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110 results on '"Carrere, Sebastien"'

6. 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, Carrère, Sébastien, Gouzy, Jérôme, Legrand, Ludovic, Mayjonade, Baptiste, Pouilly, Nicolas, André, Thierry, Coque, Marie, Piquemal, Joël, Laporte, Marion, Vincourt, Patrick, Muños, Stéphane, and Langlade, Nicolas B.

Subjects
Quantitative Biology - Genomics
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., Comment: 12 pages, 5 figures, Plant, Cell and Environment

Published
2017
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10. A metabolic crosstalk between liposarcoma and muscle sustains tumor growth.

Author

Manteaux, Gabrielle, Amsel, Alix, Riquier-Morcant, Blanche, Prieto Romero, Jaime, Gayte, Laurie, Fourneaux, Benjamin, Larroque, Marion, Gruel, Nadège, Quignot, Chloé, Perot, Gaelle, Jacq, Solenn, Cisse, Madi Y., Pomiès, Pascal, Sengenes, Coralie, Chibon, Frédéric, Heuillet, Maud, Bellvert, Floriant, Watson, Sarah, Carrere, Sebastien, and Firmin, Nelly

Subjects
MUSCLE tumors, TUMOR growth, LIPOSARCOMA, MUSCLE cells, CELL survival
Abstract

Dedifferentiated and Well-differentiated liposarcoma are characterized by a systematic amplification of the Murine Double Minute 2 (MDM2) oncogene. We demonstrate that p53-independent metabolic functions of chromatin-bound MDM2 are exacerbated in liposarcoma and mediate an addiction to serine metabolism to sustain tumor growth. However, the origin of exogenous serine remains unclear. Here, we show that elevated serine levels in mice harboring liposarcoma-patient derived xenograft, released by distant muscle is essential for liposarcoma cell survival. Repressing interleukine-6 expression, or treating liposarcoma cells with Food and Drugs Administration (FDA) approved anti-interleukine-6 monoclonal antibody, decreases de novo serine synthesis in muscle, impairs proliferation, and increases cell death in vitro and in vivo. This work reveals a metabolic crosstalk between muscle and liposarcoma tumor and identifies anti-interleukine-6 as a plausible treatment for liposarcoma patients. During tumorigenesis, liposarcoma has been reported to develop a dependence on serine metabolism but it is unclear how this high energetic demand is met. Here, the authors identify a crosstalk mechanism between tumor and distant muscle cells wherein liposarcoma cell-derived IL-6 drives muscle cell release of serine, in turn accelerating tumor growth. [ABSTRACT FROM AUTHOR]

Published
2024
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11. NBTXR3, a first-in-class radioenhancer hafnium oxide nanoparticle, plus radiotherapy versus radiotherapy alone in patients with locally advanced soft-tissue sarcoma (Act.In.Sarc): a multicentre, phase 2–3, randomised, controlled trial

Author

Bonvalot, Sylvie, Rutkowski, Piotr L, Thariat, Juliette, Carrère, Sébastien, Ducassou, Anne, Sunyach, Marie-Pierre, Agoston, Peter, Hong, Angela, Mervoyer, Augustin, Rastrelli, Marco, Moreno, Victor, Li, Rubi K, Tiangco, Béatrice, Herraez, Antonio Casado, Gronchi, Alessandro, Mangel, László, Sy-Ortin, Teresa, Hohenberger, Peter, de Baère, Thierry, Le Cesne, Axel, Helfre, Sylvie, Saada-Bouzid, Esma, Borkowska, Aneta, Anghel, Rodica, Co, Ann, Gebhart, Michael, Kantor, Guy, Montero, Angel, Loong, Herbert H, Vergés, Ramona, Lapeire, Lore, Dema, Sorin, Kacso, Gabriel, Austen, Lyn, Moureau-Zabotto, Laurence, Servois, Vincent, Wardelmann, Eva, Terrier, Philippe, Lazar, Alexander J, Bovée, Judith V M G, Le Péchoux, Cécile, and Papai, Zsusanna

Published
2019
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13. A fully sequenced collection of homozygous EMS mutants for forward and reverse genetic screens inArabidopsis thaliana

Author

Carrere, Sebastien, primary, Routaboul, Jean-Marc, additional, Savourat, Pauline, additional, Bellenot, Caroline, additional, Lopez, Hernan, additional, Quiroz-Monnens, Thomas, additional, Ricou, Anthony, additional, Camilleri, Christine, additional, Laufs, Patrick, additional, mercier, raphael, additional, and Noel, Laurent D, additional

Published
2023
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15. Prognostic factors and outcomes of adult spermatic cord sarcoma. A study from the French Sarcoma Group

Author

Achard, Gilles, primary, Charon-Barra, Céline, additional, Carrere, Sebastien, additional, Bonvalot, Sylvie, additional, Meeus, Pierre, additional, Fau, Magali, additional, Honoré, Charles, additional, Delhorme, Jean-Baptiste, additional, Tzanis, Dimitri, additional, Le Loarer, François, additional, Karanian-Philippe, Marie, additional, Ngo, Carine, additional, Le Guellec, Sophie, additional, Bertaut, Aurélie, additional, Causeret, Sylvain, additional, and Isambert, Nicolas, additional

