists in modulating the set points for heating (lower during the night) and ventilation (higher during the day) keeping similar mean 24h temperature for plant development. Four variety-rootstock combinations of tomato plants were studied for two consecutive years (2010 and 2011). Two climate managements were compared: a temperature integration technique (TI) and a control (grower’s technique). In order to test the limit of TI system, TI application lasted longer in 2011 and with temperature settings colder compared to 2010. During the first year of experiment (2010), energy saving was about 22% during TI period. Yield was not modified, nor leaf growth. In 2011, TI led to an 8.6% energy saving compared to control. Yield significantly increased for Plaisance-Beaufort combination and was not affected in other variety-rootstock combinations. In conclusion, for both years TI increased energy use efficiency. Plant development rate was not significantly modified by TI. Leaf area slightly decreased (-11%). Fruit size and composition (sugars, acids, vitamin C) were not modified by TI. Carotenoids (specifically phytoene and lycopene) were improved by TI in particular for Plaisance-Beaufort; this might be related to the reduced leaf area that allowed more light to reach the fruit and consequently promoted carotenoid synthesis. Temperature integration appears as a profitable alternative to classic management of greenhouse climate.
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Evolution of diversity of fruits and vegetables crops
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Michel Pitrat, Jean Marc Audergon
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2. Symposium on Horticulture in Europe, Jul 2012, ANGERS, France
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We will answer only to a part of the session title (Horticulture and biodiversity: contribution to its loss, conservation or increase?) which includes the impact of the cultivars and cultivation methods on the biodiversity. Our presentation will focus on the diversity of fruits and vegetables crops in Europe at the species, cultigroup and cultivar levels and its evolution with time. Due to climatic conditions and cultural traditions, only a part of the world fruit and vegetable diversity is cultivated in Europe. Until the Second World War, most of the cultivars were locally based. Since the 1950', major evolutions have affected most of the cultivated species at several levels:
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https://hal.inrae.fr/hal-02746535/file/Pitrat_Audergon%202012%20SHE%20230_1.pdf BibTex
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A multi-Ievel omic approach of tomato fruit quality
auteur
Jiaxin Xu, Laura Pascual, Nelly Desplat, Mireille Faurobert, Yves Gibon, Annick Moing, Mickaël Maucourt, Patricia Ballias, Catherine Deborde, Yan Liang, Jean-Paul Bouchet, Dominique Brunel, Marie-Christine Le Paslier, Mathilde Causse
article
2. Symposium on Horticulture in Europe, Jul 2012, Angers, France
resume
Tomato fruit quality is an important trait for tomato consumers, but complex to improve due to the number of components involved and by their polygenic nature. ln order to decipher the genetic diversity and the inheritance of fruit qua lity components at a global level, we conducted a large multi-Ievel omic experiment. A set of 8 contrasted lines and 4 of their F1 hybrids were phenotyped for fruit development traits. Fruits were harvested and pericarp samples analysed at 2 stages (cell expansion and orange) and different scales: (1) primary and secondary metabolome profiles, (2) activities of 28 enzymes involved in primary metabolism, (3) proteome profiles revealed by 2D-PAGE and sequencing of 470 spots showing quantitative variations and (4) gene expression analysis by Digital Gene Expression. ln parallel, the 8 lines were resequenced and more than 3 millions SNPs identified when aligned on the reference tomato genome. This experiment allowed us to address several questions: the range of variability for the metabolic traits and expression data. Correlation networks can be constructed within and between levels of analysis to identify regulatory networks. Diversity of chosen candidate genes can be analysed, relating the polymorphisms at the sequence levels with their expression. Some examples will be presented.
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https://hal.inrae.fr/hal-02748459/file/Faurobert_Bouchet%202012%20SHE%20294_1.pdf BibTex
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Selection pressure exerted by host resistance genes shapes the population genetic structure of the lettuce downy mildew, Bremia lactucae, in France
auteur
Romain Valade, Aurélie Ducasse, Brigitte Maisonneuve, Claire Neema
article
8° Colloque de la Société Française de Phytopathologie (SFP), Societe Francaise de Phytopathologie (SFP). Paris, FRA., Jun 2012, Paris, France
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Compromising NSGA-II performances and stopping criteria: case of virtual peach design
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Mohamed Ould Sidi, Abdeslam Kadrani, Bénédicte Quilot-Turion, Francoise Lescourret, Michel Génard
article
International Conference on Metamaterials, Photonic Crystals and Plasmonics, Apr 2012, Paris, France. 2 p
resume
Multiobjective evolutionary optimization algorithms allow exploring highly dimensional search (decision) spaces in a reasonable computation time. These methods provide the decision-maker with a set of diversified solutions. The decision-maker will thus have the final choice of the best suited trade-off between criteria. However, a difficulty when using these algorithms is the convenient time to stop computation. Generally, one uses a predefined maximum number of generations as stopping criterion. Unfortunately, this can lead to many unnecessary generations and thus decrease the ratio of solution quality by computation time. Authors of [4] discussed this aspect, and illustrated it with the well-known NSGA-II (Non-dominated Sorting Genetic Algorithm II)[2]. They introduced a new stopping criterion which may partly remedy to this drawback. This criterion consists of stopping the process when the algorithm has performed a given number of iterations without improvement. It is based on the standard deviation of the crowding distance, a diversity control measure of NSGA-II, during a given number of iterations. Authors have tested their criterion only in the case of unconstrained and bi-objective problems and they claimed that it is difficult to use this criterion with NSGA-II for more than 2 criteria and for constrained optimization problems. Consequently, the question we address here is the possibility to use this stopping criterion to improve NSGA-II computation time in case of a constrained three-objective optimization problem. Thus, we compared the results obtained with the original version of NSGA-II to those obtained when modifying this original version by including this stopping criterion. In both studies we used the ‘Virtual Fruit’, a process-based model [3]. Six genetic parameters of the model constitute the decision variables of our problem and will be combined to create the genotypes by optimization. Three traits of fruit quality and sensitivity to brown rot simulated by the model were taken into account to evaluate the solutions (genotypes). Six constraints were also considered. The population size, 400, and the number of generations, 1500, were chosen after performing many preliminary simulations with the original version of the NSGA-II algorithm (data not shown). In order to choose the best values of the two parameters involved in the stopping criterion (L the length of the time window and the threshold value δ lim) adapted to the population size considered, we tested different combinations of values (20, 40, 60, and 80 generations for L combined with values of 0.001, 0.005, 0.0075, and 0.0001 for δ lim). Values of 0.001 and 20 were selected respectively for the threshold and length of time window. We repeat simulations of both versions 13 times. We compared the performances of the two versions using standard performance metrics and statistical analysis. Coverage set, spacing, and dominated volumes ration metrics[1] were used together with the computational time to compare the performances of the original (or) and the modified (sd: standard deviation) versions of NSGA-II. Results are given in table 1. We concluded that the NSGA-II with the stopping criterion based on the standard deviation find very similar results compared to the original NSGA-II but in less computational time.
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Méthodes multicritères pour le tri de fruits virtuels
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Mohamed-Mahmoud Ould-Sidi, Bénédicte Quilot-Turion, Antoine Rolland
article
13. Congrès Annuel de la Société Française de Recherche Opérationnelle et d’Aide à la Décision, Apr 2012, Angers, France. 2 p
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https://hal.inrae.fr/hal-02811362/file/ROADEF_2012_MMOS_BQT_AR_1.pdf BibTex
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Molecular basis of virus resistance mediated by host factors required for the infectious cycle
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Carole Caranta, S. Lacombe, Sophie Ewert, Jean-Luc Gallois, Laurence Ouibrahim, André Moretti, Joan Estevan, L. Albar, A. Ghesquiere, J. Bouniol, D. Thiemele, E. Hébrard, D. Fargette, F. Vignols, N. Poulicard, Amal Moumène, Emilce Prado, Monique Beuve, Vincent Dumas, Veronique Komar, Emmanuelle Vigne, Gerard Demangeat, Olivier Lemaire, Didier Merdinoglu
article
Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France. 2 p
resume
ln recent year, one of the most interesting results that has enabled plant virology to make a significant step forward is the identification of components of the translation initiation complex as essential host factors required for RNA virus multiplication. Although translation initiation factors were demonstrated to be highly conserved determinants of plant resistance to viruses, preliminary data indicate that the molecular basis underlying translation initiation factors-mediated resistance are highly variable. ln parallel, several recessive resistance genes against viruses were identified and demonstrated to be distinct from translation initiation factors. These genes are therefore very good candidates for the discovery of new susceptibility factors. ln this context, the MOVle project airns at (i) the characterization of mechanisms underlying molecular specificity of translation initiation factors mediated resistance, (ii) the study of the potential role of translation initiation factors in RNA virus resistance in economically important crops such as grapevine, and (iii) the identification of new host factors required for viral infection The project is likely to provide fundamental insights into the molecular basis of plant-virus interactions and to greatly facilitate the exploitation of host factors required for the viral cycle as targets to improve plant resistance to viruses.
