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2. Projet INSPIR : Circuit inter-laboratoires du Réseau National INRAE NIRS

Author

Naudet-Huart, Myriam, Touratier, Michaël, Regulier, Jennifer, Desfontaines, Lucienne, Leinster, Jocelyne, Bureau, Sylvie, Serino, Sylvie, Gouble, Barbara, Lepoittevin, Camille, Alvarez, David, Gardet, Olivier, Barotin, Charlène, Dorlac, Alexis, Compan, Frédéric, Ecarnot, Martin, Segura, Vincent, Sotillo, Armelle, Singer, Mathilde, Chaix, Gilles, Crespin, Paul, Roger, Jean-Michel, Cornet, Denis, Zeller, Bernhar, Rossard, Virginie, Flutre, Timothée, Fievet, Julie, Enjalbert, Jérôme, Serre, Valentin, Breuil, Sébastien, Thoisy, Jeanne-Chantal, Habrant, Annouck, Gaudard, François, Rolland, Sophie, Ganier, Philippe, Perrin, Pierre, Lecloux, Eric, Levasseur, Cécile, Griveau, Yves, Dufayet, Valérie, Colombet, Céline, Naudet-Huart, Myriam, Touratier, Michaël, Regulier, Jennifer, Desfontaines, Lucienne, Leinster, Jocelyne, Bureau, Sylvie, Serino, Sylvie, Gouble, Barbara, Lepoittevin, Camille, Alvarez, David, Gardet, Olivier, Barotin, Charlène, Dorlac, Alexis, Compan, Frédéric, Ecarnot, Martin, Segura, Vincent, Sotillo, Armelle, Singer, Mathilde, Chaix, Gilles, Crespin, Paul, Roger, Jean-Michel, Cornet, Denis, Zeller, Bernhar, Rossard, Virginie, Flutre, Timothée, Fievet, Julie, Enjalbert, Jérôme, Serre, Valentin, Breuil, Sébastien, Thoisy, Jeanne-Chantal, Habrant, Annouck, Gaudard, François, Rolland, Sophie, Ganier, Philippe, Perrin, Pierre, Lecloux, Eric, Levasseur, Cécile, Griveau, Yves, Dufayet, Valérie, and Colombet, Céline

Abstract

Au sein d'INRAE, il existe le réseau national INRAE NIRS qui est en fait un groupe de compagnonnage entre 80 utilisateurs de la spectrométrie proche infra-rouge. Suite à une enquête réalisée en 2021 auprès de ses membres, il a été décidé de créer un circuit inter-laboratoires entre les 18 implantations INRAE volontaires totalisant initialement une trentaine de spectromètres proche-infrarouges. En effet, les données spectrales proche infra-rouges sont de plus en plus exploitées pour des caractérisations à haut-débit des échantillons car c'est une technique d'analyse physico-chimique, rapide et non destructive. Mais, pour chaque paramètre étudié, il est nécessaire de développer en amont un étalonnage entre la base spectrale et les valeurs de référence associées (via une calibration). Par conséquent, la qualité et la fiabilité des spectres sont indispensables. Début 2024, le projet multi-départements INSPIR, qui porte l'ambition de ce circuit inter-laboratoires, a été accepté. Il est prévu de faire circuler les mêmes échantillons de farines de blé tendre pour réaliser l'acquisition des spectres proche infrarouge au sein des différents sites et ainsi comparer : - les différentes méthodologies de prise de spectres (bonnes pratiques) - la qualité des spectres pris par les différents instruments (gamme de longueur d'onde, résolution et performances prédictives) - les instruments entre eux (appareils de labo et portatifs de terrain) Une base de données avec les spectres obtenus sur les différents appareils, les métadonnées associées et leur teneur respective en protéines (Kjeldahl) sera établie par notre stagiaire Master 2 Paul CRESPIN, puis publiée sous forme de Data paper et rendue disponible sur le Dataverse INRAE. Cette base de données pourra également être très utile pour standardiser les spectromètres entre eux et entre sites INRAE. Cette possibilité de standardisation permettra d'assurer l'interopérabilité mais aussi le suivi en cas de panne ou de renouvellement d'un

Published
2024

3. Enhancing grapevine breeding efficiency through genomic prediction and selection index

Author

Brault, Charlotte, primary, Segura, Vincent, additional, Roques, Maryline, additional, Lamblin, Pauline, additional, Bouckenooghe, Virginie, additional, Pouzalgues, Nathalie, additional, Cunty, Constance, additional, Breil, Matthieu, additional, Frouin, Marina, additional, Garcin, Léa, additional, Camps, Louise, additional, Ducasse, Marie-Agnès, additional, Romieu, Charles, additional, Masson, Gilles, additional, Julliard, Sébastien, additional, Flutre, Timothée, additional, and Le Cunff, Loïc, additional