Published
2023
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16. Stereotactic MR-Guided Adaptive Radiotherapy for Pancreatic Tumors: Updated Results of the Montpellier Prospective Registry Study

Author

Bordeau, Karl, primary, Michalet, Morgan, additional, Keskes, Aïcha, additional, Valdenaire, Simon, additional, Debuire, Pierre, additional, Cantaloube, Marie, additional, Cabaillé, Morgane, additional, Portales, Fabienne, additional, Draghici, Roxana, additional, Ychou, Marc, additional, Assenat, Eric, additional, Mazard, Thibault, additional, Samalin, Emmanuelle, additional, Gauthier, Ludovic, additional, Colombo, Pierre-Emmanuel, additional, Carrere, Sebastien, additional, Souche, François-Régis, additional, Aillères, Norbert, additional, Fenoglietto, Pascal, additional, Azria, David, additional, and Riou, Olivier, additional

Published
2022
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19. The genomics of linkage drag in sunflower

Author

Huang, Kaichi, primary, Jahani, Mojtaba, additional, Gouzy, Jérôme, additional, Legendre, Alexandra, additional, Carrere, Sebastien, additional, Lázaro-Guevara, José Miguel, additional, González Segovia, Eric Gerardo, additional, Todesco, Marco, additional, Mayjonade, Baptiste, additional, Rodde, Nathalie, additional, Cauet, Stéphane, additional, Dufau, Isabelle, additional, Staton, S Evan, additional, Pouilly, Nicolas, additional, Boniface, Marie-Claude, additional, Tapy, Camille, additional, Mangin, Brigitte, additional, Duhnen, Alexandra, additional, Gautier, Véronique, additional, Poncet, Charles, additional, Donnadieu, Cécile, additional, Mandel, Tali, additional, Hübner, Sariel, additional, Burke, John M., additional, Vautrin, Sonia, additional, Bellec, Arnaud, additional, Owens, Gregory L., additional, Langlade, Nicolas, additional, Muños, Stéphane, additional, and Rieseberg, Loren H., additional

Published
2022
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20. The middle class in Argentina: Dynamics, characteristics and implications for public policies

Author

Carrere, Sebastien, Mathieu, Clement, Combarnous, Francois, Kessker, Gabriel, Rougier, Eric, Wilkis, Ariel, and Admin, Oskar

Subjects
Classes moyennes, politique publiques, mobilité sociale, [QFIN] Quantitative Finance [q-fin]
Abstract

L'Argentine est généralement considérée comme le pays typique de la classe moyenne en Amérique latine. Pourtant, si les crises successives qui ont frappé l'économie argentine au cours des quatre dernières décennies ont manifestement affecté à la fois la taille et la stabilité de sa classe moyenne, les études universitaires manquent quant aux conséquences de ces crises sur la stratification socio-économique et sur les préférences et les attentes de la classe moyenne. Le présent article comble cette lacune en se concentrant sur la période la plus récente. Pour ce faire, nous adoptons un plan de recherche original basé sur une combinaison d'enquêtes quantitatives, fondées sur des enquêtes auprès des ménages existantes et des matériaux qualitatifs originaux, qui vise à : (1) identifier la classe moyenne argentine et sa structure, ainsi que de décrire sa dynamique ; (2) examiner le comportement et les perceptions subjectives du groupe, ainsi que ses attentes en termes de politiques publiques ; et (3) évaluer dans quelle mesure la conception des politiques publiques et des stratégies du marché privé est influencée par la composition et la dynamique de la classe moyenne argentine. Premièrement, notre analyse montre que la tendance à la mobilité ascendante qui a été dominante jusqu'en 2007 et a conduit à l'expansion d'une nouvelle classe moyenne (inférieure) argentine s'est progressivement ralentie et même inversée après 2014. Deuxièmement, la mise en oeuvre d'une analyse en cluster nous a conduit à identifier cinq groupes distincts au sein de la classe moyenne argentine, confirmant ainsi son hétérogénéité.Troisièmement, l'enquête qualitative menée auprès de 40 individus issus de ménages de la classe moyenne à Buenos Aires et Tucuman fournit des comptes rendus détaillés des perceptions et attentes subjectives des différents segments de la classe moyenne argentine. Quatrièmement, notre analyse confirme que la classe moyenne argentine est hétérogène en termes d'orientations politiques. Enfin, une enquête institutionnelle qualitative menée auprès de 12 représentants d'institutions publiques et privées met en évidence la mise en oeuvre récente de programmes publics ou privés spécifiquement dédiés aux ménages de la classe moyenne.

