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52. Genomic prediction of hybrid crops allows disentangling dominance and epistasis

Author

González-Diéguez, David, Legarra, Andres, Charcosset, Alain, Moreau, Laurence, Lehermeier, Christina, Teyssèdre, Simon, Vitezica, Zulma, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), 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]-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), Genetics and Analytics Unit, RAGT2n, France Genetique PorcRAGTINRA1500041600000837INRA SELGEN metaprogram (project OptiMaGics)Toulouse Midi-Pyrenees bioinformatics platform, and ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010)

Subjects
Crops, Agricultural, AcademicSubjects/SCI01140, epistasis, AcademicSubjects/SCI00010, [SDV]Life Sciences [q-bio], AcademicSubjects/SCI01180, dominance, Linkage Disequilibrium, shared data resources, heterosis, Inbreeding, ComputingMilieux_MISCELLANEOUS, genomic prediction, Investigation, Models, Genetic, Chimera, Genetic Variation, Epistasis, Genetic, Genomics, Plants, Plant Breeding, GenPred, genomic models, Hybridization, Genetic, AcademicSubjects/SCI00960, genetic variance, Statistical Genetics and Genomics, Forecasting
Abstract

We revisited, in a genomic context, the theory of hybrid genetic evaluation models of hybrid crosses of pure lines, as the current practice is largely based on infinitesimal model assumptions. Expressions for covariances between hybrids due to additive substitution effects and dominance and epistatic deviations were analytically derived. Using dense markers in a GBLUP analysis, it is possible to split specific combining ability into dominance and across-groups epistatic deviations, and to split general combining ability (GCA) into within-line additive effects and within-line additive by additive (and higher order) epistatic deviations. We analyzed a publicly available maize data set of Dent × Flint hybrids using our new model (called GCA-model) up to additive by additive epistasis. To model higher order interactions within GCAs, we also fitted “residual genetic” line effects. Our new GCA-model was compared with another genomic model which assumes a uniquely defined effect of genes across origins. Most variation in hybrids is accounted by GCA. Variances due to dominance and epistasis have similar magnitudes. Models based on defining effects either differently or identically across heterotic groups resulted in similar predictive abilities for hybrids. The currently used model inflates the estimated additive genetic variance. This is not important for hybrid predictions but has consequences for the breeding scheme—e.g. overestimation of the genetic gain within heterotic group. Therefore, we recommend using GCA-model, which is appropriate for genomic prediction and variance component estimation in hybrid crops using genomic data, and whose results can be practically interpreted and used for breeding purposes.

Published
2020

55. The genetic architecture of grain yield and related traits in Zea maize L. revealed by comparing intermated and conventional populations

Author

Yung-Fen Huang, Madur, Delphine, Combes, Valerie, Chin Long Ky, Coubriche, Denis, Jamin, Philippe, Jouanne, Sophie, Dumas, Fabrice, Bouty, Ellen, Bertin, Pascal, Charcosset, Alain, and Moreau, Laurence

Subjects
Corn -- Physiological aspects, Corn -- Genetic aspects, Gene mutations -- Research, Population genetics -- Research, Quantitative trait loci -- Research, Biological sciences
Published
2010

57. Fine mapping and haplotype structure analysis of a major flowering time quantitative trait locus on maize chromosome 10

Author

Ducrocq, Sebastien, Giauffret, Catherine, Madur, Delphine, Combes, Valerie, Dumas, Fabrice, Jouanne, Sophie, Coubriche, Denis, Jamin, Philippe, Moreau, Laurence, and Charcosset, Alain

Subjects
Corn -- Physiological aspects, Corn -- Genetic aspects, Genetic code -- Research, Population genetics -- Research, Quantitative trait loci -- Research, Biological sciences
Published
2009

61. Patterns of molecular evolution associated with two selective sweeps in the Tb1-Dwarf8 region in maize

Author

Camus-Kulandaivelu, Letizia, Chevin, Luis-Miguel, Tollon-Cordet, Christine, Charcosset, Alain, Manicacci, Domenica, and Tenaillon, Maud I.