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https://hal.inrae.fr/hal-02746501/file/Caranta_Gallois%202012%20Genoplante%2098-100_1.pdf BibTex
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Identification of a candidate gene for the key broad-spectrum resistance QTL to late blight in pepper
auteur
Véronique Lefebvre, Helene Berges, Abdelhafid Bendahmane
article
Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France
resume
Determining the gene responsible for a QTL controlling broad-spectrum resistance to pathogens Phytophthora agents are the most devastating pathogens of Dicotyledons. Chemical controls against these pathogens are insufficiently effective, and have serious consequences on the environ ment and human health. An alternative more environmentally friendly is the use of pathogen-resistant varieties. However, monogenic resistances are rare and often specifie to a strain of the pathogen (narrow spectrum); they are thus frequently overcome because of the emergence of new virulent strains. Polygenic resistances have often the advantage of being broad-spectrum. ln addition, they have been demonstrated for some of them more durable. But their use in selection is limited because the controlling loci (named QTLs for Quantitative Trait Loci) are difficult to identify due to their number and their partial individual effect on resistance. ln addition, it is not known in what resistance QTLs differ from monogenic resistance genes. Consequently, we aim to determine the molecular basis of a QTL involved in polygenic resistance to Phytophthora capsici, the agent of late blight in pepper (Capsicum annuum). From the fine genetic map to the identification of a candidate gene: chromosome walking, seguencing and gene annotation The QTL Phy-PS confers a high level of broad-spectrurn resistance towards P. capsici. Identified in several resistant genitors of C annuum, it was mapped to chromosome P5. To facilitate its fine mapping, we derived a population that segregates for the QTL alone. Then a physical map of the locus was constructed by chromosome walking based on two BAC libraries (BACfor Bacterial Artificial Chromosome), and anchored to the fine genetic map. BAC clones covering the locus have been sequenced by classical and new generation sequencing approaches. An automatic annotation pipeline has been adapted to the pepper genome to characterize sequence repeats that are very common in this species, and to predict the coding sequences corresponding to hypothetical functional genes. An analysis of nucleotide and protein homology and a search for protein domains have been achieved to identify among them candidate genes. Finally, severa 1 methods for functional validation have been considered and developed to study the role of candidate genes in the resistance to P. capsici.
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A generic tool for managing and exploiting genetic association studies results using high throughput genotyping and phenotyping
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Célia Michotey, Frédéric Sapet, Pierre Dubreuil, Jacques Le Gouis, Mathilde Causse, Cyril Pommier, Sophie Durand, Nacer Mohellibi, Raphaël Flores, Catherine Delaitre, Stephane Nicolas, Alain Charcosset, Yannick de Oliveira, Patrice This, Roberto Bacilieri, Alexis Dereeper, Philippe Lashermes, Hadi Quesneville, Delphine Steinbach
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Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France
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Valorisation of genetic and genomic resources of tomato for the improvement of fruit quality
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Mathilde Causse, Dominique Brunel, Paul Amouroux
article
Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France
resume
ln this project we intend to develop the resources necessary for high throughput QTL studies in tomato by combining the development of genomic and plant resources including: (1) a large set of SNPs in expressed sequences and flanking regions based on high throughput sequencing technology. (2) a set of 4 Illumina VeraCode chips carrying a total of 1536 SNP (3) Creation and phenotype characterisation of a multiparent advanced generation intercross (MAGIC) population to be used for QTL mapping and latter for fine mapping, as a complement to genetic resources gathered in collections. The population will be characterised for yield related traits and fruit quality (composition in sugars and acids, colour, texture). (4) Differentiai Gene Expression profiles and proteome profiles of the 8 parental lines of the MAGIC populations and the 4 Fl hybrids These resources are developed to be used in the subsequent analyses: (1) Genotyping a biallelic population in order to precisely map ail the markers present on the VeraCode chips (2) Genotypinç the MAGIC population with the Illumina VeraCode chips in order to map QTL (3) Genotyping several genetic resources (collections of cherry tomato cultivars, of old cultivars and a set of elite genotypes), in order to assess linkage disequilibrium and search for associations between SNP markers and fruit related traits (4) Expression profile analysis of the genes and proteins characterised at the 2 stages of expression; comparison among genotypes and Fl hybrids. The final expected result is a genetic map of more than 1000 SNPs which will be associated with QTL locations and expression variations of the parental lines and Fl hybrids.
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https://hal.inrae.fr/hal-02749148/file/Causse%202012%20Genoplante%2085-86_1.pdf BibTex
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Modifications of antioxidant enzymes as a tool to improve yield in tomato under water deficit
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Noé Gest, Cecile Garchery, Mathilde Causse, Hélène Gautier, Pierre Baldet, Rebecca Stevens
article
2nd International Symposium on Biotechnology of Fruit Species, Mar 2012, Nelson, New Zealand. 228 p
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https://hal.inrae.fr/hal-02745000/file/Stevens%202012%20Biotech%20fruit_1.pdf https://hal.inrae.fr/hal-02745000/file/Stevens%202012%20Biotech%20fruit_2.doc BibTex
titre
Variation in tomato fruit ascorbate levels and consequences of manipulation of ascorbate metabolism on drought stress tolerance
auteur
Vincent Truffault, Noé Gest, Cecile Garchery, Mathilde Causse, Renaud Duboscq, Gisèle Riqueau, Christopher Sauvage, Hélène Gautier, Pierre Baldet, Rebecca Stevens
article
2. International Symposium on Biotechnology of Fruit Species, Mar 2012, Nelson, New Zealand
resume
Tomato is an important crop worldwide and one of the major sources of vitamin C (ascorbate) in the human diet. Ascorbate contributes both to tomato nutritional quality and has roles in stress tolerance and adaptation to the environment. In this study we show the variability that exists in tomato germplasm in terms of ascorbate content (10 to 90 mg/100 g fwt) which could be starting point for evaluating correlations with physiological traits potentially linked to ascorbate. We have then manipulated genes involved in ascorbate metabolism, using RNA interference, to investigate their influence on fruit ascorbate levels, fruit physiology and yield under both normal and drought stress conditions. There is some evidence that one of the genes chosen affects fruit size and yield under different conditions, but clear effects on the fruit ascorbate pool are not seen. We conclude that ascorbate metabolism is complex and can also have wider effects on fruit physiology and growth.
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L'abricot, fruit d'un terroir. La diversité de l'abricot, une richesse attachée au terroir
auteur
Jean Marc Audergon, Eric Martin, Alain Blanc, Frederic Gilles, Anne Marie Ferréol, Guy Clauzel, Laurent Brun, Vincent Mercier, Barbara Gouble, Sylvie Bureau, Catherine Renard, Claire Lamine, Véronique Decroocq, Thierry Candresse, Guillaume Roch
article
Abricot de Rhône-Alpes, une stratégie d'avance!, Mar 2012, Mercurol, France
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titre
Apricot susceptibility to blossom brown rot (Monilia spp.) and leaf rust (Tranzschelia spp.) under low-input production system
auteur
Claude Eric Parveaud, Jm Broquaire, Vincent Mercier, Christelle Gomez, Laurent Brun, Guy Clauzel, Armand Guillermin, Jean Marc Audergon
article
15. international conference on organic fruit-Growing, Feb 2012, Hohenheim, Germany. 427 p
resume
Disease-susceptibility of apricot cultivars is a key-stone towards low-input production systems. Among the main diseases, the susceptibility to Monilinia spp. and leaf rust of apricot cultivars are economically important but rarely assessed. A 5-years study in two sites was conducted to assess the susceptibilities to Monilinia spp. and leaf rust of 16 apricot cultivars under natural conditions (no inoculation). No fungicide and insecticide were applied during the experiment. In Torreilles site, no significant Monilinia spp. was observed. In Gotheron site, the percentage of shoots necrosed by Monilinia spp. ranged from 13% to 100% during 2010-2011. A Genotype x Environment interaction was observed for Monilinia spp. damages. Concurrently a high variability to leaf rust was observed in both sites. The ranking of cultivars susceptibility to leaf rust was similar between both sites
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https://hal.inrae.fr/hal-02746309/file/Apricot_ssceptibility_Conference%20Organic%20Fruit_1.pdf BibTex
titre
Peach molecular breeding at the INRA Avignon and links to a new European initiative to increase fruit breeding efficiency: FP7 KBBE FruitBreedomics
auteur
Patrick Lambert
article
1. International Congress for Bacterial Diseases of Stone Fruits and Nuts, Feb 2012, Zurich, Switzerland. 28 p
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titre
Genetic diversity of Phytophthora capsici recovered from pepper in Southern France
auteur
D. Gobena, Melissa Cantet, Véronique Lefebvre, K. Lamour
article
2012 APS Southern Division Meeting, Feb 2012, Birmingham, Alabama, United States
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titre
Az almalisztharmat okozza az őszibarack-gyümölcsök rozsdás foltosságát?
auteur
Levente Kiss, Tünde Jankovics, Nenad Dolovac, Aleksandra Bulajic, Branta Krstic, Thierry Pascal, Marc Bardin, Philippe C. Nicot
article
22. Keszthelyi Növényvédelmi Fórum (22nd Plant Protection Forum), Jan 2012, Keszthely, Hungary. 85 p
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titre
Populations de Bremia Lactucae en Provence
auteur
Brigitte Maisonneuve, Sandrine Jeuniaux, Emilie Juillard, Marion Lovera, Jérémy Gaudin, Romain Valade, Claire Neema
article
9. Rencontres de Phytopathologie-Mycologie de la Société française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.5.11
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absent
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https://hal.archives-ouvertes.fr/hal-01000208/file/49307_20120116092127326_1.pdf BibTex
titre
The new EU project FruitBreedomics: an integrated approach for increasing breeding efficiency in fruit tree crops
auteur
Francois Laurens, M.J. Aranzana, P. Arus, D. Bassi, J. Bonany, L. Corelli, Charles Eric Durel, J. Mes, Thierry Pascal, A. Patocchi, A. Peil, Bénédicte Quilot-Turion, S. Salvi, S. Tartarini, M. Troggio, A. Vecchietti, R. Velasco, E. van de Weg
article
XX. PAG Plant & Animal Genome, Jan 2012, SanDiego, United States. 8 p
resume
The european fruit industry is facing economic challenges imposed by increasingly fierce international competition and decreasing fruit consumption, societal demand for a more sustainable production, and biological problems caused by climate changes. Releasing new cultivars that meet these challenges is a major goal of all european breeding programmes. However, addressing them has been slow due to the nature of fruit tree breeding: long term, low efficiency and high cost. For the past 15 years, efficient networks of fruit geneticists and genomicists have progressively been built thanks in particular to EU-funded projects. Europe has thus become a leader in research on fruit genetics aimed at enhancing fruit quality traits as well as resistance to biotic stresses. European teams working on fruit genetics have developed up-to-date tools and skills covering most of the "omics" fields as well as statistics and software development. Although fruit breeding is very active in Europe, very few breeding programmes are really using the output of the fruit genetics/genomics research. A few bottlenecks can explain this situation. To solve that, a new european initiative has been set up by the fruitbreedomic. This large collaborative project, has the strategic goal of improving the efficiency of current fruit breeding programmes by bridging the existing gap between molecular genetics research and application in breeding.