Published
2022

21. Stereotactic MR-Guided Radiotherapy for Pancreatic Tumors: Dosimetric Benefit of Adaptation and First Clinical Results in a Prospective Registry Study

Author

Michalet, Morgan, primary, Bordeau, Karl, additional, Cantaloube, Marie, additional, Valdenaire, Simon, additional, Debuire, Pierre, additional, Simeon, Sebastien, additional, Portales, Fabienne, additional, Draghici, Roxana, additional, Ychou, Marc, additional, Assenat, Eric, additional, Dupuy, Marie, additional, Gourgou, Sophie, additional, Colombo, Pierre-Emmanuel, additional, Carrere, Sebastien, additional, Souche, François-Regis, additional, Aillères, Norbert, additional, Fenoglietto, Pascal, additional, Azria, David, additional, and Riou, Olivier, additional

Published
2022
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22. Symbiotic Nodule Development and Efficiency in the Medicago truncatula Mtefd-1 Mutant Is Highly Dependent on Sinorhizobium Strains.

Author

Jardinaud, Marie-Françoise, Carrere, Sebastien, Gourion, Benjamin, and Gamas, Pascal

Subjects
*MEDICAGO truncatula, *NITROGEN fixation, *NITROGEN fertilizers, *PLANT genes, *TRANSCRIPTION factors, *RHIZOBIUM
Abstract

Symbiotic nitrogen fixation (SNF) can play a key role in agroecosystems to reduce the negative impact of nitrogen fertilizers. Its efficiency is strongly affected by the combination of bacterial and plant genotypes, but the mechanisms responsible for the differences in the efficiency of rhizobium strains are not well documented. In Medicago truncatula , SNF has been mostly studied using model systems, such as M. truncatula A17 in interaction with Sinorhizobium meliloti Sm2011. Here we analyzed both the wild-type (wt) A17 and the Mtefd-1 mutant in interaction with five S. meliloti and two Sinorhizobium medicae strains. ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes a transcription factor, which contributes to the control of nodule number and differentiation in M. truncatula. We found that, in contrast to Sm2011, four strains induce functional (Fix+) nodules in Mtefd-1 , although less efficient for SNF than in wt A17. In contrast, the Mtefd-1 hypernodulation phenotype is not strain-dependent. We compared the plant nodule transcriptomes in response to SmBL225C, a highly efficient strain with A17, versus Sm2011, in wt and Mtefd-1 backgrounds. This revealed faster nodule development with SmBL225C and early nodule senescence with Sm2011. These RNA sequencing analyses allowed us to identify candidate plant factors that could drive the differential nodule phenotype. In conclusion, this work shows the value of having a set of rhizobium strains to fully evaluate the biological importance of a plant symbiotic gene. [ABSTRACT FROM AUTHOR]

Published
2023
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23. Stereotactic MR-Guided Adaptive Radiotherapy for Pancreatic Tumors: Updated Results of the Montpellier Prospective Registry Study.

Author

Bordeau, Karl, Michalet, Morgan, Keskes, Aïcha, Valdenaire, Simon, Debuire, Pierre, Cantaloube, Marie, Cabaillé, Morgane, Portales, Fabienne, Draghici, Roxana, Ychou, Marc, Assenat, Eric, Mazard, Thibault, Samalin, Emmanuelle, Gauthier, Ludovic, Colombo, Pierre-Emmanuel, Carrere, Sebastien, Souche, François-Régis, Aillères, Norbert, Fenoglietto, Pascal, and Azria, David

Subjects
PANCREATIC tumors, CONFIDENCE intervals, CANCER chemotherapy, MAGNETIC resonance imaging, TREATMENT effectiveness, RADIOSURGERY, LONGITUDINAL method, DISEASE management, RADIATION dosimetry
Abstract