Subjects
Corn -- Natural history, Corn -- Genetic aspects, Molecular evolution -- Research, Genetic polymorphisms -- Identification and classification, Adaptation (Physiology) -- Genetic aspects, Biological sciences
Abstract

We focused on a region encompassing a major maize domestication locus, Tb1, and a locus involved in the flowering time variation, Dwarf8 (D8), to investigate the consequences of two closely linked selective sweeps on nucleotide variation and gain some insights into maize geographical diffusion, through climate adaptation. First, we physically mapped D8 at ~300 kb 3' of Tb1. Second, we analyzed patterns of nucleotide variation at Tb1, D8, and seven short regions (400-700 bp) located in the Tb1-D8 region sequenced on a 40 maize inbred lines panel encompassing early-flowering temperate and late-flowering tropical lines. The pattern of polymorphism along the region is characterized by two valleys of depleted polymorphism while the region in between exhibits an appreciable amount of diversity. Our results reveal that a region ~100 kb upstream of the D8 gene exhibits hallmarks of divergent selection between temperate and tropical lines and is likely closer than the D8 gene to the target of selection for climate adaptation. Selection in the tropical lines appears more recent than in the temperate lines, suggesting an initial domestication of early-flowering maize. Simulation results indicate that the polymorphism pattern is consistent with two interfering selective sweeps at Tb1 and D8.

Published
2008

62. Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information

Author

Ducrocq, Sebastien, Madur, Delphine, Veyrieras, Jean-Baptiste, Camus-Kulandaivelu, Letizia, Kloiber-Maitz, Monika, Presterl, Thomas, Ouzunova, Milena, Manicacci, Domenica, and Charcosset, Alain

Subjects
Plants, Flowering of -- Physiological aspects, Plants, Flowering of -- Genetic aspects, Chromosome mapping -- Methods, Adaptation (Physiology) -- Genetic aspects, Corn -- Genetic aspects, Corn -- Physiological aspects, Biological sciences
Abstract

An association study conducted on 375 maize inbred lines indicates a strong relationship between Vgt1 polymorphisms and flowering time, extending former quantitative trait loci (QTL) mapping results. Analysis of allele frequencies in a landrace collection supports a key role of Vgt1 in maize alilatitudinal adaptation.

Published
2008

63. Bridging genomics and genetic diversity: linkage disequilibrium structure and association mapping in maize and other cereals

Author

Veyrieras, Jean-Baptiste, Camus-Kulandaivelu, Letizia, Gouesnard, Brigitte, Manicacci, Domenica, and Charcosset, Alain

Subjects
Genomics -- Research, Corn -- Genetic aspects, Grain -- Genetic aspects, Biological diversity -- Research, Quantitative trait loci -- Models, Linkage (Genetics) -- Research, Plant breeding -- Research, Agricultural industry, Business
Abstract

Linkage disequilibrium (LD) and association mapping s receiving considerable attention in the plant genetics community for its potential to use existing genetic resources collections to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest. Based on investigations in maize (Zea mays L.) either published or recently conducted in our group, we discuss three elements of particular importance for conducting association mapping or interpreting the results: (i) the analysis of population structure into subgroups, (ii) its use to control for spurious associations and consequences in the specific case of differential selection among subgroups, and (iii) the analysis of the local structure of LD into haplotypes and its consequences on the resolution and the application of LD mapping. Consequences and perspecutives for plant breeding are briefly discussed.

Published
2008

64. Des modèles pour répondre à quels besoins de R&D ? Les besoins du généticien

Author

Le Gouis, Jacques, Rincent, Renaud, Charcosset, Alain, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), and Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA)

