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Your search keyword '"Carrere, Sebastien"' showing total 11 results
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11 results on '"Carrere, Sebastien"'

1. Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modeling and genome-wide association

Author

Mangin, Brigitte, Casadebaig, Pierre, Cadic, Eléna, BLANCHET, Nicolas, Boniface, Marie-Claude, Carrere, Sebastien, Gouzy, Jerome, Legrand, Ludovic, mayjonade, Baptiste, Pouilly, Nicolas, André, Thierry, Coque, Marie, Piquemal, Joël, Laporte, Marion, Vincourt, Patrick, Munos, Stephane, Langlade, Nicolas, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Soltis, Biogemma, Syngenta France, RAGT, French National Research Agency : ANR-07-GPLA-0022, ANR-11-BTBR-0005, 'OLEOSOL' project, Midi Pyrenees Region, European Fund for Regional Development (EFRD), French Fund for Competitiveness Clusters (FUI), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, French National Research Agency, ANR-07-GPLA-0022,SUNYFUEL,Improving sunflower yield and quality for biofuel production by genomics and genetics(2007), and ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011)

Subjects
Genomics (q-bio.GN), stress abiotique, abiotic stress, crop model, plasticité, fungi, food and beverages, drought, cold, huile de tournesol, vegetal oil, multi-stress, FOS: Biological sciences, genetic variation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Quantitative Biology - Genomics, sunflower oil, contrôle génétique, huile végétale
Abstract

Understanding the genetic basis of phenotypic plasticity is crucial for predicting and managing climate change effects on wild plants and crops. Here, we combined crop modeling and quantitative genetics to study the genetic control of oil yield plasticity for multiple abiotic stresses in sunflower. First we developed stress indicators to characterize 14 environments for three abiotic stresses (cold, drought and nitrogen) using the SUNFLO crop model and phenotypic variations of three commercial varieties. The computed plant stress indicators better explain yield variation than descriptors at the climatic or crop levels. In those environments, we observed oil yield of 317 sunflower hybrids and regressed it with three selected stress indicators. The slopes of cold stress norm reaction were used as plasticity phenotypes in the following genome-wide association study. Among the 65,534 tested SNP, we identified nine QTL controlling oil yield plasticity to cold stress. Associated SNP are localized in genes previously shown to be involved in cold stress responses: oligopeptide transporters, LTP, cystatin, alternative oxidase, or root development. This novel approach opens new perspectives to identify genomic regions involved in genotype-by-environment interaction of a complex traits to multiple stresses in realistic natural or agronomical conditions., 12 pages, 5 figures, Plant, Cell and Environment

Published
2017
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2. Genomic Prediction of Sunflower Hybrids Oil Content

Author

Mangin, Brigitte, Bonnafous, Fanny, Blanchet, Nicolas, Boniface, Marie-Claude, Bret-Mestries, Emmanuelle, Carrere, Sebastien, Cottret, Ludovic, Legrand, Ludovic, Marage, Gwenola, Pegot - Espagnet, Prune, Munos, Stephane, Pouilly, Nicolas, Vear, Felicity, Vincourt, Patrick, Langlade, Nicolas, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Vegetal Biology, sunflower, hybrid, genomic selection, factorial design, oil content, GBS, prédiction génétique, Plant Science, lcsh:Plant culture, huile de tournesol, hybride, Agricultural sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Biologie végétale, Sciences agricoles, Original Research
Abstract

International audience; Prediction of hybrid performance using incomplete factorial mating designs is widely used in breeding programs including different heterotic groups. Based on the general combining ability (GCA) of the parents, predictions are accurate only if the genetic variance resulting from the specific combining ability is small and both parents have phenotyped descendants. Genomic selection (GS) can predict performance using a model trained on both phenotyped and genotyped hybrids that do not necessarily include all hybrid parents. Therefore. GS could overcome the issue of unknown parent GCA. Here, we compared the accuracy of classical GCA-based and genomic predictions for oil content of sunflower seeds using several GS models. Our study involved 452 sunflower hybrids from an incomplete factorial design of 36 female and 36 male lines. Re-sequencing of parental lines allowed to identify 468,194 non-redundant SNPs and to infer the hybrid genotypes. Oil content was observed in a multi-environment trial (MET) over 3 years, leading to nine different environments. We compared GCA-based model to different GS models including female and male genomic kinships with the addition of the female-by-male interaction genomic kinship, the use of functional knowledge as SNPs in genes of oil metabolic pathways, and with epistasis modeling. When both parents have descendants in the training set, the predictive ability was high even for GCA-based prediction, with an average MET value of 0.782. GS performed slightly better (+0.2%). Neither the inclusion of the female-by-male interaction, nor functional knowledge of oil metabolism, nor epistasis modeling improved the GS accuracy. GS greatly improved predictive ability when one or both parents were untested in the training set, increasing GCA-based predictive ability by 10.4% from 0.575 to 0.635 in the MET. In this scenario, performing GS only considering SNPs in oil metabolic pathways did not improve whole genome GS prediction but increased GCA-based prediction ability by 6.4%. Our results show that GS is a major improvement to breeding efficiency compared to the classical GCA modeling when either one or both parents are not well-characterized. This finding could therefore accelerate breeding through reducing phenotyping efforts and more effectively targeting for the most promising crosses.