Published
2024
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4. Clusters of grapevine genes for a burning world

Author

Coupel‐Ledru, Aude, primary, Westgeest, Adrianus J., additional, Albasha, Rami, additional, Millan, Mathilde, additional, Pallas, Benoît, additional, Doligez, Agnès, additional, Flutre, Timothée, additional, Segura, Vincent, additional, This, Patrice, additional, Torregrosa, Laurent, additional, Simonneau, Thierry, additional, and Pantin, Florent, additional

Published
2024
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5. A statistical framework for joint eQTL analysis in multiple tissues

Author

Flutre, Timothée, Wen, Xiaoquan, Pritchard, Jonathan, and Stephens, Matthew

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Genomics, Statistics - Applications
Abstract

Mapping expression Quantitative Trait Loci (eQTLs) represents a powerful and widely-adopted approach to identifying putative regulatory variants and linking them to specific genes. Up to now eQTL studies have been conducted in a relatively narrow range of tissues or cell types. However, understanding the biology of organismal phenotypes will involve understanding regulation in multiple tissues, and ongoing studies are collecting eQTL data in dozens of cell types. Here we present a statistical framework for powerfully detecting eQTLs in multiple tissues or cell types (or, more generally, multiple subgroups). The framework explicitly models the potential for each eQTL to be active in some tissues and inactive in others. By modeling the sharing of active eQTLs among tissues this framework increases power to detect eQTLs that are present in more than one tissue compared with "tissue-by-tissue" analyses that examine each tissue separately. Conversely, by modeling the inactivity of eQTLs in some tissues, the framework allows the proportion of eQTLs shared across different tissues to be formally estimated as parameters of a model, addressing the difficulties of accounting for incomplete power when comparing overlaps of eQTLs identified by tissue-by-tissue analyses. Applying our framework to re-analyze data from transformed B cells, T cells and fibroblasts we find that it substantially increases power compared with tissue-by-tissue analysis, identifying 63% more genes with eQTLs (at FDR=0.05). Further the results suggest that, in contrast to previous analyses of the same data, the majority of eQTLs detectable in these data are shared among all three tissues., Comment: Summitted to PLoS Genetics

Published
2012
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6. Blood ties: ABO is a trans-species polymorphism in primates

Author

Ségurel, Laure, Thompson, Emma E., Flutre, Timothée, Lovstad, Jessica, Venkat, Aarti, Margulis, Susan W., Moyse, Jill, Ross, Steve, Gamble, Kathryn, Sella, Guy, Ober, Carole, and Przeworski, Molly

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with a current consensus in support of convergent evolution. We show instead that genetic variation data in humans and gibbons as well as in Old World Monkeys are inconsistent with a model of convergent evolution and support the hypothesis of an ancient, multi-allelic polymorphism of which some alleles are shared by descent among species. These results demonstrate that the ABO polymorphism is a trans-species polymorphism among distantly related species and has remained under balancing selection for tens of millions of years, to date, the only such example in Hominoids and Old World Monkeys outside of the Major Histocompatibility Complex., Comment: 45 pages, 4 Figures, 4 Supplementary Figures, 5 Supplementary Tables

Published
2012
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8. Enhancing grapevine breeding efficiency through genomic prediction and selection index

Author

Brault, Charlotte, primary, Segura, Vincent, additional, Roques, Maryline, additional, Lamblin, Pauline, additional, Bouckenooghe, Virginie, additional, Pouzalgues, Nathalie, additional, Cunty, Constance, additional, Breil, Matthieu, additional, Frouin, Marina, additional, Garcin, Léa, additional, Camps, Louise, additional, Ducasse, Marie-Agnès, additional, Romieu, Charles, additional, Masson, Gilles, additional, Julliard, Sébastien, additional, Flutre, Timothée, additional, and Le Cunff, Loïc, additional

Published
2023
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10. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Author

Badouin, Hélène, Velt, Amandine, Gindraud, François, Flutre, Timothée, Dumas, Vincent, Vautrin, Sonia, Marande, William, Corbi, Jonathan, Sallet, Erika, Ganofsky, Jérémy, Santoni, Sylvain, Guyot, Dominique, Ricciardelli, Eugenia, Jepsen, Kristen, Käfer, Jos, Berges, Hélène, Duchêne, Eric, Picard, Franck, Hugueney, Philippe, Tavares, Raquel, Bacilieri, Roberto, Rustenholz, Camille, and Marais, Gabriel A. B.