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

International audience

Published
2020

65. Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering

Author

Madur Delphine, Charcosset Alain, Simon Rio, Moreau Laurence, Palaffre Carinne, Valérie Combes, Cyril Bauland, Tristan Mary-Huard, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Unité expérimentale du maïs (BORDX ST-MARTIN UE), and Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Linkage disequilibrium, [SDV]Life Sciences [q-bio], Genome-wide association study, Plant Science, QH426-470, Plant Genetics, 01 natural sciences, Linkage Disequilibrium, Gene Frequency, Plant Genomics, GWAS, Association mapping, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Genetics, 0303 health sciences, [STAT.AP]Statistics [stat]/Applications [stat.AP], food and beverages, Chromosome Mapping, Eukaryota, Genomics, Plants, Phenotype, Experimental Organism Systems, Engineering and Technology, Genetic Background, Genome, Plant, Research Article, Biotechnology, Genotype, Quantitative Trait Loci, application to maize flowering, Bioengineering, Flowers, Quantitative trait locus, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, Zea mays, Chromosomes, Plant, Molecular Genetics, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Model Organisms, specific QTL allele, Plant and Algal Models, genetic background epistasis, Genome-Wide Association Studies, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Grasses, Allele, Allele frequency, Molecular Biology, Alleles, 030304 developmental biology, Evolutionary Biology, Population Biology, Organisms, Biology and Life Sciences, Computational Biology, Epistasis, Genetic, Human Genetics, Genome Analysis, Genetic architecture, Maize, Genetic Loci, Animal Studies, Epistasis, Plant Biotechnology, Population Genetics, 010606 plant biology & botany, Genome-Wide Association Study
Abstract

When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genome-wide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred “Flint-Dent” panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species., Author summary Identification of genomic regions involved in genetic architecture of traits has become commonplace in quantitative genetics studies. Genetic structure is a common feature in human, animal and plant species and most current methods target genomic regions whose effects on traits are conserved between genetic groups. However, a heterogeneity of allele effects may be observed due to different factors: a group-specific correlation between the alleles of the tagged marker and those of the causal variant, a group-specific mutation at the causal variant or an epistatic interaction between the causal variant and the genetic background. We propose a new method adapted to structured populations including admixed individuals, which aims to identify these genomic regions and to unravel the previous factors. The method was applied to a maize inbred diversity panel including lines from the dent and the flint genetic groups, as well as admixed lines, evaluated for flowering time. Several genomic regions were detected with various configurations of allele effects, with evidence of epistatic interactions between some of the loci and the genetic background.

Published
2020

66. Levier génétique et stress abiotiques : principaux acquis et perspectives des projets nationaux BreedWheat (blé) et Amaizing (maïs)

Author

Le Gouis, Jacques, Charcosset, Alain, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Arvalis - Institut du Végétal, and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

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

International audience

Published
2020

67. A Long Read project to find optimal technologic combinations for genome assembly and variability, epigenetic marks detection and metagenomic analysis

Author

Iampietro, Carole, Eché, Camille, Castinel, Adrien, Serre, Rémy-Félix, Klopp, Christophe, Denis, Erwan, Bouchez, Olivier, Kuchly, Claire, Vandecasteele, Céline, BROHA, Amandine, THERVILLE, Romain, Di Franco, Arnaud, Djebali Quelen, Sarah, DREAU, Andreea, Hoede, Claire, KOROVINA, Oleksandra, BIRBES, CLEMENT, Laborie, Didier, Mainguy, Jean, Noirot, Céline, Salin, Gerald, Terzian, Paul, Trotard, Marie-Stéphane, Boichard, Didier, Boussaha, Mekki, Grohs, Cécile, Charcosset, Alain, Belcram, Harry, Joets, Johann, Combes, Sylvie, Pascal, Géraldine, Pitel, Frederique, Leroux, Sophie, Riquet, Juliette, Demars, Julie, Tosser-Klopp, Gwenola, Vitte, Clémentine, Iannuccelli, Nathalie, Lluch, Jérôme, Lopez-Roques, Celine, Faraut, Thomas, Zytnicki, Matthias, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, 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), 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-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), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-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), FEDER-Région Occitanie, 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)-Université Toulouse III - Paul Sabatier (UT3), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

71. Place des agricultures européennes dans le monde à l’horizon 2050 : Entre enjeux climatiques et défis de la sécurité alimentaire mondiale: Effets du changement climatique sur la production agricole végétale : synthèse de la littérature scientifique internationale pour documenter les projections des variables d’entrée du modèle GlobAgri-AE2050