Simple Summary: While the role of radiation therapy in the management of pancreatic tumors remains controversial, new technological modalities allow for safer and more effective radiotherapy treatments. Stereotactic MR-guided Adaptive RadioTherapy (SMART) is an attractive treatment for pancreatic tumors, taking advantage of this challenging tumor location from the continuous image guidance and target tracking, as well as the daily adaptive process. We report in this prospective registry study the largest series of pancreatic SMART to date. Our study confirms the interest of this technique with a high therapeutic index since it is very well tolerated and gives encouraging results in our selected population. Pancreatic SMART could contribute to the improvement of the management of pancreatic adenocarcinoma, whose prognosis remains poor. Its exact place remains to be confirmed in further studies. Introduction: Stereotactic MR-guided Adaptive RadioTherapy (SMART) is a novel process to treat pancreatic tumors. We present an update of the data from our prospective registry of SMART for pancreatic tumors. Materials and methods: After the establishment of the SMART indication in a multidisciplinary board, we included all patients treated for pancreatic tumors. Primary endpoints were acute and late toxicities. Secondary endpoints were survival outcomes (local control, overall survival, distant metastasis free survival) and dosimetric advantages of adaptive process on targets volumes and OAR. Results: We included seventy consecutive patients in our cohort between October 2019 and April 2022. The prescribed dose was 50 Gy in 5 consecutive fractions. No severe acute SMART related toxicity was noted. Acute and late Grade ≤ 2 gastro intestinal were low. Daily adaptation significantly improved PTV and GTV coverage as well as OAR sparing. With a median follow-up of 10.8 months since SMART completion, the median OS, 6-months OS, and 1-year OS were 20.9 months, 86.7% (95% CI: (75–93%), and 68.6% (95% CI: (53–80%), respectively, from SMART completion. Local control at 6 months, 1 year, and 2 years were, respectively, 96.8 % (95% CI: 88–99%), 86.5 (95% CI: 68–95%), and 80.7% (95% CI: 59–92%). There was no grade > 2 late toxicities. Locally Advanced Pancreatic Cancers (LAPC) and Borderline Resectable Pancreatic Cancers (BRPC) patients (52 patients) had a median OS, 6-months OS, and 1-year OS from SMART completion of 15.2 months, 84.4% (95% CI: (70–92%)), and 60.5% (95% CI: (42–75%)), respectively. The median OS, 1-year OS, and 2-year OS from initiation of induction chemotherapy were 22.3 months, 91% (95% CI: (78–97%)), and 45.8% (95% CI: (27–63%)), respectively. Twenty patients underwent surgical resection (38.7 % of patients with initially LAPC) with negative margins (R0). Conclusion: To our knowledge, this is the largest series of SMART for pancreatic tumors. The treatment was well tolerated with only low-grade toxicities. Long-term OS and LC rates were achieved. SMART achieved high secondary resection rates in LAPC patients. [ABSTRACT FROM AUTHOR]

Published
2023
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26. GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5′ and 3′ ends of its target genes

Author

Ruggieri, Valentino, Alexiou, Konstantinos, Morata, Jordi, Argyris, Jason, Pujol, Marta, Yano, Ryoichi, Nonaka, Satoko, Ezura, Hiroshi, Cigliano, Riccardo Aiese, Sanseverino, Walter, Puigdomenech, Pere, Casacuberta, Josep, Kirienko, Anna, Porozov, Yuri, Malkov, Nikita, Akhtemova, Gulnara, Le Signor, Christine, Thompson, Richard, Saffray, Christine, Dalmais, Marion, Tikhonovich, Igor, Dolgikh, Elena, Boucheham, Anouar, Sommard, Vivien, Zehraoui, Farida, Batouche, Mohamed, Israeli, David, Tahi, Fariza, Jacob, Pierre, Avni, Adi, Ligerot, Yasmine, De Saint Germain, Alexandre, Waldie, Tanya, Kadakia, Nikita, Pillot, Jean-Paul, Prigge, Michael, Aubert, Gregoire, Leyser, Ottoline, Estelle, Mark, Debellé, Frederic, Rameau, Catherine, GOUZY, Jerome, Badouin, Hélène, Lemainque, Arnaud, Vergne, Philippe, Moja, Sandrine, Choisne, Nathalie, Pont, Caroline, Carrere, Sebastien, Caissard, Jean-Claude, Couloux, Arnaud, Cottret, Ludovic, Aury, Jean-Marc, Szécsi, Judit, Madoui, Mohammed-Amin, Yang, Shu-Hua, Piola, Florence, Larrieu, Antoine, Perez, Magali, Labadie, Karine, Perrier, Lauriane, govetto, Benjamin, LABROUSSE, Yoan, Villand, Priscilla, Bardoux, Claudia, Boltz, Véronique, Lopez-Roques, Celine, Heitzler, Pascal, Vernoux, Teva, Quesneville, Hadi, Boualem, Adnane, Liu, Chang, Le Bris, Manuel, Salse, Jerome, Baudino, Sylvie, Wincker, Patrick, François, Léa, Verdenaud, Marion, Fu, Xiaopeng, Ruleman, Darcy, Dubois, Annick, Vandenbussche, Michiel, Raymond, Olivier, Just, Jérémy, Bendahmane, Mohammed, Giner, Ana, Pascual, Laura, Bourgeois, Michael, Gyetvai, Gabor, Rios, Pablo, Picó, Belén, Troadec, Christelle, Bendahmane, Abdel, Garcia-Mas, Jordi, MARTIN-HERNANDEZ, Ana Montserrat, Kim, Soonkap, Piquerez, Sophie, Ramirez-Prado, Juan, Mastorakis, Emmanouil, Veluchamy, Alaguraj, Latrasse, David, Manza-Mianza, Deborah, Brik-Chaouche, Rim, Huang, Ying, Rodriguez-Granados, Natalia, Concia, Lorenzo, Blein, Thomas, Citerne, Sylvie, Bendahmane, Abdelhafid, Bergounioux, Catherine, Crespi, Martin, Mahfouz, Magdy, Raynaud, Cécile, Hirt, Heribert, Ntoukakis, Vardis, BENHAMED, Moussa, Centre for Research in Agricultural Genomics (CRAG), IRTA, Center for Research in Agricultural Genomics, University of Tsukuba, Sequentia Biotech SL, LAboratoire PLasma et Conversion d'Energie (LAPLACE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, 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, Université Bourgogne Franche-Comté [COMUE] (UBFC)-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, 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), All-Russia Research Institute for Agricultural Microbiology, University Salah Boubnider Constantine 3, Laboratoire d'Informatique de Paris-Nord (LIPN), Université Sorbonne Paris Cité (USPC)-Institut Galilée-Université Paris 13 (UP13)-Centre National de la Recherche Scientifique (CNRS), LIRE laboratory, Constantine, University of Constantine, GENETHON 3, Université Paris Saclay (COmUE), Tel Aviv University [Tel Aviv], Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Sainsbury Laboratory, University of Cambridge [UK] (CAM), University of California [San Diego] (UC San Diego), University of California, Laboratoire de chimie organique et organométallique (LCOO), Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), Division of Biology [La Jolla], University of California-University of California, UMR 0441 INRA / CNRS : Laboratoire de Biologie moléculaire des relations plantes-microorganismes, Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), Unité de Recherche Génomique Info (URGI), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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)-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)-Université Paris-Saclay, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), GeT PlaGe, Genotoul, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sun Yat-Sen University [Guangzhou] (SYSU), Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Huazhong Agricultural University, Division of Biology [Pasadena], California Institute of Technology (CALTECH), Unité de recherche Génétique et amélioration des fruits et légumes (GAFL), Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universitat Politecnica de Valencia (UPV), Institute of Agrifood Research and Technology (IRTA), Institut de Recerca i Tecnologia Agroalimentaries, King Abdullah University of Science and Technology (KAUST), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Economics and Management [Beijing] (BUAA), Beihang University, Institut de biotechnologie des plantes (IBP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Warwick [Coventry], AgroParisTech, and ANR-18-CE20-0015,EPICLIPSE,Dynamique des marques épigénétiques dans les cellules hôtes infectées et subversion de l'épigénome par le pathogène.(2018)