Published
2020
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12. New insights towards breeding for mixed cropping of spring pea and barley to increase yield and yield stability

Author

Haug, Benedikt, Messmer, Monika, Enjalbert, Jérôme, Goldringer, Isabelle, Flutre, Timothée, Mary-Huard, Tristan, Hohmann, Pierre, Haug, Benedikt, Messmer, Monika, Enjalbert, Jérôme, Goldringer, Isabelle, Flutre, Timothée, Mary-Huard, Tristan, and Hohmann, Pierre

Abstract

Mixed cropping (MC) is a key strategy to harness agriculture for climate-change. Breeding adapted genotypes can unleash the full potential of MC, both in terms of yield potential and yield stability. To achieve this goal, concepts from both breeding and ecology have to be fused in order to develop a suitable methodology for breeding for MC. In order to advance the field of breeding for MC, we evaluated yield and trait data of pure stands (PS) and mixed stands (MS) of pea (P. sativum L.) and barley (H. vulgare L.) as a legume-cereal model system. Twenty-eight pea and seven barley lines, representing European breeding material, were grown in an incomplete factorial design at two organically managed sites across two years. The general mixing ability (GMA) of pea for total mixture yield was predominant as specific mixing ability (SMA) was absent, facilitating future breeding and seed marketing efforts. The most promising pea cultivar ‘Volt’ resulted in an average total mixture yield increase of 11% (+0.43 t/ha) in MC compared to the average, while the cultivar ’Florida’ led to a yield decrease of − 31% (−1.23 t/ha), highlighting the importance of the choice of the genotype in MS. The analysis of separated MS yields allowed to investigate the underlying mechanistic principles in genotypes’ contribution to MS yields and we revealed the major role of producer (Pr) effects in this context. The correlation between Pr effects and GMA revealed that GMA can be maximized by selecting for high Pr effects. Early vigor, onset of flowering, shoot biomass and stipule length were identified as key traits for indirect selection for high GMA in pea accounting for up to 17% of the identified variation in total mixture yield. PS yields were moderately correlated with mixture yields (r = 0.52, P = 0.013) and can serve as an additional selection criterion. Discrepancies between correlations with PS and MS yields can be exploited to identify unique MS traits that confer niche complementarity

Published
2023

13. Efficient Bayesian automatic calibration of a functional–structural wheat model using an adaptive design and a metamodelling approach.

Author

Blanc, Emmanuelle, Enjalbert, Jérôme, Flutre, Timothée, and Barbillon, Pierre

Subjects
OPTIMIZATION algorithms, CALIBRATION, BOTANISTS, GLOBAL optimization, GAUSSIAN processes
Abstract

Functional–structural plant models are increasingly being used by plant scientists to address a wide variety of questions. However, the calibration of these complex models is often challenging, mainly because of their high computational cost, and, as a result, error propagation is usually ignored. Here we applied an automatic method to the calibration of WALTer: a functional–structural wheat model that simulates the plasticity of tillering in response to competition for light. We used a Bayesian calibration method to jointly estimate the values of five parameters and quantify their uncertainty by fitting the model outputs to tillering dynamics data. We made recourse to Gaussian process metamodels in order to alleviate the computational cost of WALTer. These metamodels are built from an adaptive design that consists of successive runs of WALTer chosen by an efficient global optimization algorithm specifically adapted to this particular calibration task. The method presented here performed well on both synthetic and experimental data. It is an efficient approach for the calibration of WALTer and should be of interest for the calibration of other functional–structural plant models. [ABSTRACT FROM AUTHOR]

Published
2023
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14. The ecologically relevant genetics of plant–plant interactions

Author

Becker, Claude, primary, Berthomé, Richard, additional, Delavault, Philippe, additional, Flutre, Timothée, additional, Fréville, Hélène, additional, Gibot-Leclerc, Stéphanie, additional, Le Corre, Valérie, additional, Morel, Jean-Benoit, additional, Moutier, Nathalie, additional, Muños, Stéphane, additional, Richard-Molard, Céline, additional, Westwood, James, additional, Courty, Pierre-Emmanuel, additional, de Saint Germain, Alexandre, additional, Louarn, Gaëtan, additional, and Roux, Fabrice, additional

Published
2023
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17. Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality

Author

Nsibi, Mariem, Gouble, Barbara, Bureau, Sylvie, Flutre, Timothée, Sauvage, Christopher, Audergon, Jean-Marc, Regnard, Jean-Luc, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, multivariate modeling, Models, Genetic, accuracy, prunus armeniaca, Bayes Theorem, Genomics, prediction, QH426-470, Polymorphism, Single Nucleotide, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, genetic architecture, genomic, Plant Breeding, Genomic Prediction, Fruit, shared data resources, Genetics, Animals, genpred, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Selection, Genetic, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Genome, Plant
Abstract