Author

Tibi, Anaïs, Debaeke, Philippe, Ben Ari, Tamara, Bérard, Annette, Bispo, Antonio, Charcosset, Alain, Durand, Jean-Louis, Le Gouis, Jacques, Makowski, David, Marrou, Hélène, Planton, Serge, Sauquet, Eric, Savary, Serge, Willocquet, Laetitia, Guyomard, Hervé, Schmitt, Bertrand, Direction de l'Expertise scientifique collective, de la Prospective et des Etudes, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agronomie, AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), InfoSol (InfoSol), 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), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Météo France, Riverly (Riverly), Services déconcentrés d'appui à la recherche Bretagne-Normandie, Institut National de la Recherche Agronomique (INRA), Centre d'Economie et de Sociologie Rurales Appliquées à l'Agriculture et aux Espaces Ruraux (CESAER), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Le présent document a été élaboré dans le cadre d'une Étude réalisée à la demande et grâce au soutien de l’association Pluriagri. Cette Étude a été conduite par la Direction de l’Expertise scientifique collective, de la prospective et des études d’INRAE, et selon les principes et règles de conduite établies par cette structure et disponibles sur le site internet d’INRAE., INRAE, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Météo-France Direction Interrégionale Sud-Est (DIRSE), Météo-France, RiverLy - Fonctionnement des hydrosystèmes (RiverLy), and Services déconcentrés d'appui à la recherche Bretagne-Normandie (SDAR Bretagne Normandie)

Subjects
Changement climatique, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, Marché mondial des produits agricoles, Sécurité alimentaire, Rendement, [SHS]Humanities and Social Sciences
Abstract

Le présent rapport rassemble les revues de la littérature scientifique internationale réalisées par le collectif d’experts scientifiques constitué dans le cadre de l’étude « Place des agricultures européennes dans le monde à l’horizon 2050 : entre enjeux climatiques et défis de la sécurité alimentaire » (ci-après désignée par l’acronyme AE2050).Pour rappel, l’étude AE2050 consiste à examiner, au moyen d’un modèle de bilans (GlobAgri-AE2050 ), l’évolution des surfaces, des niveaux de productions, et des échanges mondiaux de produits agricoles à l’horizon 2050 dans chacune des régions du monde , en fonction (i) de celle de la demande en produits agricoles (notamment liée à la croissance démographique et aux évolutions des régimes alimentaires) et (ii) des caractéristiques clefs des systèmes agricoles que sont les rendements (végétaux et animaux), les intensités culturales et les disponibilités en terres. On cherche, dans cette étude, à intégrer autant que possible les effets du changement climatique dans la projection des variables clefs décrivant les systèmes agricoles.

Published
2020

72. Additional file 4 of Optimized breeding strategies to harness genetic resources with different performance levels

Author

Allier, Antoine, Teyssèdre, Simon, Lehermeier, Christina, Moreau, Laurence, and Charcosset, Alain

Abstract

Additional file 4:Supplementary Figures contain the supplemental Figure S1. (Evolution of the additive genetic variance intra- and inter-family components in the breeding population); Figure S2. (Summary statistics on the introduction crosses); Figure S3. (Effect of TS composition on intra-family prediction accuracies); Figure S4. (Evolution of the breeding population over generations for two different weightings α).

Published
2020
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73. Evaluating the reliability of Structure outputs in case of relatedness between individuals

Author

Camus-Kulandaivelu, Letizia, Veyrieras, Jean-Baptiste, Gouesnard, Brigitte, Charcosset, Alain, and Manicacci, Domenica

Subjects
Plant breeding -- Research, Plant populations -- Analysis, Agricultural industry, Business
Abstract

Inference of population structure from neutral marker loci is a key issue for association genetics. However, the presence of highly related individuals, commonly observed in breeders' panels, may lead to deviation from model hypotheses and therefore unreliable group assignment. The present note proposes a tool to help interpret Structure software outputs on populations that include highly related individuals, such as plant breeding material. We ran Structure software on simple sequence repeat (SSR) data from two maize (Zea mays L. ssp. mays) inbred panels. We propose a criterion to evaluate Structure stability based on Euclidian distance between outputs. This approach shows a high stability across runs for the panel composed of first cycle inbred lines. On the contrary, the presence of highly related individuals in the second panel induces strong instability in Structure outputs.