Subjects
0106 biological sciences, Transcription, Genetic, AcademicSubjects/SCI00010, [SDV]Life Sciences [q-bio], Arabidopsis, Biology, Genes, Plant, 01 natural sciences, Histones, 03 medical and health sciences, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Homeostasis, Plant Immunity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Epigenetics, Promoter Regions, Genetic, QH426, ComputingMilieux_MISCELLANEOUS, Histone Acetyltransferases, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Arabidopsis Proteins, Lysine, Gene regulation, Chromatin and Epigenetics, Acetylation, Biotic stress, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Cell biology, Chromatin, enzymes and coenzymes (carbohydrates), Histone, Acetyltransferase, Transcription Coactivator, biology.protein, 5' Untranslated Regions, Salicylic Acid, 010606 plant biology & botany
Abstract

The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions.

Published
2020
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27. Genomic structure and phylogeny of the plant pathogen Ralstonia solanacearum inferred from gene distribution analysis

Author

Guidot, Alice, Prior, Philippe, Schoenfeld, Jens, Carrere, Sebastien, Genin, Stephane, and Boucher, Christian

Subjects
Genomes -- Structure, Genomes -- Research, Phylogeny (Botany) -- Research, Bacteria, Phytopathogenic -- Research, Biological sciences
Abstract

In the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic [beta]-proteobacterium Ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. Based on the use of comparative genomic hybridization on a pangenomic microarray for the GMI1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representative of the biodiversity of the R. solanacearum species. This identified a list of 2,690 core genes present in all tested strains. As a corollary, a list of 2,338 variable genes within the R. solanacearum species has been defined. The hierarchical clustering based on the distribution of variable genes is fully consistent with the phylotype classification that was previously defined from the nucleotide sequence analysis of four genes. The presence of numerous pathogenicity-related genes in the core genome indicates that R. solanacearum is an ancestral pathogen. The results establish the long coevolution of the two replicons that constitute the bacterial genome. We also demonstrate the clustering of variable genes in genomic islands. Most genomic islands are included in regions with an alternative codon usage, suggesting that they originate from acquisition of foreign genes through lateral gene transfers. Other genomic islands correspond to genes that have the same base composition as core genes, suggesting that they either might be ancestral genes lost by deletion in certain strains or might originate from horizontal gene transfers.