International audience; Genomic selection (GS) is a breeding approach which exploits genome-wide information and whose unprecedented success has shaped several animal and plant breeding schemes through delivering their genetic progress. This is the first study assessing the potential of GS in apricot (Prunus armeniaca) to enhance postharvest fruit quality attributes. Genomic predictions were based on a F1 pseudo-testcross population, comprising 153 individuals with contrasting fruit quality traits. They were phenotyped for physical and biochemical fruit metrics in contrasting climatic conditions over two years. Prediction accuracy (PA) varied from 0.31 for glucose content with the Bayesian LASSO (BL) to 0.78 for ethylene production with RR-BLUP, which yielded the most accurate predictions in comparison to Bayesian models and only 10% out of 61,030 SNPs were sufficient to reach accurate predictions. Useful insights were provided on the genetic architectureof apricot fruit quality whose integration in prediction models improved their performance, notably for traits governed by major QTL. Furthermore, multivariate modeling yielded promising outcomes in terms of PA within training partitions partially phenotyped for target traits. This provides a useful framework for the implementation of indirect selection based on easy-to-measure traits. Thus, we highlighted the main levers to take into account for the implementation of GS for fruit quality in apricot, but also to improve the genetic gain in perennial species.

Published
2020

19. A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs

Author

Flutre, Timothée, primary, Le Cunff, Loïc, additional, Fodor, Agota, additional, Launay, Amandine, additional, Romieu, Charles, additional, Berger, Gilles, additional, Bertrand, Yves, additional, Terrier, Nancy, additional, Beccavin, Isabelle, additional, Bouckenooghe, Virginie, additional, Roques, Maryline, additional, Pinasseau, Lucie, additional, Verbaere, Arnaud, additional, Sommerer, Nicolas, additional, Cheynier, Véronique, additional, Bacilieri, Roberto, additional, Boursiquot, Jean-Michel, additional, Lacombe, Thierry, additional, Laucou, Valérie, additional, This, Patrice, additional, Péros, Jean-Pierre, additional, and Doligez, Agnès, additional

Published
2022
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20. A quantitative geneticist’ journey from grapevine vineyards to wheat mixtures

Author

Flutre, Timothée, Flutre, Timothée, and Combining innovation in vineyard management andgenetic diversity for a sustainable European viticulture - INNOVINE - - EC:FP7:KBBE2013-01-01 - 2016-12-31 - 311775 - VALID

Subjects
[SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, education
Published
2021

21. From cultivar mixtures to allelic mixtures: opposite effects of allelic richness between genotypes and genotype richness in wheat

Author

Montazeaud, Germain, primary, Flutre, Timothée, additional, Ballini, Elsa, additional, Morel, Jean‐Benoit, additional, David, Jacques, additional, Girodolle, Johanna, additional, Rocher, Aline, additional, Ducasse, Aurélie, additional, Violle, Cyrille, additional, Fort, Florian, additional, and Fréville, Hélène, additional

Published
2022
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23. Estimation des proportions variétales de grains de blé par SPIR et imagerie hyperspectrale

Author

Belny, Adrien, Ecarnot, Martin, Flutre, Timothée, AgroParisTech, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and INRAE

Subjects
[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, ComputingMilieux_MISCELLANEOUS, [CHIM.CHEM]Chemical Sciences/Cheminformatics
Abstract

National audience

Published
2021

26. Advances in Breeding for Mixed Cropping – Incomplete Factorials and the Producer/Associate Concept

Author

Haug, Benedikt, Messmer, Monika, Enjalbert, Jérôme, Goldringer, Isabelle, Forst, Emma, Flutre, Timothée, Mary-Huard, Tristan, Hohmann, Pierre, Haug, Benedikt, Messmer, Monika, Enjalbert, Jérôme, Goldringer, Isabelle, Forst, Emma, Flutre, Timothée, Mary-Huard, Tristan, and Hohmann, Pierre

Abstract

Mixed cropping has been suggested as a resource-efficient approach to meet high produce demands while maintaining biodiversity and minimizing environmental impact. Current breeding programs do not select for enhanced general mixing ability (GMA) and neglect biological interactions within species mixtures. Clear concepts and efficient experimental designs, adapted to breeding for mixed cropping and encoded into appropriate statistical models, are lacking. Thus, a model framework for GMA and SMA (specific mixing ability) was established. Results of a simulation study showed that an incomplete factorial design combines advantages of two commonly used full factorials, and enables to estimate GMA, SMA, and their variances in a resource-efficient way. This model was extended to the Producer (Pr) and Associate (As) concept to exploit additional information based on fraction yields. It was shown that the Pr/As concept allows to characterize genotypes for their contribution to total mixture yield, and, when relating to plant traits, allows to describe biological interaction functions (BIF) in a mixed crop. Incomplete factorial designs show the potential to drastically improve genetic gain by testing an increased number of genotypes using the same amount of resources. The Pr/As concept can further be employed to maximize GMA in an informed and efficient way. The BIF of a trait can be used to optimize species ratios at harvest as well as to extend our understanding of competitive and facilitative interactions in a mixed plant community. This study provides an integrative methodological framework to promote breeding for mixed cropping.