Published
2017
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3. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Author

BADOUIN, Hélène, Gouzy, Jerome, GRASSA, Christopher, Murat, Florent, Staton, S Evan, Cottret, Ludovic, Lelandais-briere, Christine, Owens, Gregory L, Carrere, Sebastien, mayjonade, Baptiste, Legrand, Ludovic, Gill, Navdeep, Kane, Nolan C, Bowers, John E, Hubner, Sariel, Bellec, Arnaud, Berard, Aurélie, Berges, Helene, BLANCHET, Nicolas, Boniface, Marie-Claude, Brunel, Dominique, Catrice, Olivier, Chaidir, Nadia, Claudel, Clotilde, Donnadieu, Cecile, Faraut, Thomas, Fievet, Ghislain, Helmstetter, Nicolas, King, Matthew, Knapp, Steven J, Lai, Zhao, Le Paslier, Marie-Christine, Lippi, Yannick, LORENZON, Lolita, Mandel, Jennifer R, Marage, Gwenola, MARCHAND, Gwenaëlle, MARQUAND, Elodie, MESTRIES, Emmanuelle, Morien, Evan, Nambeesan, Savithri, Nguyen, Thuy, Pegot - Espagnet, Prune, Pouilly, Nicolas, Raftis, Frances, Sallet, Erika, Schiex, Thomas, Thomas, Justine, Vandecasteele, Céline, Vares, Didier, Vear, Felicity, Vautrin, Sonia, Crespi, Martin, Mangin, Brigitte, Burke, John M, Salse, Jerome, Munos, Stephane, Vincourt, Patrick, Rieseberg, Loren H, Langlade, Nicolas, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Botany and Biodiversity Research Centre, University of British Columbia (UBC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Department of Plant Biology, Miller Plant Sciences, University of Georgia [USA], Department of Biotechnology, Tel-Hai Academic College, Galilee Research Institute (Migal), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Etude du Polymorphisme des Génomes Végétaux (EPGV), Dow AgroSciences LLC, Biogemma, GeT PlaGe, Genotoul, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Department of Plant Sciences, University of California, Department of Biology, Northern Arizona University [Flagstaff], Center for Genomics and Bioinformatics, Indiana University [Bloomington], Indiana University System-Indiana University System, Department of Biological Sciences, The Open University [Milton Keynes] (OU), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Department of Horticulture, University of Wisconsin-Madison, The Wellcome Trust Sanger Institute [Cambridge], Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), French National Research Agency : SUNYFUEL/ANR-07-GPLA-0022, SUNRISE/ANR-11-BTBR-0005 Midi-Pyrenees Region, European Fund for Regional Development, French Fund for Competitiveness Clusters (FUI), Genoscope SystemSun project, Genome Canada, Genome BC's Applied Genomics Research in Bioproducts or Crops (ABC) Competition, NSF Plant Genome Program : DBI-082045, International Consortium for Sunflower Genomics Resources, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Tel-Hai College, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), ANR-07-GPLA-0022,SUNYFUEL,Improving sunflower yield and quality for biofuel production by genomics and genetics(2007), ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Galilee Research Institute [Israël] (MIGAL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), University of California (UC), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), University of British Columbia ( UBC ), Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Institut National de la Recherche Agronomique ( INRA ), UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Department of Ecology and Evolutionary Biology ( Faculty of Biology ), University of Georgia, Galilee Research Institute ( Migal ), Centre National de Ressources Génomiques Végétales ( CNRGV ), Institut National de la Recherche Agronomique ( INRA ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, The Open University [Milton Keynes] ( OU ), University of Wisconsin-Madison [Madison], Wellcome Trust Sanger Institute, and Unité de Mathématiques et Informatique Appliquées de Toulouse ( MIAT INRA )