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titre
Application of high throughput genotyping techniques in peach germplasm and breeding lines within the fruitbreedomics project
auteur
Diego Micheletti, Valeria Aramini, Pere Arus, Elisa Banchi, Teresa Barreneche, Daniele Bassi, Elisabeth Dirlewanger, Zhongshan Gao, Laura Gazza, Patrick Lambert, Francois Laurens, Xiongwei Li, Thierry Pascal, Bénédicte Quilot-Turion, Laura Rossini, Michela Troggio, Eric van de Weg, Ignazio Verde, Maria Jose Aranzana
article
20. Plant and Animal Genome, Jan 2012, San Diego, United States. 1 p
resume
Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Every year new varieties are released from breeding programmes trying to meet the requirements imposed by the market. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programmes is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium-high degree of multiplexing. FruitBreedomics is a European project conceived with the strategic goal to improve the efficiency of fruit breeding by bridging the gap between scientific knowledge and application in breeding. In the frame of this project, and with the goal of obtaining SNP closely linked to agronomic interesting traits, the 9K peach SNP chip (Illumina Inc.) developed by the International Peach SNP Consortium (IPSC) has been used in both segregating populations and in germplasm collections. This chip, containing 8144 SNPs scattered on the 8 peach chromosomes, has been used in about 1,500 individuals belonging to seventeen Prunus crosses (12 peach x peach and 5 interspecific) and in 1,300 peach cultivars from different origins, including some of the founders of the current breeding programs
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titre
The new EU project Fruitbreedomics: an integrated approach for increasing breeding efficiency in fruit tree crops
auteur
Eric van de Weg, Francois Laurens, Maria Jose Aranzana, Pere Arus, Daniele Bassi, Joan Bonany, Luca Corelli Grappadelli, Charles Eric Durel, Thierry Pascal, Andrea Patocchi, Andreas Peil, Bénédicte Quilot-Turion, Vincent Troillard, Alessandra Stella, Michela Troggio, Riccardo Velasco
article
20. Plant and Animal Genome, Jan 2012, San Diego, United States. pp.PO 482
resume
An international consortium gathering European and non European teams has designed FruitBreedomics to bridge the gap between scientific genetics research and application in breeding. The project will focus on apple and peach, two major fruits in Europe, but the tools and the knowledge gained will also benefit other species of the Rosaceae family. The aim of FruitBreedomics is to provide the European fruit tree sector with cutting-edge breeding tools for the efficient and accelerated creation of new apple and peach varieties with excellent fruit quality characteristics, improved resistances to diseases and pests, and that can be grown in sustainable agriculture systems in the context of climate change. This poster presents the aims, structure and participants of the project
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titre
Genetic diversity, inheritance and integration of multi-level omic data in tomato fruit
auteur
Jiaxin Xu, Laura Pascual-Banuls, Nelly Desplat, Jean-Paul Bouchet, Yves Gibon, Annick Moing, Dominique Brunel, Marie-Christine Le Paslier, Mathilde Causse
article
20. Plant and Animal Genome, Jan 2012, San Diego, United States. pp.W643
resume
Tomato fruit quality is an important trait for tomato breeders, but complex by the number of components and by their polygenic nature. In order to decipher the genetic diversity and the inheritance of fruit quality components at a global level, we conducted a large multi-level omic experiment. A set of 8 contrasted lines and 4 of their F1 hybrids were phenotyped for fruit development traits. Fruits were harvested and pericarp samples analysed at 2 stages (celle expansion and orange) and different scales: (1) primary and secondary metabolome profiles, (2) activities of 28 enzymes involved in primary metabolism, (3) proteome profiles revealed by 2D-PAGE and sequencing of 470 spots showing quantitative variations and (4) gene expression analysis by Digital Gene Expression. In parallel, the 8 lines were resequenced and more than 3 millions SNPs identified when aligned on the reference tomato genome. This experiment allowed us to address several questions: the range of variability for the metabolic traits and expression data. Correlation networks can be constructed within and between levels of analysis to identify regulatory networks. Diversity of chosen candidate genes can be analysed, relating the polymorphisms at the sequence levels with their expression. Some examples will be presented
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titre
Sensibilité variétale de l'abricotier au Monilia sur fleur, à la tavelure et à la rouille
auteur
Laurent Brun, Vincent Mercier, Jm Broquaire, Christelle Gomez, Claude Eric Parveaud, Guy Clauzel, Armand Guillermin, Jean Marc Audergon
article
Rencontre Phytosanitaire Fruits à Noyau, Jan 2012, Balandran, France. 11 p
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titre
Inheritance of phenological traits in apricot progenies.
auteur
Jean Marc Audergon, Guy Clauzel, Alain Blanc, Guillaume Roch, Patrick Lambert, D. Ruiz, J.A. Campoy, J.A. Salazar, P. Martínez-Gómez, J. Egea, Sylvie Bureau, Barbara Gouble, Marielle Boge, Patrice Reling, Catherine Renard, Luca Dondini, S. Tartarini
article
15 th International Symposium on Apricot Breeding and Culture , 2012, Yerevan, Armenia
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titre
Influence of temperature on apricot fruit respiration and ethylene production.
auteur
Barbara Gouble, Patrice Reling, Catherine Renard, Jean Marc Audergon
article
International Symposium on Apricot Breeding and Culture, 2012, Yerevan, Armenia
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titre
Infrared spectroscopy: a rapid tool for apricot characterization.
auteur
Sylvie Bureau, Marielle Boge, Catherine Renard, Jean Marc Audergon
article
International Symposium on Apricot Breeding and Culture, 2012, Yerevan, Armenia
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Poster communications

titre
Mise en œuvre d’un système de surveillance des enceintes climatiques à l’INRA-PACA
auteur
Frédéric Jean, Olivier Marloie, Marie Noëlle Corre, Damien Gounelle, Mehdi Pringarbe
article
Séminaire AQR, Dec 2012, Nouan le Fuzelier, France. 2012
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https://hal.inrae.fr/hal-02809975/file/Poster_Surveillance_Alarme_Enceintes_UERFM_2012_V2_1 BibTex
titre
Protection des laitues contre le Bremia par des stimulateurs de défenses des plantes (SDP) diversité génétique de la réactivité des variétés.
auteur
Brigitte Maisonneuve, Anne Pesme-Glemin
article
MIFFEL, salon Méditerranéen Interprofessionnel de la Filière Fruits Et Légumes, Oct 2012, Avignon, France. 2012
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titre
Effects of lettuce cultivar mixtures, differing for resistance genes, on Bremia lactucae incidence.
auteur
Brigitte Maisonneuve, Eric Martin, Loic Jean, Claude Pope de Vallavieille, Michel Pitrat
article
Plant resistance sustainability 2012. International conference, Oct 2012, La Colle sur Loup, France. 2012
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absent
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https://hal.archives-ouvertes.fr/hal-01190799/file/resumes_1.pdf BibTex
titre
Identification of genomic regions and candidate genes involved in fruit ripening in two apricot (Prunus armeniaca L.) cultivars
auteur
Patrick Lambert, David Ruiz, Barbara Gouble, Sylvie Bureau, Luis Buendia, Maryse Reich, Patrice Reling, Catherine M.G.C. Renard, Jean Marc Audergon
article
6. Rosaceous Genomics Conference, Sep 2012, Mezzocorona, Italy. 2012
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https://hal.inrae.fr/hal-02807222/file/Lambert%202012%20Rosa.%20Geno.%20Conf.%20ITA_1.pdf BibTex
titre
High or low fructose? Consequences for sugar metabolism in peach fruit
auteur
Elsa Desnoues, Yves Gibon, Valentina Baldazzi, Veronique Signoret, Michel Génard, Bénédicte Quilot-Turion
article
6. Rosaceous Genomics Conference, Sep 2012, San Michele all’Adige, Italy. 1 p., 2012
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https://hal.inrae.fr/hal-02804340/file/poster_RGC6_ED_1.pdf BibTex
titre
What do spring migrants reveal about sex and host selection in the melon aphid
auteur
Sophie Thomas, Nathalie Boissot, Flavie Vanlerberghe-Masutti
article
34. Réunion annuelle du Groupe d’Etude de Biologie et Génétique des Populations (Petit Pois Déridé 2012), Aug 2012, Avignon, France. 2012
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Poster communications
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https://hal.inrae.fr/hal-02805852/file/Thomas_Boissot%202012%20PPD%20Poster_1.ppt https://hal.inrae.fr/hal-02805852/file/Thomas_Boissot%202012%20PPD%20Poster_2.ppt BibTex
titre
Molecular marker development for introgression of nematode resistance in potato breeding programs: exploitation of [i]solanum spegazzinii[/i] resistance source
auteur
Laura Chauvin, Marie-Laure Lesage, Sylvain Fournet, Bernard Caromel, Josiane Quéré, Jean-Paul Dantec, Marie-Claire Kerlan
article
9. Solanaceae Conference (SOL2012), Aug 2012, Neuchâtel, Switzerland. 2012, SOL 2012: From the Bench to Innovative Applications
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absent
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https://hal.archives-ouvertes.fr/hal-01208704/file/Caromel%202012%20SOL2012%2044_1.pdf BibTex
titre
Comparison of metabolomic, proteomic and genomic variability in tomato fruit
auteur
Mathilde Causse, Jiaxin Xu, Laura Pascual, Yves Gibon, Annick Moing, Nelly Desplat, Dominique Brunel
article
9. Solanaceae Conference (SOL2012), Aug 2012, Neuchâtel, Switzerland. 2012, SOL 2012: From the Bench to Innovative Applications
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https://hal.inrae.fr/hal-02745839/file/Causse_Xu%202012%20SOL2012%20147_1.pdf BibTex
titre
Identification of a genetic factor determining the durability of a plant major resistance gene and quantitative resistance to virus accumulation
auteur
Julie Quenouille-Lederer, Estelle Paulhiac, Pascale Mistral, Ghislaine Nemouchi, Anne-Marie Sage-Palloix, Bruno Savio, Vincent Simon, Benoît Moury, Alain Palloix
article
15. International Congress on Molecular Plant-Microbe Interactions (IS-MPMI 2012), Jul 2012, Kyoto, Japan. 2012, IS-MPMI 2012 XV International congress. Program and abstracts
resume
Genetic resistance provides efficient control of crop diseases but is limited by pathogen counteradaptation. The durability of the pvr23 allele, conferring resistance to Potato virus Y (PVY), was demonstrated to depend on the plant genetic background. In order to identify genetic factors affecting the durability of the pvr23 resistance, QTL mapping was performed using doubled-haploid (DH) lines issued from the F1 between two Capsicum annuum lines: ‘Perennial’ carrying pvr23 in a partially resistant background and ‘Yolo Wonder’ carrying the susceptible pvr2+ allele in a susceptible background. 350 DH lines were genotyped with 234 markers and the linkage map was established. The 156 DH lines carrying the pvr23 allele but segregating for the genetic background were evaluated for two traits: the breakdown frequency of pvr23 (following inoculation with a PVY clone nonpathogenic (avirulent) towards pvr23) and the PVY accumulation (following inoculation with a mutant of the previous PVY clone carrying a single mutation conferring pathogenicity towards pvr23). Genotypic variance was highly significant for the two traits with heritabilities of 0.76 and 0.47. One major QTL, explaining 29% of the variance of pvr23 breakdown frequency was identified on chromosome 3 and two QTLs, explaining 25% and 9% of PVY accumulation variation, were identified on chromosomes 3 and 6, respectively. Interestingly, the major QTL for the 2 traits mapped to the same region of chromosome 3. A putative pleiotropic effect affecting simultaneously the two traits, the underlying mechanism and the perspective in breeding for resistance durability will be discussed.