Published
2007

29. Genome sequence of the cluster root forming white lupin;

Author

Hufnagel, Barbara, Marques, André, Soriano, Alexandre, Marquès, Laurence, Divol, Fanchon, Doumas, Patrick, Sallet, Erika, Mancinotti, Davide, Carrere, Sebastien, Marande, William, Arribat, Sandrine, Keller, Jean, Huneau, Cecile, Blein, Thomas, Aime, Delphine, Laguerre, Malika, Taylor, Jemma, Schubert, Veit, Nelson, Matthew, Geu-Flores, Fernando, Crespi, Martin, Gallardo-Guerrero, Karine, Delaux, Pierre-Marc, Salse, Jerome, Berges, Helene, Guyot, Romain, Gouzy, Jerome, and PERET, Benjamin

Subjects
Vegetal Biology, lupinus albus, absorption azotée, aliment sans gluten, racine laterale, Biologie végétale, nutrition protéique
Abstract

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch)1–5. White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi6. Nevertheless, its root system is well adapted to poor soils: it produces cluster roots, constituted of dozens of determinate lateral roots that improve soil exploration and phosphate remobilization7. As phosphate is a limited resource that comes from rock reserves8, the production of cluster roots is a trait of interest to improve fertilizers efficiency. Using long reads sequencing technologies, we provide a high-quality genome sequence of a modern variety of white lupin (2n=50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe how domestication impacted soil exploration capacity through the early establishment of lateral and cluster roots. We identify the APETALA2 transcription factor LaPUCHI-1, homolog of the Arabidopsis morphogenesis coordinator9, as a potential regulator of this trait. Our high-quality genome and companion genomic and transcriptomic resources enable the development of modern breeding strategies to increase and stabilize yield and to develop new varieties with reduced allergenic properties (caused by conglutins10), which would favor the deployment of this promising culture.

Published
2019

30. Transcriptome database resource and gene expression atlas for the rose

Author

Dubois Annick, Carrere Sebastien, Raymond Olivier, Pouvreau Benjamin, Cottret Ludovic, Roccia Aymeric, Onesto Jean-Paul, Sakr Soulaiman, Atanassova Rossitza, Baudino Sylvie, Foucher Fabrice, Bris Manuel, Gouzy Jérôme, and Bendahmane Mohammed

Subjects
Rose, Transcriptome, Gene expression atlas, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. Results Here, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways. Conclusions The study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.

Published
2012
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33. Pathobiome entomopathogenic nematodes Development of methodology for a taxonomic assignation at the species level in the the pathobiome of entomopathogenic nematodes from the Steinernema genus

Author

Ogier, Jean-Claude, Gaudriault, Sophie, Heuillard, Pauline, Zemb, Olivier, Carrere, Sebastien, Galan, Maxime, Barret, Matthieu, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), 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], Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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)-Université Toulouse III - Paul Sabatier (UT3), 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, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] ( DGIMI ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ), Institut National de la Recherche Agronomique ( INRA ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Interactions plantes-microorganismes et santé végétale, Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Recherche Agronomique ( INRA ), Centre de Biologie pour la Gestion des Populations ( CBGP ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, 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-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), 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), AGROCAMPUS OUEST, and 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)

Subjects
[ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, taxonomy, amplification d'adn, activité intestinale, sol, microbiote, taxonomie, interaction microorganisme insecte, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, steinernema, écologie des populations, soil, nématode
Abstract

Pathobiome entomopathogenic nematodes Development of methodology for a taxonomic assignation at the species level in the the pathobiome of entomopathogenic nematodes from the [i]Steinernema[/i] genus . 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens)

Published
2017

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

Author

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, Mangin, Brigitte, and Langlade, Nicolas

Subjects
stress abiotique, Vegetal Biology, plasticité, fungi, food and beverages, cold, crop model, drought, genetic variation, multi-stress, Biologie végétale, contrôle génétique, huile végétale, huile de tournesol
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.

Published
2017

36. Partial chromosome sequence of Spiroplasma citri reveals extensive viral invasion and important gene decay

Author

Carle, Patricia, Saillard, Colette, Carrere, Nathalie, Carrere, Sebastien, Duret, Sybille, Eveillard, Sandrine, Gaurivaud, Patrice, Gourgues, Geraldine, Gouzy, Jerome, Salar, Pascal, Verdin, Eric, Breton, Marc, Blanchard, Alain, Laigret, Frederic, Bove, Joseph-Marie, Renaudin, Joel, and Foissac, Xavier

Subjects
Spiroplasma -- Genetic aspects, Spiroplasma -- Physiological aspects, Chromosomes -- Research, Nucleotide sequence -- Research, Biological sciences
Abstract

The partial chromosome sequence of Spiroplasma citri strain GII3-3X and the functional assignment of the predicted coding sequences is reported. The overall gene conservation in the S. citri genome is more related to the phylogenetic origin than to the ecological niche, hence spiroplasmas and phytoplasmas have rather divergent genome information, despite sharing a similar biological cycle between plants and insects.