Published
2007

75. Number and fitness of selected individuals in marker-assisted and phenotypic recurrent selection

Author

Bernardo, Rex, Moreau, Laurence, and Charcosset, Alain

Subjects
Natural selection -- Research, Phenotype -- Research, Agricultural industry, Business
Abstract

Selected individuals in recurrent selection usually have equal fitness, i.e., they contribute the same number of progenies to the next cycle of selection. Our objective was to determine if varying the fitness of selected individuals increases the response to recurrent selection. We developed and evaluated an optimum method (Unequal Fitness) and a simplified method (Better Half) for determining the appropriate fitness of selected individuals. By computer simulation we found that if the number of selected individuals ([N.sub.Sel]) is constant, the short-term response (cycles 1-5) to phenotypic recurrent selection was generally higher with the Better Half and Unequal Fitness methods than with the Equal Fitness method. In practice, however, breeders would find it easier to change [N.sub.Sel] than to manipulate the fitness of selected individuals. Reducing [N.sub.Sel] often negated any short-term advantage of the Better Half and Unequal Fitness methods. Likewise, the Better Half and Unequal Fitness methods were not advantageous in markerassisted recurrent selection, which is a short-term procedure. Across different [N.sub.Sel] values, the Better Half and Unequal Fitness methods were superior to the Equal Fitness method for medium- and longterm phenotypic recurrent selection (cycles 6-30). We recommend the Better Half method over the Unequal Fitness method because of its simplicity and because it remained superior to the Equal Fitness method over more cycles of selection. As a rule-of-thumb, we suggest that [N.sub.Sel] should be roughly equal to the number of cycles for which selection will be conducted. This rule of thumb leads to [N.sub.sel] values lower than those typically used in selection programs.

Published
2006

76. Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene

Author

Camus-Kulandaivelu, Letizia, Veyrieras, Jean-Baptiste, Madur, Delphine, Combes, Valerie, Fourmann, Marie, Barraud, Stephanie, Dubreuil, Pierre, Gouesnard, Brigitte, Manicacci, Domenica, and Charcosset, Alain

Subjects
Corn -- Genetic aspects, Corn -- Research, Gene mutations -- Research, Genetic polymorphisms -- Research, Dwarf plants -- Genetic aspects, Dwarf plants -- Research, Biological sciences
Abstract

To investigate the genetic basis of maize adaptation to temperate climate, collections of 375 inbred lines and 275 landraces, representative of American and European diversity, were evaluated for flowering time under short- and long-day conditions. The inbred line collection was genotyped for 55 genomewide simple sequence repeat (SSR) markers. Comparison of inbred line population structure with that of landraces, as determined with 24 SSR loci, underlined strong effects of both historical and modern selection on population structure and a clear relationship with geographical origins. The late tropical groups and the early 'Northern Flint' group from the northern United States and northern Europe exhibited different flowering times. Both collections were genotyped for a 6-bp insertion/deletion in the Dwarf8 (D8idp) gene, previously reported to be potentially involved in flowering time variation in a 102 American inbred panel. Among-group D8idp differentiation was much higher than that for any SSR marker, suggesting diversifying selection. Correcting for population structure, D8idp was associated with flowering time under long-day conditions, the deletion allele showing an average earlier flowering of 29 degree days for inbreds and 145 degree days for landraces. Additionally, the deletion allele occurred at a high frequency (>80%) in Northern Flint while being almost absent (

Published
2006

77. Usefulness of gene information in marker-assisted recurrent selection: a simulation appraisal

Author

Bernardo, Rex and Charcosset, Alain

Subjects
Quantitative trait loci -- Research, Corn -- Breeding, Agricultural industry, Business, Research
Abstract