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https://hal.inrae.fr/hal-02745421/file/2012-Quenouille-MPMI-Poster_1.pdf https://hal.inrae.fr/hal-02745421/file/2012-Quenouille-MPMI-Abstract_2.pdf BibTex
titre
Integrative approach using multiblock analysis to explain a complex trait of tomato fruit quality: texture
auteur
Rémy Aurand, Mireille Faurobert, Mohamed Hanafi, Gerard Mazerolles, Raphael Tisiot, Laurent Rosso, Brigitte Navez, Nadia Bertin
article
2. Symposium on Horticulture in Europe, Jul 2012, Angers, France. 2012
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https://hal.inrae.fr/hal-02746679/file/Faurobert%202010%20SHE%20310_1.pdf BibTex
titre
The use of a multi-locus mixed model approach for GWAS reveals associations for metabolic traits in the tomato, Solanum lycopersicum
auteur
Christopher Sauvage, Vincent Segura, Guillaume Bauchet, Rebecca Stevens, Thi Phuc Do, Alisdair Fernie, Mathilde Causse
article
4. International Conference on Quantitative Genetics: Understanding Variation in Complex Traits, Jun 2012, Edinburgh, United Kingdom. 2012, 4. International Conference on Quantitative Genetics: Understanding Variation in Complex Traits
resume
Genome-wide association studies have been successful in identifying genes involved in polygenic traits notably in crops, towards their improvement. We propose to apply in a major crop, such as tomato, a recently developed multi-Iocus mixed model as a general method for mapping complex traits in structured populations (Segura et al., 2012). Among major crops, tomato (Solanum Iycopersicum), is an highly valuable vegetable in the world for its health value (Causse et 201 0). SNP beadchip (Hamilton et al., 2012) are available and enable GWAS for traits of interest. Recently, a pilote study defined the optimal conditions for GWAS by using cherry tomato accessions (Ranc et al., 2012). ln our study, we examined a core collection of 180 tomato varieties composed of 20 wild a cessions (S.pimpinellifollium), 130 admixed accessions (S. cerasiforme) and 30 domesticated accessions (S. Iycopersicum). Multi-Iocus GWAS analysis was conducted using the MLMM package (Segura et al., 2012) with 7700 SNP markers and a set of sugar-related, Vitamin C-related and morphological traits as weil as a broad range of metabolites related to central carbon metabolism. The present study is the first one in tomato reporting associations for a large set of traits at the genome scale. We found significant associations for 89 loci with a total of 19 traits including fresh weight, sucrose, ascorbate dehydrogenase, malate or citrate, notably. Identified loci were also concordant with published quantitative trait loci (i.e. Malate), while new loci were identified (for Tocopherol). Moreover, several related metabolites, such as citrate and malate (both involved in Krebs cycle) displayed two identical associations. These results (1) provide a list of candidate loci to be functionally validated and (2) provide a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex trait.
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https://hal.archives-ouvertes.fr/hal-01268380/file/Sauvage%202012%20ICQG%20235_1.pdf BibTex
titre
Identification and validation of reference genes for normalization of transcripts levels in roots of potatoes infected by nematodes
auteur
Patricio Castro Quezada, Jawad Aarrouf, Michel Claverie, Eric Grenier, Marie-Claire Kerlan, Bruno Favery, Véronique Lefebvre, Bernard Caromel
article
5. Congrès de la Société Française de Phytopathologie, Jun 2012, Paris, France. 2012
resume
Potato cyst nematodes induce changes in gene expression after infecting the roots. For studying gene expression, reverse transcription quantitative real-time PCR (RT-qPCR) is now a standard method. However, for accurate quantication of transcripts, a set of internal control genes, stable under different experimental conditions, is necessary for transcript normalization.[br/] Very few experimental data on suitable reference genes are available for plant-nematode interactions. In this study, we tested eight potential candidate reference genes identied through a microarray study performed on the pathosystem Arabidopsis/Meloigodygne for normalizing levels of potato gene transcripts, after invasion by nematodes. The transcription proles of these genes were assessed by RT-qPCR. Samples used in these experiments were RNAs, issued from roots of infected and uninfected potato plants, carrying resistant or susceptible alleles against Globodera pallida, following a kinetic of four days. Analyses were performed using the geNorm and NormFinder softwares.[br/] Our results showed that the eight candidate reference genes were stably expressed in our conditions. For accurate normalization in RT-qPCR studies, RPN7 (26S proteasome regulatory subunit, involved in protein synthesis) and MST2 (mercaptopyruvate sulfurtransferase) were the top ranked genes and, therefore, are reliable reference genes in compatible and incompatible potato-nematode interactions.
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https://hal.archives-ouvertes.fr/hal-01208737/file/Lefebvre_Caromel%202012%20SFP_1.pdf BibTex

Reports

titre
Analyse et évaluation de la durabilité d'une résistance partielle au Watermelon mosaic virus (WMV) chez le melon
auteur
Michel Pitrat
article
[Contrat] C07-2008, 2012
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titre
A tool to conveive sustainable production systems_case of the peach-brown rot couple
auteur
Abdeslam Kadrani
article
[Contract] 0902-011, 2012
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https://hal.inrae.fr/hal-02805946/file/rapport%20final%20Quilot%20turion%202012%20Kadrani_1.pdf https://hal.inrae.fr/hal-02805946/file/rapport%20final%20Quilot%20turion%202012%20Kadrani_2.docx BibTex
titre
Rapport de fin de contrat de recherche - Contrat Resist-laitue : Analyse du mildiou de la laitue et mise en place de stratégies pour apporter des résistances durables
auteur
Brigitte Maisonneuve
article
[Contrat] AgroParisTech; Gautier semences; Rijk Zwaan. 2012
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2011

Conference papers

titre
Disease resistance in melon and its modification by molecular breeding techniques
auteur
Michel Pitrat
article
8. Joint Conference on Solanaceae Genomics (SOL), Nov 2011, Kobe, France. ⟨10.1007/978-3-662-48535-4⟩
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titre
Phenotypic and genetic trends in the evolution under domestication of melon
auteur
Michel Pitrat
article
8. Solanaceae Genome Joint conference; 2. Cucurbitaceae Genome Joint conference, Nov 2011, Kobe, Japan
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titre
Insect resistance in melon and its modification by molecular breeding
auteur
Catherine Dogimont, Nathalie Boissot
article
8. Joint Conference on Solanaceae Genomics (SOL), Nov 2011, Kobe, Japan. 265 p., ⟨10.1007/978-3-662-48535-4_12⟩
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titre
Phenotypic and genetic trends in the evolution under domestication of Solanaceae
auteur
M-Christin Daunay, Christopher Sauvage, Mathilde Causse, Alain Palloix, Jaime Prohens
article
8. Solanaceae Genome Joint conference; 2. Cucurbitaceae Genome Joint conference, Nov 2011, Kobe, Japan
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titre
Sensibilités variétales. Pêchers & Abricotier. Bilan de 14 années d’observation
auteur
Claude Eric Parveaud, Christelle Gomez, Gilles Libourel, François Warlop, Laurent Brun, Vincent Mercier, Armand Guillermin, Guy Clauzel, Jean Marc Audergon
article
MIFFEL, salon Méditerranéen Interprofessionnel de la Filière Fruits Et Légumes, Oct 2011, Avignon, France. 19 p
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https://hal.inrae.fr/hal-02805555/file/Sensibilite%20abricot%20peche%20MIFFEL%202011%20Parveaud%20et%20al_1.pdf BibTex
titre
Genetic and genomic tools in pepper to decipher disease resistance traits: Progress and prospects
auteur
Véronique Lefebvre
article
Chinese-French Workshop on Pepper Genetics and Breeding, Oct 2011, Bejing, China
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titre
Combination of field margin manipulation and genetic resistance to limit Aphis gossypii outbreaks and virus epidemics in melon crops
auteur
Alexandra Schoeny, Patrick Gognalons, Nathalie Boissot, Pascale Mistral, Virginie Chareyron, Catherine Wipf-Scheibel, Hervé Lecoq
article
Towards a multi-scale approach for improving pest management. System management for sustainable insect pest control: from local to regional approaches, Oct 2011, Montpellier, France
resume
Aphis gossypii is a major pest of Cucurbitaceae crops as much by causing primary damages (sap uptake) as by being an important vector of viruses. The Vat gene confers to the melon a resistance to the colonization by A. gossypii as well as a resistance to the not persistent viruses (CMV, WMV,..) transmitted by these aphids. It is however ineffective to block the transmission of the viruses carried by other aphid species. The use of Vat is thus generally coupled with aphicid treatments to limit the viral transmission by the not colonizing aphids. However, the progressive reduction of the usage of the phytosanitary products in the crop protection imposed by the evolution of the regulation (plan Ecophyto 2018) leads to look for new strategies integrating cultural practices and genetics for the management of the bioagressors. The bibliography suggests that the management of field margins (strips sown with non host grass or flower mixtures) could be an effective option to decrease 1) the aphid pressure (and thus the risk of bypassing Vat) by favoring the development of natural enemies and 2) the virus pressure by constituting a filter reducing the viral load of aphids before they reach the crop. The hypothesis tested in this project is that an adequate manipulation of the environment of the crop can contribute to regulate the populations of aphids and\or their viral load and therefore to reduce the risk of viral epidemics. The effect of three types of field margins (naked soil, grassy strips and flower strips) is evaluated on the efficiency of the Vat-mediated resistance.