Published
2010

38. Identification de gènes liés à la résistance aux herbicides non liée à la cible chez les Ivraies : vers des tests « moléculaires » de diagnostic

Author

Délye, Christophe, Duhoux, Arnaud, Carrere, Sebastien, Bonin, Ludovic, 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, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), ARVALIS - Institut du végétal [Paris], Association Française de Protection des Plantes (AFPP). FRA., 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-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), ProdInra, Archive Ouverte, 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-Université Bourgogne Franche-Comté ( UBFC ), 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 ), and ARVALIS - Institut du Végétal

Subjects
[SDV] Life Sciences [q-bio], PCR, [ SDV ] Life Sciences [q-bio], rye-grass, [SDV]Life Sciences [q-bio], detection, ivraie, ALS, non-target-site-based resistance, résistance non liée à la cible
Abstract

Identification of genes linked to non-target-site resistance to herbicides in ryegrass : towards "molecular" diagnosis assays. Setting up molecular diagnosis tools would greatly foster preventing and managing non-target-sitebased resistance to herbicides (NTSR). This is currently hampered by the complexity of NTSR genetic determinism, which is largely based upon differences in the expression of an unknown number of genes between resistant and sensitive plants. Identifying NTSR genes is thus a challenging task. Herein, we report the identification of 19 genes which expression patterns are correlated to NTSR to ALS-inhibiting herbicides in rye-grasses (Lolium sp.). We demonstrate the potential of using combined expression data from several of these genes to predict NTSR, Le développement de tests moléculaires de détection serait un grand pas en avant dans la prévention et la gestion de la résistance non liée à la cible (RNLC). Les déterminismes génétiques de la RNLC sont cependant complexes, et font largement appel à des différences d’expression d’un nombre inconnu de gènes entre plantes résistantes et plantes sensibles. Leur identification est donc ardue. Dans ce travail, nous décrivons l’identification de 19 gènes dont les profils d’expression sont corrélés à la RNLC à des herbicides inhibiteurs de l’ALS chez les Ivraies (Lolium sp.), et nous montrons le potentiel de l’utilisation des données d’expression combinées de plusieurs de ces gènes pour la prédiction de la RNLC.

Published
2016

39. 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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40. Robotic Versus Laparoscopic Total Mesorectal Excision (TME) for Sphincter-Saving Surgery: Is There Any Difference in the Transanal TME Rectal Approach?

Author

Colombo, Pierre-Emmanuel, Bertrand, Martin, Alline, Mathias, Boulay, Eric, Mourregot, Anne, Carrere, Sebastien, Quenet, François, Jarlier, Marta, Rouanet, Philippe, Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Université de Montpellier (UM), and Unité de biostatistiques

Subjects
[SDV.CAN]Life Sciences [q-bio]/Cancer, sense organs, [SDV.MHEP.CHI]Life Sciences [q-bio]/Human health and pathology/Surgery
Abstract

International audience; BACKGROUND:Robotic total mesorectal excision (R-TME), a novel way for minimally invasive treatment of rectal cancer, was shown in previous studies to be safe and effective. However, comparison with laparoscopic total mesorectal excision (L-TME) has drawn contradictory disputes, especially concerning operative high-risk patients. The aim of this study was to compare R-TME and L-TME on the rectal technical approach.METHODS:Between October 2009 and March 2013, a total of 120 consecutive rectal carcinomas, operated for sphincter-saving procedure, were enrolled. The patient population included the last 60 laparoscopic procedures and the first 60 robotic surgeries (six hybrid approaches, then 54 full robotic surgeries). There were no exclusions.RESULTS:Patients' baseline characteristics were similar in both the R-TME and L-TME groups. Outcomes were equivalent for blood loss (200 vs. 100 mL), postoperative hospital stay (12 vs. 11 days), conversion rate (3.2 vs. 4.8 %), lymph nodes yield (15 vs. 19), no positive distal margin (0 %), positive radial margin (6.4 vs. 9.3 %), diverting ileostomy (73 vs. 58 %) and severe morbidity (28 vs. 20 %). Significant differences were found for median operative time (274 vs. 228 min; p = 0.003) and proctectomy performed via transanal approach (1.7 vs. 16.7 %; p = 0.004). The R-TME operative time curve stabilized to 245 min after the first 25 procedures.CONCLUSIONS:For rectal cancer, R-TME may be as feasible and safe as L-TME in terms of technique. In our practice and for difficult cases, R-TME allows complete rectal dissection by an abdominal approach, while L-TME requires a transanal approach.

Published
2016
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41. Transcriptome-based identification of the Sinorhizobium meliloti NodD1 regulon

Author

Capela, Delphine, Carrere, Sebastien, and Batut, Jacques

Subjects
Genetic transcription -- Research, Rhizobium meliloti -- Genetic aspects, Biological sciences
Abstract

The NodD1 regulon of Sinorhizobium meliloti was determined through the analysis of the S. meliloti transcriptome in response to the plant flavone luteolin and the overexpression of nodD1. The results demonstrate that NodD1 controls few functions behind nodulation in S. meliloti.