Published
2021

27. Breeding for mixed cropping – New concepts and statistical methodology

Author

Haug, Benedikt, Messmer, Monika, Forst, Emma, Mary-Huard, Tristan, Enjalbert, Jérôme, Goldringer, Isabelle, Flutre, Timothée, and Hohmann, Pierre

Subjects
Breeding, genetics and propagation, Cereals, pulses and oilseeds
Abstract

A contribution to an online conference in the framework of the EU H2020 project LIVESEED dealing with the producer-associate concept and key traits, as well as with statistical methods to analyze mixed-crop data.

Published
2020

28. Comparison of univariate and multivariate models for marker selection and genomic prediction

Author

Brault, Charlotte, Doligez, Agnes, Chiquet, Julien, Le Cunff, Loic, This, Patrice, Flutre, Timothée, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Français de la Vigne et du Vin (IFV), Géno-vigne® (UMT Géno-vigne®), Institut Français de la Vigne et du Vin (IFV)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Diversité, Adaptation et Amélioration de la Vigne [AGAP] (DAAV), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), and AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[STAT]Statistics [stat], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

29. WHEAMM: a functional-structural model to study plant growth and interactions with neighbors in wheat variety mixtures

Author

Gawinowski, Meije, Enjalbert, Jérôme, Cournède, Paul-Henry, Flutre, Timothée, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique pour la Complexité et les Systèmes (MICS), and CentraleSupélec-Université Paris-Saclay

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

30. Additional file 7 of The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Author

Badouin, Hélène, Velt, Amandine, Gindraud, François, Flutre, Timothée, Dumas, Vincent, Vautrin, Sonia, Marande, William, Corbi, Jonathan, Sallet, Erika, Ganofsky, Jérémy, Santoni, Sylvain, Guyot, Dominique, Ricciardelli, Eugenia, Jepsen, Kristen, Käfer, Jos, Berges, Hélène, Duchêne, Eric, Picard, Franck, Hugueney, Philippe, Tavares, Raquel, Bacilieri, Roberto, Rustenholz, Camille, and Marais, Gabriel A. B.

Abstract

Additional file 7. Review History.

Published
2020
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31. Additional file 1 of The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Author

Badouin, Hélène, Velt, Amandine, Gindraud, François, Flutre, Timothée, Dumas, Vincent, Vautrin, Sonia, Marande, William, Corbi, Jonathan, Sallet, Erika, Ganofsky, Jérémy, Santoni, Sylvain, Guyot, Dominique, Ricciardelli, Eugenia, Jepsen, Kristen, Käfer, Jos, Berges, Hélène, Duchêne, Eric, Picard, Franck, Hugueney, Philippe, Tavares, Raquel, Bacilieri, Roberto, Rustenholz, Camille, and Marais, Gabriel A. B.

Abstract

Additional file 1: Figures S1 to S9, Tables S1 to S12, Text S1.

Published
2020
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32. VviUCC1 Nucleotide Diversity, Linkage Disequilibrium and Association with Rachis Architecture Traits in Grapevine

Author

Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Tello, Javier, Torres-Pérez, Rafael, Flutre, Timothée, Grimplet, Jérôme, Ibáñez Marcos, Javier, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Tello, Javier, Torres-Pérez, Rafael, Flutre, Timothée, Grimplet, Jérôme, and Ibáñez Marcos, Javier

Abstract

Cluster compactness is a trait with high agronomic relevance, affecting crop yield and grape composition. Rachis architecture is a major component of cluster compactness determinism, and is a target trait toward the breeding of grapevine varieties less susceptible to pests and diseases. Although its genetic basis is scarcely understood, a preliminary result indicated a possible involvement of the VviUCC1 gene. The aim of this study was to characterize the VviUCC1 gene in grapevine and to test the association between the natural variation observed for a series of rachis architecture traits and the polymorphisms detected in the VviUCC1 sequence. This gene encodes an uclacyanin plant-specific cell-wall protein involved in fiber formation and/or lignification processes. A high nucleotide diversity in the VviUCC1 gene promoter and coding regions was observed, but no critical effects were predicted in the protein domains, indicating a high level of conservation of its function in the cultivated grapevine. After correcting statistical models for genetic stratification and linkage disequilibrium effects, marker-trait association results revealed a series of single nucleotide polymorphisms (SNPs) significantly associated with cluster compactness and rachis traits variation. Two of them (Y-984 and K-88) affected two common cis-transcriptional regulatory elements, suggesting an effect on phenotype via gene expression regulation. This work reinforces the interest of further studies aiming to reveal the functional effect of the detected VviUCC1 variants on grapevine rachis architecture.