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https://hal.inrae.fr/hal-02744706/file/43994_20111011083541165_1.pdf BibTex
titre
Exploitation of knowledge on Oomycete effectors to drive the discovery of durable late blight resistance in tomato
auteur
Véronique Lefebvre
article
4. Effectome Meeting, Sep 2011, Lauret, France
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Genetics and genomics of disease resistance in pepper: focus on Phytophthora threats
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Véronique Lefebvre
article
international symposium commemorating the 20th anniversary of Korea Capsicum Research Cooperative, Sep 2011, South Korea
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https://hal.inrae.fr/hal-02744884/file/Lefebvre%202011%20Symposium%20Korea%20205-223_1.pdf BibTex
titre
La conservation et la connaissance des ressources génétiques d'espèces végétales cultivées: un enjeu pour l'agriculture et un défi pour les acteurs
auteur
Emmanuel Geoffriau, Michel Pitrat, Pascal Coquin, François Balfourier, M-Christin Brand-Daunay, Florence Esnault, Chrystelle Jouy, Jean-Eric Chauvin, Alain Label-Richardson, Francois Boulineau, Helene Burck, Laurence Feugey, Brigitte Maisonneuve, Emilie Balsemin, Claudie Lambert, Anne-Marie Sage-Palloix, Teresa Barreneche, Catherine Delaitre, Stéphane Fourtier, Anne Zanetto, Agnès Grapin, Jean-Marie Prosperi, Audrey Didier
article
Les ressources génétiques face aux nouveaux enjeux environnementaux économiques et sociétaux, Sep 2011, Montpellier, France
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absent
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https://hal.archives-ouvertes.fr/hal-01189505/file/43650_20111213111414976_1.pdf https://hal.archives-ouvertes.fr/hal-01189505/file/43650_20120106122142128_2.PDF BibTex
titre
Metabolite profiling and feeding bioassays suggest a major role for a dicaffeoylquinic acid in induced resistance of peach to Myzus persicae aphid
auteur
Jean-Luc Poëssel, Marie-Hélène Sauge, Michael Staudt, Claire Dufour, Catherine Deborde, Yves Rahbé, B. Jackson, Cédric Renaud, Mickael Maucourt, Marie-Noëlle Corre, H. El-Aouni, Jean Philippe Lacroze, Annick Moing
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PRIR 2011 Joint International Workshop: "PR-proteins Workshop" and the "Working Group Induced Resistance in Plants Against Insects and Diseases", Sep 2011, Neuchâtel, Switzerland
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Signatures de sélection et évolution d'effecteurs candidats dans des populations pathogènes soumises aux résistances de l'hôte
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Romain Valade, Aurélie Ducasse, Jean-Baptiste Genty, Brigitte Maisonneuve, R. Michelmore, Claire Neema
article
Petit Pois Déridé 2011; 33. Réunion annuelle du Groupe d'Etude de Biologie et Génétique des Populations, Aug 2011, Toulouse, France. 1 p
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absent
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https://hal.archives-ouvertes.fr/hal-00999904/file/48349_20120210012231551_1.pdf BibTex
titre
Population structure of Bremia lactucae isolated from lettuce culture in France
auteur
Romain Valade, Claire Neema, Brigitte Maisonneuve
article
Eucarpia leafy Vegetables 2011, Aug 2011, Lille, France. pp.33
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absent
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https://hal.archives-ouvertes.fr/hal-00999915/file/49390_20120210101109176_1.pdf BibTex
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Current diseases and pests in lettuce in Western Europe
auteur
Brigitte Maisonneuve, Dominique Blancard
article
Eucarpia Leafy Vegetables 2011, Aug 2011, Lille, France
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https://hal.inrae.fr/hal-02745687/file/51050_20120210100304137_1.pdf BibTex
titre
Virulence of Bremia lactucae populations in Southern France between 2006 and 2011
auteur
Brigitte Maisonneuve, Sandrine Jeuniaux, Emilie Juillard, Marion Lovera
article
Eucarpia Leafy Vegetables 2011, Aug 2011, Lille, France
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https://hal.inrae.fr/hal-02745037/file/51518_20120210103754638_1.pdf BibTex
titre
Impact of selection pressure exerted by host resistance gene on population genetic structure of Bremia lactucae
auteur
Romain Valade, Aurélie Ducasse, Brigitte Maisonneuve, Claire Neema
article
13. congress of the European Society for Evolutionnary Biology, Aug 2011, Tübingen, Germany. 1 p
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absent
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MDHAR links the ascorbate-glutathione cycle to carbohydrate metabolism and sink organ development in tomato
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Noé Gest, Cecile Garchery, Rebecca Stevens
article
Annual Meeting of the American Society of Plant Biologists, Aug 2011, Minneapolis, United States
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Ascorbate redox control of plant growth, carbon metabolism and source-sink regulation in tomato
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Noé Gest, Cecile Garchery, Mathilde Causse, Hélène Gautier, T Do Phuc, Allistair R. Fernie, Ana Jimenez, Pierre Baldet, Christophe Rothan, Rebecca Stevens
article
10. International Conference on reactive Oxygen and Nitrogene species in Plants, Jul 2011, Budapest, Hungary
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https://hal.inrae.fr/hal-02747094/file/49885_20120106025601491_1.pdf BibTex
titre
Breeding for disease resistance in plants, moving from efficiency to durability
auteur
Alain Palloix
article
4. Plant Protection Congress of Turkey, Jun 2011, Kahramanmaras, Turkey
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https://hal.inrae.fr/hal-02744503/file/Palloix%202011%20NPP-Turkey_1.pdf https://hal.inrae.fr/hal-02744503/file/Palloix%202011%20NPP-Turkey_2.doc BibTex
titre
Inheritance of phenological traits in apricot progenies
auteur
Jean Marc Audergon, Guy Clauzel, Alain Blanc, Guillaume Roch, Patrick Lambert, D. Ruiz, J. A. Campoy, J. A. Salazar, P. Martínez-Gómez, J. Egea, Sylvie Bureau, Barbara Gouble, Marielle Boge, Patrice Reling, Catherine Renard, L. Dondini, S. Tartarini
article
15. International Symposium on Apricot Breeding and Culture, Jun 2011, Yerevan, Armenia
resume
The impact of global changes is becoming a serious concern at a world scale, and its influence could be rather large on perennial plant behaviour. Within fruit species, advances in blooming dates and floral disorders in relation to temperature increase during period of dormancy and bud burst have already been shown. Unfortunately among fruit species, apricot is expected to be one of the most susceptible in relation to the restricted adaptation of the local cultivars to narrow geographic areas. Thus, in order to overcome the negative trends and to safeguard apricot fruit production, the identification of the genetic components involved in blooming and maturity periods becomes of major interest. A global genetic analysis has been conducted on 4 apricot progenies issued from different genetic backgrounds; two progenies were cultivated in Avignon (Fr), one in Bologna (It), and one in Murcia (Sp). The four progenies were phenotyped for blooming and maturity dates at least for 2 years (except the Italian one evaluated only for the maturity date). The segregations have been examined and QTL analyses have been performed on the whole data set. The QTL stability across years has been analysed for the two traits. The influence of the genetic background has been discussed.
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Inheritance of fruit quality traits in apricot progenies
auteur
D Ruiz, L. Dondini, J.A. Salazar, Stefano Tartarini, M.D. Nortes, P. Martínez-Gómez, J. Egea, Guy Clauzel, Patrick Lambert, Alain Blanc, Sylvie Bureau, Maryse Reich, Patrice Reling, Barbara Gouble, Catherine Renard, Jean Marc Audergon
article
15. International Symposium on Apricot Breeding and Culture, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02749079/file/46585_20110908112901220_1.pdf BibTex
titre
A rapid tools for physiological study of apricot fruit
auteur
Sylvie Bureau, Barbara Gouble, Jean Marc Audergon, Catherine Renard
article
15. International Symposium, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02745371/file/42568_20111031100213921_1.pdf BibTex
titre
Infrared spectroscopy: a rapid tool for apricot characterization
auteur
Sylvie Bureau, Marielle Boge, Catherine Renard, Jean Marc Audergon
article
15. International Symposium on Apricot Breeding and Culture, Jun 2011, Yerevan, Armenia
resume
The objective of this work, using the infrared spectroscopy applied to predict some apricot fruit quality traits, was to test on fruit harvested in 2010 the robustness of models established in 2005 (Bureau et al., 2009a,b). Two wavelength regions have been tested for apricot fruit quality analysis, the near-infrared (NIR, 800-2500 nm) applied on intact fruits and the mid-infrared (MIR, 4000-650 cm(-1)) on fruit slurries. Results of prediction were acceptable for SSC in NIR and for SSC and TA in MIR independently of the year. A methodology was then proposed for each year with i) a selection of a representative set of samples, ii) the development of prediction models using both spectral and classical measurements, and iii) the use of these models to predict quality traits in all other samples of the same year.