Subjects
[ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, sunflower, Acclimatization, résistance au stress, génome végétal, Flowers, genome evolution, résilience, Evolution, Molecular, Gene Expression Regulation, Plant, Stress, Physiological, Gene Duplication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Oils, Sunflower Oil, genome, food and beverages, Genetic Variation, Genomics, Sequence Analysis, DNA, tournesol, genêtic variation, stress biotique, diversité génétique, Helianthus, Transcriptome, Genome, Plant
Abstract

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.

Published
2016
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4. Using Ecology, Physiology, and Genomics to Understand Host Specificity inXanthomonas: French Network on Xanthomonads (FNX)

Author

Jacques, Marie Agnes, Arlat, Matthieu, Boulanger, Alice, Boureau, Tristan, Carrere, Sebastien, Cesbron, Sophie, Chen, Nicolas W.G., Cociancich, Stéphane, Darrasse, Armelle, Denance, Nicolas, Le Saux, Marion, Gagnevin, Lionel, Koebnik, Ralf, Lauber, Emmanuelle, NOEL, Laurent, Pieretti, Isabelle, Portier, Perrine, PRUVOST, Olivier, Rieux, Adrian, Robene-Soustrade, Isabelle, Royer, Monique, Szurek, Boris, Verdier, Valérie, Vernière, Christian, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université de Montpellier (UM), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Institut de Recherche pour le Développement (IRD [France-Ouest]), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de La Réunion (UR)-Institut National de la Recherche Agronomique (INRA)

Subjects
bactérie phytopathogène, type III effectors, habitat, emergence, host specificity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, adaptation, spécificité de l'hôte, host jump, effecteur type III, phytopathogenic bacteria, analyse phylogénétique
Abstract

How pathogens coevolve with and adapt to their hosts are critical to understanding how host jumps and/or acquisition of novel traits can lead to new disease emergences. The Xanthomonas genus includes Gram-negativeplant-pathogenic bacteria that collectively infect a broad range of crops and wild plant species. However, individual Xanthomonas strains usually cause disease on only a few plant species and are highly adapted to their hosts,making them pertinent models to study host specificity. This review summarizes our current understanding of the molecular basis of host specificity in the Xanthomonas genus, with a particular focus on the ecology, physiology,and pathogenicity of the bacterium. Despite our limited understanding of the basis of host specificity, type III effectors, microbe-associated molecular patterns, lipopolysaccharides, transcriptional regulators, and chemotacticsensors emerge as key determinants for shaping host specificity.

Published
2016
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5. Pea in the genomic era

Author

Alves Carvalho, Susete, Aluome, Christelle, Aubert, Gregoire, Cruaud, Corinne, Klein, Anthony, Jacquin, Françoise, Carrere, Sebastien, Brochot, Anne-Lise, Kreplak, Jonathan, Martin, Chantal, Boucherot, Karen, Da Silva, Corinne, Gamas, Pascal, Wincker, Patrick, Brunel, Dominique, Le Paslier, Marie-Christine, Gouzy, Jerome, Burstin, Judith, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2014

6. Recent pea genomic resources will enhance complementary improvement strategies in this crop

Author

Burstin, Judith, Alves Carvalho, Susete, Tayeh, Nadim, Aluome, Christelle, Bourion, Virginie, Klein, Anthony, Carrere, Sebastien, Brochot, Anne-Lise, Salloignon, P., Siol, Mathieu, Delaitre, Catherine, Cruaud, C, Kreplak, Jonathan, Truntzer, C., Balzergue, Sandrine, Wincker, P., Le Paslier, Marie-Christine, Brunel, Dominique, Gouzy, Jerome, Lejeune-Henaut, Isabelle, Duc, Gérard, Aubert, Gregoire, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), Institut National de la Recherche Agronomique (INRA)-Université de Lille, Sciences et Technologies, University of Saskatchewan. CAN., Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, pea genomic ressources, improvement, high density marker genotypes, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract

BAP GEAPSI BAP CT2 Événement(s) lié(s) : - 7. International Conference on Legume Genetics and Genomics (ICLGG VII); Saskatoon (CAN) - (2014-07-07 - 2014-07-11); International audience; The recent development of high-throughput sequencing and genotyping technologies has permitted pea genomics to catch up and enter into the genomic era. We will present the development of functional and structural genomic resources in pea and their application in pea breeding. We developed a pea Unigene expression atlas that allows visualization of expression profiles for any gene of interest in various tissues subjected to different conditions. This was the basis for generating a high density microarray for functional genomics and a high-throughput genotyping BeadChip array for genotyping. These tools will be extremely useful in three breeding strategies followed by the team: (i) ideotype breeding, which pursue an ideal plant model that is expected to meet the desired yield and quality requirements of producers and users; (ii) targeted breeding, which chase the good combinations of genetic factors controlling traits of interest; and (iii) genome-wide breeding, which models phenotypes from high density marker genotypes.

Published
2014

7. Characterisation of rye-grass (Lolium sp.) transcriptome-wide response to ALS-inhibiting herbicides

Author

Duhoux, Arnaud, Gouzy, Jerome, Carrere, Sebastien, Bonin, Ludovic, Delye, Christophe, ProdInra, Migration, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), ARVALIS - Institut du végétal [Paris], and European Weed Research Society (EWRS). GBR.

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, enhanced metabolism, Illumina, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, herbicide resistance, Lolium, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, RNA-Seq, transcriptome sequencing
Abstract

International audience; Non-target-site-resistance (NTSR) to herbicides is a major cause for failure in the chemical control of a number of weeds, and is especially widespread and important in grass weeds. Although several gene families have been shown to be involved in NTSR (cytochromes p450, glutathione-S-transferases, glycosyl-transferases, ABC transporters, esterases…), the genetic determinants of NTSR are still poorly known to date. NTSR is part of the response of weeds to herbicides. To unravel NTSR, it is thus of interest to firstly characterise the processes involved in herbicide stress response in grasses. For this purpose, we implemented a comparative whole-transcriptome sequencing (RNA-seq) of resistant and sensitive plants of Lolium sp. before and after the application of an herbicide inhibiting ALS. The expression of transcripts encoding a total of 81,663 potential peptides was monitored over a time-course experiment ranging from before herbicide application to 48 hours after herbicide application. Comparison among experimental modalities allowed to identify Gene Ontology biological processes and molecular functions with a potential role in herbicide response and in NTSR. The role of the main gene families known to be involved in herbicide detoxification was confirmed in this study. We identified additional processes regulated by the herbicide application (e.g., transcripts involved in plant defence, in drug response, in the regulation of gene expression, in the branched amino-acid biosynthesis pathway, in photosynthesis or in excretion transport). Several transcripts with an expression pattern differentiating herbicide-resistant and herbicide-sensitive plants were also identified that are candidates of interest for NTSR diagnosis purposes.

Published
2014

8. Transcriptome screening-based identification of candidate genes endowing non-target-site-based resistance to herbicides inhibiting ALS in Lolium sp

Author

Duhoux, Arnaud, Gouzy, Jerome, Carrere, Sebastien, Délye, Christophe, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and European Weed Research Society (EWRS). GBR.

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2013

9. Alopecurus myosuroides transcriptome database (ALOMYBase): unravelling the genetic bases of non-target-site-based resistance to herbicides

Author

Gardin, Jeanne, Gouzy, Jerome, Carrere, Sebastien, Beffa, Roland, Delye, Christophe, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Bayer Pharma AG [Berlin], and European Weed Research Society (EWRS). GBR.

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2013

10. Génomique comparative dans le genre Xenorhabdus : l'espèce X. Poinarii caractérisée par un pouvoir pathogène atténué et un génome de petite taille

Author

Ogier, Jean-Claude, Pages, Sylvie, Tailliez, Patrick, Bisch, Gaëlle, Teyssier, Corinne, Carrere, Sebastien, Medigue, Claudine, Rouy, Zoé, Givaudan, Alain, Gaudriault, Sophie, Diversité, Génomes et Interactions Microorganismes-Insectes, Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Ecologie des systèmes marins côtiers (Ecosym), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2012

11. Genomic resources for functional analysis in Medicago truncatula and related crop species

Author

Debellé, Frederic, Belser, C., Aury, J.M., Labadie, K., Roux, Brice, Sallet, Erika, Carrere, Sebastien, Wincker, P., Schiex, Thomas, Julier, Bernadette, Gamas, Pascal, Gouzy, Jerome, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), International Crops Research Institute for the Semi-Arid Tropics, CGIAR (ICRISAT). Patancheru, IND., Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA)

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2012

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