Published
2020

38. Genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs

Author

Flutre, Timothée, primary, Le Cunff, Loïc, additional, Fodor, Agota, additional, Launay, Amandine, additional, Romieu, Charles, additional, Berger, Gilles, additional, Bertrand, Yves, additional, Terrier, Nancy, additional, Beccavin, Isabelle, additional, Bouckenooghe, Virginie, additional, Roques, Maryline, additional, Pinasseau, Lucie, additional, Verbaere, Arnaud, additional, Sommerer, Nicolas, additional, Cheynier, Véronique, additional, Bacilieri, Roberto, additional, Boursiquot, Jean-Michel, additional, Lacombe, Thierry, additional, Laucou, Valérie, additional, This, Patrice, additional, Péros, Jean-Pierre, additional, and Doligez, Agnès, additional

Published
2020
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40. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Author

Badouin, Hélène, primary, Velt, Amandine, additional, Gindraud, François, additional, Flutre, Timothée, additional, Dumas, Vincent, additional, Vautrin, Sonia, additional, Marande, William, additional, Corbi, Jonathan, additional, Sallet, Erika, additional, Ganofsky, Jérémy, additional, Santoni, Sylvain, additional, Guyot, Dominique, additional, Ricciardelli, Eugenia, additional, Jepsen, Kristen, additional, Käfer, Jos, additional, Berges, Hélène, additional, Duchêne, Eric, additional, Picard, Franck, additional, Hugueney, Philippe, additional, Tavares, Raquel, additional, Bacilieri, Roberto, additional, Rustenholz, Camille, additional, and Marais, Gabriel, additional

Published
2020
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41. Genetic diversity and structure of sweet chestnut (Castanea sativa Mill.) in France: At the intersection between Spain and Italy

Author

Bouffartigue, Cathy, Debille, Sandrine, Fabreguette, Olivier, Cabrer, Ana Ramos, Pereira-Lorenzo, Santiago, Flutre, Timothée, and Harvengt, Luc

Abstract

Context Renewed interest in European chestnut in France is focussed on finding locally adapted populations partially resistant to ink disease and identifying local landraces. Aims We genotyped trees to assess (i) the genetic diversity of wild and cultivated chestnut across most of its range in France, (ii) their genetic structure, notably in relation with the sampled regions, and (iii) relations with its neighbors in Spain and Italy. Methods A total of 1,401 trees in 17 sampling regions in France were genotyped at 13 SSRs, and a subset of 693 trees at 24 SSRs. Results Genetic diversity was high in most sampling regions, with redundancy between them. No significant differentiation was found between wild and cultivated chestnut. A genetic structure analysis with no a priori information found a low, yet significant structure, and identified three clusters. Two clusters of sampling regions, south east France and Corsica, were less admixed than the others. A substructure was detected in the admixed cluster suggesting differentiation in wild chestnut trees in Finistère and Aveyron sampling regions. Conclusion The genetic structure within and between our sampling regions is likely the result of natural events (recolonization after the last glaciation) and human activities (migration and exchanges). Notably, we provide evidence for a common origin of most French and Iberian chestnut trees, except those from, south east France that were associated with the Italian gene pool. This advance in our knowledge of chestnut genetic diversity and structure will benefit conservation and help our local partners’ valorization efforts. Key message This paper presents the results of the first assessment of genetic diversity and structure of wild and cultivated sweet chestnut in France. It reveals high diversity, a low but significant structure, and strongly suggests that the French gene pool is at the intersection between the Italian and Spanish gene pools.

Published
2019
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42. Genomic selection - which prospects in Prunus armeniaca?