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Temperature effect on respiration and ethylene production of two apricot varieties
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Barbara Gouble, Patrice Reling, Jean Marc Audergon, Catherine Renard
article
15. International Symposium, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02745887/file/40073_20110912091210918_1.pdf BibTex
titre
An integrated apricot breeding program in France joining CEP Innovation - Centrex and INRA
auteur
Jean Marc Audergon, Alain Blanc, Frederic Gilles, Guy Clauzel, J.M. Broquaire, Barbara Gouble, Marie Grotte, Maryse Reich, Sylvie Bureau, C. Pitiot
article
15. International Symposium on Apricot Breeding and Culture, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02749046/file/47306_20110908102623142_1.pdf BibTex
titre
Influence of temperature on apricot fruit respiration and ethylene production
auteur
Barbara Gouble, Patrice Reling, Catherine Renard, Jean Marc Audergon
article
15. International Symposium on Apricot Breeding and Culture, Jun 2011, Yerevan, Armenia
resume
To define optimal permeability of a composite wheat gluten-paper material for a new packaging film, elaborated in the Tailorpack project, physiological parameters modelling was conducted on two contrasted apricot cultivars ('Ravicille' and 'Bergeron'). Effects of temperature on respiration and ethylene production have been monitored and Q(10) were estimated at picking time and during postharvest storage. 'Ravicille' presented higher respiration and ethylene production rates, at all analysed temperatures, than 'Bergeron', while Q(10) values were more or less similar. For both cultivars, Q(10) increased with storage time. This result, added to the variability between cultivars, will have major impact on film conception.
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Performance of a model to predict the flowering date of apricot in three different regions of South France
auteur
Lucia Andreini, Patrick Bertuzzi, Jean Marc Audergon, Sylvain Satger, Marie Elise Liennard, Raffaella Viti
article
15. International Symposium, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02749445/file/43331_20110912094142240_1.pdf BibTex
titre
Apricot diffusion in the mediterranean basin : a serious loss of genetic diversity
auteur
Hedia Bourguiba, Lamia Krichen, Neïla Trifi-Farah, Bouchaib Khadari, Ali Mamouni, Samia Trabelsi, Claudio d'Onofrio, José Egea-Caballero, Bayram-Murat Asma, Jean Marc Audergon
article
15. International Symposium, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02749357/file/47861_20111031113806408_1.pdf BibTex
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Results of French apricot rootstock trials
auteur
Henri Duval, Martin Masse, Michel Jay, Jean Lichou
article
15. International Symposium on Apricot Breeding and Culture, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02746087/file/40311_20110908024041711_1.pdf BibTex
titre
Inheritance of phenological traits in apricot progenies
auteur
Jean Marc Audergon, David Ruiz, J.A. Campoy, J.A. Salazar, Stefano Tartarini, P. Martínez-Gómez, J. Egea, Patrick Lambert, Alain Blanc, Guillaume Roch, Guy Clauzel, L. Dondini
article
15. International Symposium, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02747058/file/40268_20111031092439465_1.pdf BibTex
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Apricot core collection assessment using morphological characterization
auteur
Lamia Krichen, Hedia Bourguiba, Jean Marc Audergon, Neïla Trifi-Farah
article
15. International Symposium, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02747317/file/47659_20111031111036415_1.pdf BibTex
titre
Suceptibility to Sharka (Plum pox virus) of several Prunus rootstocks against Dideron and Marcus strains
auteur
Manuel Rubio, Federico Dicenta, Martin Masse, Henri Duval
article
15. International Symposium on Apricot Breeding and Culture, Jun 2011, Yerevan, Armenia
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https://hal.inrae.fr/hal-02747149/file/45104_20110908030221119_1.pdf BibTex
titre
Heuristic value of a ‘Virtual fruit’ model of peach fruit quality and sensitivity to brown rot
auteur
Michel Génard, Bénédicte Quilot-Turion, Mohamed Ahmed Ould Sidi, Abdeslam Kadrani, Nadine Hilgert, Francoise Lescourret
article
9. International Symposium on modelling in Fruit Research and Orchard management, Jun 2011, Saint-Jean-sur-Richelieu, Canada. 7 p
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This work aimed at investigating the heuristic potential of a process-based model of peach fruit expressing seasonal changes in several quality attributes of fruit (e.g., size, percentages of flesh, water, sugar and acid contents) and fruit sensitivity to brown rot (skin density of cracks). Firstly, we showed that this “Virtual Fruit” could be used to analyze the impact of a single mutation which decreased the fruit’s requirement for carbon on peach fruit behavior. The mutation triggered large effects on several variables of the fruit development model (growth, respiration and metabolism) and delayed the fruit developmental rate. Such a virtual approach could lead to new ways of exploring the impact of mutations, or naturally occurring genetic variations, in silico, under different environmental conditions. Secondly, we illustrated how the “Virtual Fruit” could be possibly used to design peach ideotypes with high fruit mass and sweetness and low skin density of cracks. Since these traits are antagonists, we treated this design as a multi-objective optimization problem. An evolutionary algorithm was applied to solve this multi-objective optimization problem based on the “Virtual Fruit”. The optimized variables were six genetic parameters of the “Virtual Fruit”. This optimization procedure provided a large diversity of solutions (ideotypes). Ideotypes with low fruit mass had a high sweetness and low skin density of cracks. In a current breeding scheme, fruit mass would be the only criterion, but alternative schemes could be considered for the future, favoring organoleptic quality or environment friendly practices, or more generally, aiming at finding acceptable trade-offs between several criteria. In this case, modelling and model-based optimization would be helpful.
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Particle swarm optimization for designing ideotypes for sustainable production systems
auteur
Abdeslam Kadrani, Mohamed Mahmoud Ould Sidi, Bénédicte Quilot-Turion, Michel Génard, Francoise Lescourret
article
ICSI 2011: International conference on swarm intelligence, Jun 2011, Cergy, France. 3 p
resume
Agricultural systems have to adapt, in a changing climatic context, to face the growing social demand in terms of organoleptic, nutritional and environmental quality of food products. Thus, a crucial question for the future is how to manage fruit quality by finding the best combinations of genetic resources and cultural practices adapted to, and respectful of specific environments. This question was addressed using a particle swarm optimization and a process-based model. The obtained results show the interest of such as approach.
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Inheritance of fruit quality traits in apricot progenies
auteur
D. Ruiz, Luca Dondini, J.A. Salazar, Stefano Tartarini, M.D. Nortes, Pedro Martínez-Gómez, J. Egea, Guy Clauzel, Patrick Lambert, A. Blanc, Sylvie Bureau, M. Reich, Patrice Reling, Barbara Gouble, Catherine Renard, Jean Marc Audergon
article
15 th International Symposium on Apricot Breeding and Culture , Jun 2011, Yerevan, Armenia
resume
The knowledge on the transmission of fruit quality traits has a great importance in order to optimize the inter-cultivar crosses design and to improve the efficiency of apricot breeding programmes. Four apricot progenies issued from different genetic origins were evaluated during two years; two apricot progenies cultivated in Avignon (France), one in Bologna (Italy), and other one in Murcia (Spain). Fruit quality characterization was based on physical measurements (fruit weight, colour, and firmness) and biochemical measurements (soluble solids content, and titratable acidity). Phenotypic datasets showed distribution of seedlings with regard to the parents, with a high variability for all analyzed quality parameters. An inter-annual variation was observed for the mean values of all the genotypes between the two years of the study, indicating the influence of the environmental conditions on fruit characteristics. Results indicated a quantitative inheritance of all quality traits in the apricot progenies indicating their polygenic nature. In general we observed in most cases a normal distribution of quality traits in the observed populations. However, in contrast to intermediate expected values between the parents, a large number of seedlings showed lower or higher values than their parents for many quality parameters. In this sense, results evidenced an extra genetic influence of the parents (the whole genetic background) on the transmission of fruit quality traits in apricot, which should be taken into consideration with inter-cultivar crosses design.