Published
2005

42. 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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43. Pea in the genomic era

Author

Burstin, Judith, Alves Carvalho, Susete, Aluome, Christelle, Tayeh, Nadim, Brochot, Anne-Lise, Carrere, Sebastien, Kreplak, Jonathan, Klein, Anthony, Lecomte, Christophe, Bourion, Virginie, Delaitre, Catherine, Falque, Matthieu, Cruaud, Corinne, Salloignon, Pauline, Truntzer, Caroline, Moreau, Sandra, Balzergue, Sandrine, Lejeune-Henaut, Isabelle, Gamas, Pascal, Gouzy, Jerome, Wincker, Patrick, Le Paslier, Marie-Christine, Brunel, Dominique, Aubert, Gregoire, Duc, Gérard, 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, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-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), Plate-forme Protéomique CLIPP - Clinical and Innovation Proteomic Platform [Dijon] (CLIPP), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut Charles Viollette (ICV) - EA 7394 (ICV), Université d'Artois (UA)-Institut National de la Recherche Agronomique (INRA)-Université du Littoral Côte d'Opale (ULCO)-Institut Supérieur d'Agriculture-Université de Lille, Etude du Polymorphisme des Génomes Végétaux (EPGV), and Institut National de la Recherche Agronomique (INRA)

Subjects
pois, [SDV]Life Sciences [q-bio], pea
Abstract

BAPPôle Geapsi; Pea in the genomic era. Séminaire IFR AIB (Agrobiosciences, Interactions & Biodiversité)

Published
2015

44. Pea in the genomic era

Author

Burstin , Judith, Alves Carvalho , Susete, Aluome , Christelle, Tayeh , Nadim, Brochot , Anne-Lise, Carrere , Sebastien, Kreplak , Jonathan, Klein , Anthony, Lecomte , Christophe, Bourion , Virginie, Delaitre , Catherine, Falque , Matthieu, Cruaud , Corinne, Salloignon , Pauline, Truntzer , Caroline, Moreau , Sandra, Aubourg-Balzergue , Sandrine, Lejeune-Henaut , Isabelle, Gamas , Pascal, Gouzy , Jerome, Wincker , Patrick, Le Paslier , Marie-Christine, Brunel , Dominique, Aubert , Gregoire, Duc , Gérard, 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, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique ( INRA ), 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 ), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Plate-forme Protéomique CLIPP - Clinical and Innovation Proteomic Platform [Dijon] ( CLIPP ), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies ( FEMTO-ST ), Université de Technologie de Belfort-Montbeliard ( UTBM ) -Ecole Nationale Supérieure de Mécanique et des Microtechniques ( ENSMM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ) -Université de Technologie de Belfort-Montbeliard ( UTBM ) -Ecole Nationale Supérieure de Mécanique et des Microtechniques ( ENSMM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ) -Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] ( ICMUB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Institut Charles Viollette (ICV) - EA 7394 ( ICV ), Université d'Artois ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -Université du Littoral Côte d'Opale ( ULCO ) -Institut Supérieur d'Agriculture-Université de Lille, and Etude du Polymorphisme des Génomes Végétaux ( EPGV )

Subjects
[ SDV ] Life Sciences [q-bio], pois, pea
Abstract

BAPPôle Geapsi; Pea in the genomic era. Séminaire IFR AIB (Agrobiosciences, Interactions & Biodiversité)

Published
2015

45. Making sense out of phytoviral metagenomics: what have we learned from the Kerguelen Islands phytovirome?

Author

Candresse, Thierry, Marais, Armelle, Theil, Sébastien, Faure, Chantal, Svanella-Dumas, Laurence, Carrere, Sebastien, Bergey, Bernard, Couture, Carole, Laizet, Yec'han, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Laboratoire des interactions plantes micro-organismes (LIPM), and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2015

46. 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

47. 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

48. Genome sequence of the [beta]-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia

Author

Amadou, Claire, Pascal, Geraldine, Mangenot, Sophie, Glew, Michelle, Bontemps, Cyril, Capela, Delphine, Carrere, Sebastien, Cruveiller, Stephane, Dossat, Carole, Lajus, Aurelie, Marchetti, Marta, Poinsot, Verena, Rouy, Zoe, Servin, Bertrand, Saad, Maged, Schenowitz, Chantal, Barbe, Valerie, Batut, Jacques, Medigue, Claudine, and Masson-Boivin, Catherine

Subjects
Cladistic analysis -- Usage, Genomics -- Research, Rhizobium -- Genetic aspects, Health
Abstract

Several analyses are conducted to explain the first complete genome sequence of the [beta]-rhizobium nitrogen-fixing symbiont of legumes, namely Cupriavidus taiwanensis LMG19424. The phylogenetic position of Cupriavidus taiwanensis proved to be extremely significant for the comparison of the genomics of all the available rhizobium genes.

Published
2008

50. Feasibility and impact on resectability of FOLFIRINOX in locally-advanced and borderline pancreatic cancer.

Author

Portales, Fabienne, primary, Gagniard, Benedicte, additional, Thezenas, Simon, additional, Samalin, Emmanuelle, additional, Assenat, Eric, additional, Alline, Matthias, additional, Colombo, Pierre-Emmanuel, additional, Rouanet, Philippe, additional, Carrere, Sebastien, additional, Quenet, François, additional, Riou, Olivier, additional, Llacer, Carmen, additional, Mazard, Thibault, additional, and Ychou, Marc, additional

Published
2016
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