Author

Nsibi, Mariem, Confolent, Carole, Gouble, Barbara, Bureau, Sylvie, Blanc, Alain, Roch, Guillaume, Lambert, Patrick, Flutre, Timothée, Regnard, Jean-Luc, Sauvage, Christopher, Audergon, Jean Marc, and Gouble, Barbara

Subjects
[SDV] Life Sciences [q-bio]
Published
2019

43. Integrating novel genotyping and phenotyping technologies for grape genetics. International Congress on Grapevine and Wine Sciences

Author

Tello Moro, Javier, Roux, Catherine, Laucou, Valerie, Sarah, Gautier, Bidel, Luc, Flutre, Timothée, Chouiki Alilou, Hajar, Weber, Audrey, Santoni, Sylvain, Peros, Jean-Pierre, Doligez, Agnes, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Géno-Vigne® Technological Unit, Agropolis Fondation under the ARCAD project No 0900-001., European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ProdInra, Migration, and AgreenSkills+ - AGREENSKILLSPLUS - - EC:FP7:PEOPLE2014-05-05 - 2019-05-04 - 609398 - VALID

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

AGAP : équipes DAAV, GE2pop; International audience; Understanding the genetic determinism of crop yield, grape quality traits and adaptation potential is of paramount importance both for practical viticulture and for breeding new varieties to face future climate change challenges. The rapid development of advanced phenotyping and genotyping technologies will provide the information needed to cope with the efficient analysis of these complex traits by the use of relatively low-cost and robust systems. Here, we report the use of genotyping-by-sequencing (GBS, Keygene patents) to a large half-diallel grapevine population (N ~ 600) from 10 connected segregating progenies. The approach was useful to identify a total of 71,720 genetic polymorphisms, including biallelic SNPs and multiallelic markers. A subset of fully-informative and/or common markers to all (or 9) progenies were selected for the subsequent genetic grouping and mapping within each progeny. This process led to individual consensus maps with similar length than those previously published, but higher marker density. Individual maps were then merged to create a high-density grapevine integrated genetic map, with high informative content and acceptable marker order agreement between progenies. On the other hand, novel image-based phenotyping systems are designed for the automatic and non-destructive estimation of flower number, berry number and berry size, and available high-throughput phenotyping technologies are used to evaluate stress indicators of photosystems in selected individuals from the population. This novel genetic and phenotypic information will be integrated to identify QTLs and candidate genes involved in the genetic determinism of these relevant grapevine traits.

Published
2018

44. New physiological and genetic approaches to breed grapevines challenging climate warming

Author

Romieu, Charles, BIGARD, Antoine, Breil, Matthieu, Shahood, Rezk, Savoi, Stefania, Pellegrino, Anne, Doligez, Agnes, Flutre, Timothée, Torregrosa, Laurent, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), General Commission for Scientific Agricultural Research, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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), 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)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), ProdInra, Archive Ouverte, and Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
vitis vinifera, maturation, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, analyse de qtl, vigne, réchauffement climatique, grapevine
Abstract

UMR AGAP équipe DAAV; Global warming already induced a drift towards earlier ripening, higher sugars and lower pH in grapevine. Resilient cultivars should be selected everywhere this metabolic syndrome is detrimental to wine quality. Two major innovations may help to elucidate the physiological and genetic bases of grapevine fruit response to warming: i) Reconsidering fruit ripening quantitative bases : RNA and metabolic profiles confirmed that berries at different stages coexist in clusters; circumventing artefacts of non‐synchronous samples elucidated water and osmoticum fluxes and their respective timings ; a H+/sucrose exchange, consistent with VVHT6 activation, is induced at the tonoplast; sugar accumulation continues after malate breakdown continues after malate breakdown completion without membrane energization; phloem loading stops around 26 days when sugar concentration continues by berry shriveling. ii) Microvine accelerates fruit genetics and breeding , due to the continuous production of reproductive organs and the lack of juvenile period. We have screened Vitis vinifera germplasm for fruit water and primary metabolite accumulation. Genotypes limiting sugars accumulation below 1 M at ripe stage were crossed to generate two microvine populations segregating for berry development and composition. GBS was performed to identify QTLs controlling fruit growth and primary metabolite accumulation, as new targets in breeding programs.

Published
2018

45. A novel high-density grapevine integrated linkage map using GBS in a multi-parental population: preliminary results

Author

Tello Moro, Javier, Roux, Catherine, Laucou, Valerie, Sarah, Gautier, Flutre, Timothée, Chouiki, Hajar, Veber, Amandine, Santoni, Sylvain, Peros, Jean-Pierre, Doligez, Agnes, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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), Diversité, Adaptation et Amélioration de la Vigne [AGAP] (DAAV), 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)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
Vegetal Biology, phénotypage, génotypage, plant breeding, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, vigne, Biologie végétale, grapevine, amélioration des plantes
Abstract

UMR AGAP équipe DAAV; A novel high-density grapevine integrated linkage map using GBS in a multi-parental population: preliminary results. 12. International Conference on Grapevine Breeding and Genetics

Published
2018

46. Genome-wide association study of a diverse grapevine panel to uncover the genetic architecture of numerous traits of interest