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Replication of inaccurate viruses and transmissible genetic diversity: crosstalk between modelling and high-throughput sequencing
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Gael Thébaud, Marco Morelli, Sylvie Dallot, Joel Chadoeuf, Gerard Labonne, Daniel Haydon
article
4. Plant Virus Ecology Network Workshop (PVEN), May 2011, Montpellier, France
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Bien choisir les espèces et les variétés
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M-Christin Daunay, Richard Brand, Dominique Blancard
article
13. Colloque Scientifique, May 2011, Montpellier, France
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https://hal.inrae.fr/hal-02749852/file/46786_20111109025649439_1.pdf BibTex
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Genome admixture of Solanum lycopersicum var. cerasiforme allows successful association mapping of quality-traits and adds insights in tomato domestication
auteur
Mathilde Causse, Nicolas Ranc, Stephane Munos, Dominique Brunel
article
Eucarpia Tomato 2011, 17. Eucarpia Meeting Section Vegetables Working Group Tomato, Apr 2011, Malaga, Spain. 1 p
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Application des algorithmes génétiques pour la conception de systèmes de culture durable
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Mohamed Mahmoud Ould Sidi, Bénédicte Quilot-Turion, Abdeslam Kadrani, Nadine Hilgert, Michel Génard, Francoise Lescourret
article
12. Congrès annuel de la société française de la recherche opérationnelle et de l'aide à la décision., Mar 2011, Saint-Etienne, France. 2 p
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https://hal.inrae.fr/hal-02809734/file/43547_20110728021149244_1.pdf BibTex
titre
Evolution des souches de Bremia. Durabilité des méthodes de protection
auteur
Brigitte Maisonneuve
article
Rencontres phytosanitaires CTIL/SDQPV légumes et fraise, Feb 2011, Plan d'Orgon, France. pp.1-13
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https://hal.inrae.fr/hal-02808721/file/50628_20120217085355550_1.pdf BibTex
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Vers des cultures fruitières et légumières à hautes performances environnementales
auteur
Benoit Jeannequin, Francoise Dosba, Daniel Plénet, Michel Pitrat, Jean-Eric Chauvin
article
Salon International de l'Agriculture, Feb 2011, Paris, France. pp.73-85
resume
En France, les productions fruitières et légumières qui occupent moins de 2% de la SAU sont caractérisés par la diversité des espèces cultivées et les multiples systèmes de culture qui peuvent avoir des impacts environnementaux divers. Face aux nouveaux enjeux de développement d’une horticulture sensu lato à haute performance environnementale, l’Inra contribue aux travaux visant à réduire l’impact environnemental de ces cultures et à concevoir des systèmes de culture innovants. Les principaux résultats acquis au cours des dernières années concernent l’optimisation de la gestion du climat sous serre, le raisonnement optimisé de pratiques d’irrigation et de fertilisation, la création de variétés multi résistantes et la gestion durable des résistances aux bio agresseurs, l’élaboration de systèmes de cultures innovants limitant les risques phytosanitaires. Outre les recherches conduites en agriculture biologique, le développement de la protection fruitière intégrée et, plus récemment, de la protection biologique intégrée sous serre constituent des apports importants dans cette démarche de protection de l’environnement. Les approches actuelles de l’Inra sont plus globales et concernent l’étude des systèmes de culture à bas intrants et à hautes performances environnementales et économiques. Elles nécessitent des approches de modélisation des systèmes complexes et des partenariats multiples. Pour nourrir et étudier ces questions, l’Inra renforce ses structures d’interface notamment au travers de Groupements d’Intérêt Scientifique tels que le GIS PIClég et très prochainement le GIS « Fruits »
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https://hal.archives-ouvertes.fr/hal-01512047/file/Jeannequin_2011_1.pdf BibTex
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Génétique d'association pour la qualité chez la tomate
auteur
Mathilde Causse, Nicolas Ranc, Stephane Munos, Dominique Brunel
article
Assemblée Générale de l'ASF : Génétique d’association et Amélioration des Plantes, Evolution des outils de génotypage et de phénotypage à haut débit, Feb 2011, Versailles, France. 9 p
resume
Chez la tomate, l’amélioration pour la qualité du fruit est rendue difficile par la multiplicité et la complexité des caractères. La cartographie de QTL a permis la caractérisation génétique de ces caractères. L’objectif est maintenant d’identifier les gènes sous-jacents aux QTL. Nous avons utilisé la cartographie par déséquilibre de liaison (DL) dans ce but. Pour éviter les fausses associations entre les caractères et les polymorphismes moléculaires, la structure génétique a été prise en compte dans l’analyse. La tomate cultivée montre un faible niveau de diversité génétique, ce qui réduit la résolution de cartographie. Le génome des tomates de type cerise (S. lycopersicum var. cerasiforme) est une mosaïque entre celui de la tomate cultivée et celui de l’ancêtre sauvage. Ce mélange devrait augmenter la résolution des études d’association. Nous avons utilisé une « core collection » focalisée sur des accessions de type cerise pour réaliser une étude d’association, focalisée sur le chromosome 2. Nous avons analysé l’étendue du DL en fonction de la distance génétique et physique. Des associations entre des polymorphismes et les phénotypes étudiés ont été détectés avec des méthodes prenant en compte la structure génétique. Nous avons montré l’intérêt d’utiliser la structure en mosaïque du génome des accessions de type cerise pour surmonter les limitations de résolution dans les analyses d’associations chez une espèce cultivée autogame. Nous avons validé des QTL identifiés précédemment et nous avons trouvé des associations avec de nouveaux QTL et de nouveaux gènes candidats.
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Mejoramiento genético en el melocotonero: novedades y perspectivas para la resistencia a los bioagresores y la calidad del fruto
auteur
Thierry Pascal, Patrick Lambert, Bénédicte Quilot-Turion, Véronique Decroocq, Marie-Helene Sauge-Collet
article
Jornada de Especializacion - Innovacion Varietal en Melocoton, Nectarina y Paragueyo: Actualizacion, Cogullada, Feb 2011, Zaragoza, España
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Pourquoi une résistance polygénique est-elle plus durable qu’une résistance monogénique ?
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Julie Quenouille, Josselin Montarry, Alain Palloix, Benoît Moury
article
13. Rencontres de Virologie Végétale, Jan 2011, Aussois, France
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https://hal.inrae.fr/hal-02750189/file/47732_20110131102352846_1.pdf BibTex
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Estimating risk factors for virus dissemination from incomplete epidemiological surveillance data
auteur
David Pleydell, Gael Thébaud, Samuel Soubeyrand, Sylvie Dallot, Sylvain Grizard, Joel Chadoeuf, Gerard Labonne
article
13. Rencontres de Virologie Végétale (RVV 2011), Jan 2011, Aussois, France
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titre
Des régions clé de la protéine pvr2-eIF4E1 du piment gouvernent la résistance au potyvirus et son spectre
auteur
Séverine Lacombe, Sophie Ewert, André Moretti, Claire Fouet, Carole Caranta
article
13. Rencontres de Virologie Végétale, Jan 2011, Aussois, France. p. 27
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Conference papers
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https://hal.inrae.fr/hal-02811302/file/50322_20120402090926901_1.pdf BibTex
titre
Genome-wide association genetics to identify loci involved in responses to Potyviruses in plants
auteur
Valerie Schurdi-Levraud, Zofia Nehr, Patrick Cosson, Carole Caranta, F. Roux, Frederic Revers
article
13. Rencontres de Virologie Végétale, Jan 2011, Aussois, France. p. 82
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Conference papers
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https://hal.inrae.fr/hal-02807052/file/50374_20120402090450412_1.pdf BibTex
titre
Towards the identification of new host factors required for plant susceptibility to potyviruses: novel routes to resistance
auteur
Laurence Ouibrahim, André Moretti, Aurélie Salgues, Ana Giner Rubio, Hervé Lecoq, Christophe Robaglia, Carole Caranta
article
13. Rencontres de Virologie Végétale, Jan 2011, Aussois, France
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Conference papers
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https://hal.inrae.fr/hal-02747103/file/50751_20120402092050925_1.pdf BibTex
titre
Réplication des virus "infidèles" et diversité génétique transmissible : apports croisés de la modélisation et du séquençage à haut débit
auteur
Gael Thébaud, Marco Morelli, Sylvie Dallot, Joel Chadoeuf, Gerard Labonne, Daniel Haydon
article
13. Rencontres de Virologie Végétale (RVV 2011), Societe Francaise de Phytopathologie (SFP). FRA. Institut National de la Recherche Agronomique (INRA).; Agropolis International. Montpellier, FRA., Jan 2011, Aussois, France
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titre
Analyse et enjeux de la valeur agronomique technologique et environnementale chez les espèces fruitières
auteur
Gilbert Grivault, Richard Brand, Laurent Brun, Charles Eric Durel, Daniel Plenet, François Warlop, Jean Marc Audergon
article
6. Rencontres du Végétal, Jan 2011, Angers, France
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https://hal.inrae.fr/hal-02750112/file/42626_20110222085517852_1.pdf BibTex
titre
Le Groupe « Espèces Fruitières » du Département Génétique et Amélioration des Plantes de l'INRA, un partenaire au service de l’environnement et de l’innovation pour les territoires à vocation fruitière, les producteurs et les consommateurs
auteur
Jean Marc Audergon, Teresa Barreneche, Mathilde Causse, Elisabeth Chevreau, Evelyne Costes, Beatrice Denoyes-Rothan, Olivier Pailly, Yves Lespinasse
article
6. Rencontres du Végétal, Jan 2011, Angers, France
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Conference papers
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https://hal.inrae.fr/hal-02750402/file/41794_20110222093648304_1.pdf BibTex
titre
Temperature effect on respiration and ethylene production of two apricot varieties.
auteur
Barbara Gouble, Patrice Reling, Jean Marc Audergon, Catherine Renard
article
15 th International Symposium on Apricot Breeding and Culture , 2011, Yerevan, Armenia
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titre
An integrated apricot breeding program in France joining CEP Innovation - Centrex and INRA.
auteur
Jean Marc Audergon, Alain Blanc, Gilles Fréderic, Guy Clauzel, M. Broquaire, Barbara Gouble, Marie Grotte, Maryse Reich, Sylvie Bureau, C. Pitiot
article
International Symposium on Apricot Breeding and Culture, 2011, Yerevan, Armenia
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titre
A rapid tools for physiological study of apricot fruit.