Author

Flutre, Timothée, Bacilieri, Roberto, Berger, Gilles, Bertrand, Yves, Boursiquot, Jean-Michel, Fodor, Agota, Lacombe, Thierry, Laucou, Valerie, Launay, Amandine, Le Cunff, Loïc, Romieu, Charles, This, Patrice, Peros, Jean-Pierre, Doligez, Agnes, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-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), ANR, INRA, CASDAR, and European Project: 311775,EC:FP7:KBBE,FP7-KBBE-2012-6-singlestage,INNOVINE(2013)

Subjects
Vitis vinifera, genotyping by sequencing, berry weight, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, gwas, heritability, genetic architecture, ComputingMilieux_MISCELLANEOUS, grapevine
Abstract

International audience

Published
2018

47. Twelve new QTLs for phenological traits in Vitis vinifera L

Author

Doligez, Agnes, Bertrand, Yves, Gago, Pilar, Grolier, Michel, Berger, Gilles, Ballester, Jean Francois, Flutre, Timothée, Dias, S., This, Patrice, Peros, Jean-Pierre, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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), Diversité, Adaptation et Amélioration de la Vigne [AGAP] (DAAV), 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)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
changement climatique, Vegetal Biology, vitis vinifera, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, analyse de qtl, polygenie, vigne, Biologie végétale, global change, grapevine
Abstract

UMR Agap équipe DAAV; Twelve new QTLs for phenological traits in [i]Vitis vinifera[/i] L.. 12. International Conference on Grapevine Breeding and Genetics

Published
2018

48. Genomic selection - which prospects in Prunus armeniaca? Preliminary results issued from fruit quality traits and phenology

Author

Nsibi, Mariem, Confolent, Carole, Gouble, Barbara, Bureau, Sylvie, Blanc, Alain, Roch, Guillaume, Lambert, Patrick, Flutre, Timothée, Regnard, Jean-Luc, Sauvage, Christopher, Audergon, Jean Marc, Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Institut National de la Recherche Agronomique (INRA), Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), CEP Innovation, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Avignon Université (AU)-Institut National de la Recherche Agronomique (INRA), Génétique et Amélioration des Fruits et Légumes (GAFL), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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)-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), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), 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)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
Vegetal Biology, Bi-parental population, Apricot, abricot, cross validation, genomic selection, Prunus, Genomic selection, RR-BLUP, Cross validation, Accuracy, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, sélection génomique, Biologie végétale, validation croisée
Abstract

Genomic selection (GS) refers to a selection method which intends to assess individuals according to their genomic values using genome-wide dense markers. Particularly efficient in animal improvement strategies, opening interesting perspective in crops, it is already engaged in perennial species such as apple where, genetic gain was maximized for fruit quality traits quantitatively inherited by comparison with conventional breeding strategy. In the present work, GS was applied on a biparental apricot population (184 individuals) characterized over two consecutive years for phenology (blooming and maturity dates) and fruit quality traits (fruit weight, color, sugar nd acidity content, ethylene production). A ridge regression (RR-BLUP) modelling has been used. The performance of GS was assessed by cross validation using the accuracy defined as the correlation between true phenotypes values and the estimated ones. The effects of markers density and number, training set size and composition as well as the heritability of the investigated traits were evaluated on the accuracy of the model. The main results issued from the two years multi-annual modelling approach are showing that (i) genomic predictions are accurate even with a little number of markers (>100 markers), (ii) the accuracy increases with the training population’s size and with high heritability traits, (iii) and the optimization of the training set improves the performance of genomic selection model. To conclude, a clear interest exists in continuing the evaluation of the genomic selection in biparental apricot populations even for traits that are difficult to measure. The robustness of the approach needs to be tested both on other progenies and on a large set of genetic resources

Published
2018

49. Developing grapevine FAIR Data

Author

Pommier, Cyril, Duchêne, Eric, Lacombe, Thierry, Flutre, Timothée, Alaux, Michael, Cornut, Guillaume, Philippe, Florian, Durand, Sophie, Flores, Raphaël-Gauthier, Kimmel, Erik, Letellier, Thomas, Michotey, Célia, Mohellibi, Nacer, Quesneville, Hadi, Adam-Blondon, Anne-Francoise, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

50. Conservation and usage of chestnut biodiversity: a case study of partnership research

Author

Bouffartigue, Cathy, Couix, Nathalie, Flutre, Timothée, Barreneche, Teresa, Hazard, Laurent, 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, 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), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, European Project: 633571,H2020,H2020-SFS-2014-2,DIVERSIFOOD(2015), Université de Toulouse (UT)-Université de Toulouse (UT), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)

Subjects
genetic resources, partnership research, cultivated biodiversity, chestnut, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, management practices, ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

National audience

Published
2018

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