auteur
S. Bureau, Barbara Gouble, Jean Marc Audergon, Catherine Renard
article
15 th International Symposium on Apricot Breeding and Culture , 2011, Yerevan, Armenia
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Other publications

titre
La conservation et la connaissance des ressources génétiques d'espèces végétales cultivées : un enjeu pour l'agriculture et un défi pour les acteurs
auteur
Emmanuel Geoffriau, Michel Pitrat, Pascal Coquin, François Balfourier, Marie- Christine Daunay, Florence Esnault, Chrystelle Jouy, Jean-Eric Chauvin, Alain Label-Richardson, François Boulineau, Helène Burck, Laurence Feugey, Brigitte Maisonneuve, Emilie Balsemin, Claudie Lambert, Anne-Marie Sage-Palloix, Teresa Barreneche, Catherine Delaitre, Stéphane Fourtier, Anne Zanetto, Agnès Grapin, Jean-Marie Prosperi, Audrey Didier
article
2011, non paginé
resume
La conservation et la connaissance des ressources génétiques d'espèces végétales cultivées : un enjeu pour l'agriculture et un défi pour les acteurs
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https://hal-agrocampus-ouest.archives-ouvertes.fr/hal-00841722/file/poster_pj_Grapin.PDF BibTex

Poster communications

titre
Metabolite profiling and feeding bioassays suggest a major role for a dicaffeoylquinic acid in induced resistance of peach to Myzus persicae aphid
auteur
Jean-Luc Poessel, Marie-Hélène Sauge, Michael Staudt, Claire Dufour, Catherine Deborde, Yvan Rahbé, B. Jackson, Cédric Renaud, Mickael Maucourt, Marie Noëlle Corre, H. El-Aouni, Jean Philippe Lacroze, Annick Moing
article
PRIR 2011 Joint meeting of the "PR-proteins Workshop" and the "Working Group Induced Resistance in Plants Against Insects and Diseases", Sep 2011, Neuchatel, Switzerland. 154 p., 2011, PR-Proteins and Induced Resistance Against Pathogens and Insects. Abstracts book
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Poster communications
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https://hal.inrae.fr/hal-02748156/file/41817_20111027014430108_1.pdf BibTex
titre
Improvement of the differential lettuce set for Bremia virulence evaluation: new sativa monogenic lines
auteur
Brigitte Maisonneuve
article
Eucarpia Leafy Vegetables 2011, Aug 2011, Lille, France. 2011, Proceedings Eucarpia Leafy Vegetables 2011
typdoc
Poster communications
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https://hal.inrae.fr/hal-02747007/file/51609_20120210104128452_1.pdf BibTex
titre
Développement de biopesticides d’origine végétale pour l’horticulture : méthodes de production, spectre d’action et validation in vivo de l’efficacité des acides dicaféoylquiniques
auteur
Jean-Luc Poessel, Camille Croset, Marie Noëlle Corre, Elodie Lecerf, Jawad Aarrouf, Marie-Hélène Sauge, Stéphanie Servier, Jean Philippe Lacroze, Fanny Calmels, Claire Dufour, Michele Loonis, Philippe C. Nicot, Marc Bardin, Claire Troulet, Catherine Deborde, Vincent Lebot, Antoine Champagne, Gérard Febvay, Yvan Rahbé, Jean-Luc Verdeil
article
ANR - Grand colloque Biologie et Santé 2011, Jul 2011, Lyon, France. 1 p., 2011
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Poster communications
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titre
An Integrated Apricot Breeding Program in France Joining CEP Innovation - CENTREX and INRA
auteur
Jean Marc Audergon, Alain Blanc, Frederic Gilles, Guy Clauzel, Jean Michel Broquaire, Barbara Gouble, Marie Grotte, Maryse Reich, Sylvie Bureau, Guillaume Frémondière, Christelle Pitiot
article
15. International Symposium on Apricot Breeding and Culture, Jun 2011, Yerevan, Armenia. 2011
typdoc
Poster communications
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-02746028/file/Erev11_Audergon_apricot%20breeding_poster_1.pdf BibTex
titre
Ectopic expression of translation initiation factor eIF4E extends the resistance spectrum against Lettuce mosaic virus in lettuce
auteur
Marianne Mazier, Raquel Sanjuan, Fabrice Flamain, Verane Sarnette, Emmanuel Botton, Sylvie German-Retana, Mathieu Cammas, André Moretti, Brigitte Maisonneuve, Carole Caranta
article
13. Rencontres de virologie végétale, Jan 2011, Aussois, France. p. 70, 2011
typdoc
Poster communications
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https://hal.inrae.fr/hal-02746846/file/51777_20120330092446079_1.pdf BibTex

Reports

titre
Rapport final du projet : HortiBiope. Développement de biopesticides d'origine végétale pour l'horticulture: méthodes de production, spectre d'action et validation in vivo de l'efficacité des acides dicaféoylquiniques
auteur
Jean-Luc Poessel, Marie-Hélène Sauge, Claire Dufour, Philippe C. Nicot
article
[Contrat] 2011
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titre
Bases moléculaires des résistances aux virus contrôlés par des facteurs de l'hôte nécessaires aux cycles infectieux
auteur
Carole Caranta
article
[Contrat] 2011
typdoc
Reports
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https://hal.inrae.fr/hal-02807142/file/Compte-rendu%20final_MOVIe_%202011_1.pdf BibTex
titre
Functional confirmation of candidate genes for a broad-spectrum resistance QTL against Phytophthora in Solanaceae
auteur
Véronique Lefebvre
article
[Contract] Institut National de la Recherche Agronomique (INRA). 2011
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titre
Résistance génétique du melon à Aphis gossypii
auteur
Marion Chambrier
article
[Stage] Institut Universitaire de Technologie (IUT), Digne les Bains, FRA. 2011, 53 p
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titre
Recherche d’interactions entre la capside du Raspberry Bushy Dwarf Virus (RBDV) et les protéines eIF4G d’Arabidopsis
auteur
Aramata Marena
article
[Stage] Faculté des Sciences de Luminy. Université de la Méditerranée (Aix Marseille 2), Marseille, FRA. 2011, 25 p
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Reports
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https://hal.inrae.fr/hal-02805234/file/45379_20110721032223919_1.pdf BibTex
titre
Influence de la diversité génétique du virus et de l’hôte sur le contournement d’une résistance au virus Y de la pomme de terre chez le piment
auteur
Ludovic Saint-Félix
article
[Stage] Université Montpellier 2 (Sciences et Techniques) (UM2), Montpellier, FRA. 2011, 48 p
resume
Les résistances génétiques permettent une lutte efficace contre les maladies des cultures mais sont limitées par les capacités de contournement des pathogènes. Chez le piment, le fond génétique peut améliorer la durabilité de la résistance au virus Y de la pomme de terre (PVY) due au gène majeur pvr23 tandis que chez le PVY, le gène CI accentue ses capacités de contournement via les substitutions dans le gène d’avirulence (VPg). Nous avons déterminé une corrélation entre durabilité et résistance quantitative contrôlée par le fond génétique chez des variétés de piment non apparentées, et montré que les fonds génétiques favorisant la durabilité de pvr23 sont répandus dans la diversité génétique. Parallèlement, chez le PVY, nous avons recherché les mutations du gène CI impliquées dans l’amélioration du contournement, par création de virus recombinants. Deux acides aminés du tiers C-terminal de la protéine pourraient expliquer ces propriétés. La résistance partielle, mesurée par la concentration virale, apparaît comme un critère a priori de sélection pour la durabilité
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Reports
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https://hal.inrae.fr/hal-02811163/file/45375_20110620114946678_1.pdf BibTex
titre
Nouvelles sources de résistance au puceron Aphis gossypii chez le melon
auteur
Nathalie Boissot
article
[Contrat] 2011
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2010

Conference papers

titre
Acides caféoylquiniques et résistance au Monilinia
auteur
Bénédicte Quilot-Turion, Jean-Luc Poessel
article
Réunion finale HortiBiope, Dec 2010, Avignon, France
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titre
Vers l'intégration de composantes génétiques dans les modèles en vue de la création d'idéotypes
auteur
Bénédicte Quilot-Turion
article
Journées Modélisation du Réseau Qualité du Département EA, Nov 2010, Chateauneuf de Gadagne, France
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titre
The french peach breeding program (INRA): an integrative approach for pest/disease resistance and fruit quality
auteur
Patrick Lambert, Jean-Luc Poessel, Camille Croset, Marie Noëlle Corre, Bénédicte Quilot-Turion, Veronique Signoret, Véronique Decroocq, David Tricon, Marie-Hélène Sauge, Sylvie Bureau, Catherine Renard, Thierry Pascal
article
5. Rosacea Genomics Conference, Nov 2010, Stellenbosch, South Africa. 1p
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https://hal.inrae.fr/hal-02819259/file/47008_20110331113855581_1.pdf BibTex
titre
QTLs detection for phenological traits within the Rosaceae family.
auteur
Elisabeth Dirlewanger, José Quero-Garcia, Loick Le Dantec, Evelyne Costes, Beatrice Denoyes-Rothan, Amélia Gaston, Bénédicte Quilot-Turion, Patrick Lambert, Jean Marc Audergon, David Ruiz, Jean-Marc Celton, L. Dandini, S. Tartarini, E. Illa, P. Arus
article
5. Rosaceae Genomic Conference RGC5, Agricultural Research Council (ARC). Cape-Town, ZAF., Nov 2010, Cate-Town, South Africa
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titre
QTL detection for phenological traits within the rosaceae family
auteur
Elisabeth Dirlewanger, José Quero-Garcia, Loick Le Dantec, Patrick Lambert, David Ruiz, Jean-Marc Celton, L. Dondini, E. Illa, Bénédicte Quilot-Turion, Jean Marc Audergon, Stefano Tartarini, Pere Arus, Evelyne Costes, Beatrice Denoyes-Rothan
article
5. International Rosaceae Genomics Conference, Nov 2010, Stellenbosch, South Africa. 1 p
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titre
Towards optimization of anther culture and genotypic response for haploid plant production in sweet pepper
auteur
Alain Palloix
article
2. International Conference on Applied Biotechnology. African City of Technology, Oct 2010, Khartoum, Sudan
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titre
Analysis of the genetic determinism of phenological traits on Punus fruit species ans its interaction with envirnmental and climatic conditions
auteur
Elisabeth Dirlewanger, José Quero-Garcia, Maria-Das-Dores Lafargue, Loick Le Dantec, Jacques Joly, Jean-Yves Chevrollier, Patrick Lambert, Bénédicte Quilot-Turion, Jean Marc Audergon, Luca Dondini, Stefano Tartarini, Eudald Illa, Pere Arus, Anton Ivancic, Philippe Letourmy
article
Interdisciplinary congress ACCAE "Adapting to climate change : agriculture and ecosystems", Oct 2010, Clermont-Ferrand, France. 2 p
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titre
Étude du mode d’action des acides dicaféoylquiniques, molécules naturelles aphicides
auteur
Stéphanie Servier, Marie-Hélène Sauge, Gérard Febvay, Marie Noëlle Corre, Camille Croset, Jean Philippe Lacroze, Yvan Rahbé, Jean-Luc Poessel
article
16. Colloque de Biologie de l’Insecte, Oct 2010, Lyon, France. 1 p
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titre
Étude du mode d’action des acides dicaféoylquiniques, molécules naturelles aphicides
auteur
Stéphanie Servier, Marie-Hélène Sauge, Gérard Febvay, Marie Noëlle Corre, Camille Croset, Jean Philippe Lacroze, Yvan Rahbé, Jean-Luc Poessel
article
16. Colloque de Biologie de l’Insecte, Oct 2010, Lyon, France. 126 p
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titre
Intelligent fluorosensor: a fast tool to determine fluorescence characteristics
auteur
Alain Palloix
article
10. Nordic Phytosynthesis Congress (NPC10), Oct 2010, Tartu, Estonia
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