Genomics and post-genomics sciences are expected to uncover most, if not all, of the quantitative trait loci (QTL) in plants. Prior knowledge of QTL locations can then be exploited in marker-assisted recurrent selection (MARS). Our objectives were to determine (i) whether prior knowledge of QTL locations is advantageous in MARS, and (ii) whether knowledge of the QTL themselves, as opposed to knowledge of markers linked to QTL, is advantageous in MARS. We simulated MARS in a maize (Zea mays L.) [F.sub.2] population. We found that when 10 QTL controlled the trait, the percentage of known QTL that maximized the response to MARS was [P.sub.Max] = 100%. In contrast, [P.sub.Max] was often less than 100% when 40 or 100 QTL controlled the trait and QTL effects were estimated with a population size (N = 100) typically used in MARS. This result implied it was advantageous to exploit only the QTL with large effects and ignore those with small effects, even if the locations of all QTL were known. For a trait controlled by 40 QTL, the response was up to 50% greater when [P.sub.Max] = 70% of the QTL were known through markers for the QTL themselves rather than through linked markers. We conclude that having known QTL in MARS is most beneficial for traits controlled by a moderately large number of QTL (e.g., 40). We speculate that a combination of approaches would be needed to exploit information on markers for QTL themselves, markers linked to QTL, and unknown QTL., MAIZE BREEDING comprises three stages: (i) population improvement, (ii) inbred development, and (iii) hybrid development. Maize seed companies have successfully exploited marker-QTL associations in population improvement (Edwards and Johnson, 1994; [...]

Published
2006

81. Linkage mapping of 1454 new maize candidate gene loci

Author

Falque, Matthieu, Decousset, Laurent, Dervins, Delphine, Jacob, Anne-Marie, Joets, Johann, Martinant, Jean-Pierre, Raffoux, Xavier, Ribiere, Nicolas, Ridel, Celine, Samson, Delphine, Charcosset, Alain, and Murigneux, Alain

Subjects
Genetics -- Research, Corn -- Research, Corn -- Genetic aspects, Genetic research, Biological sciences
Abstract

Bioinformatic analyses of maize EST sequences have highlighted large numbers of candidate genes putatively involved in agriculturally important traits. To contribute to ongoing efforts toward mapping of these genes, we used two populations of intermated recombinant inbred lines (IRILs), which allow a higher map resolution than nonintermated RILs. The first panel (IBM), derived from B73 X Mo17, is publicly available from the Maize Genetics Cooperation Stock Center. The second panel (LHRF) was developed from F2 X F252 to map loci monomorphic on IBM. We built framework maps of 237 loci from the IBM panel and 271 loci from the LHRF panel. Both maps were used to place 1454 loci (1056 on map IBM_Gnp2004 and 398 on map LHRF_Gnp2004) that corresponded to 954 cDNA probes previously unmapped. RFLP was mostly used, but PCR-based methods were also performed for some cDNAs to map SNPs. Unlike in usual IRIL-based maps published so far, corrected meiotic centimorgan distances were calculated, taking into account the number of intermating generations undergone by the IRILs. The corrected sizes of our framework maps were 1825 cM for IBM_Gnp2004 and 1862 cM for LHRF_Gnp2004. All loci mapped on LHRF_Gnp2004 were also projected on a consensus map IBMconsensus_Gnp2004. cDNA loci formed clusters near the centromeres except for chromosomes 1 and 8.

Published
2005

82. Diversity patterns and selective sweeps in a Southeast European panel of maize inbred lines as combined with two West European panels

Author

Galić, Vlatko, primary, Anđelković, Violeta, additional, Kravić, Natalija, additional, Grčić, Nikola, additional, Ledenčan, Tatjana, additional, Jambrović, Antun, additional, Zdunić, Zvonimir, additional, Nicolas, Stéphane, additional, Charcosset, Alain, additional, Šatović, Zlatko, additional, and Šimić, Domagoj, additional

Published
2020
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83. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome

Author

Chardon, Fabien, Virlon, Berangere, Moreau, Laurence, Falque, Matthieu, Joets, Johann, Decousset, Laurent, Murigneux, Alain, and Charcosset, Alain

Subjects
Quantitative trait loci -- Analysis, Corn -- Genetic aspects, Biological sciences
Abstract

Genetic architecture of flowering time in maize was addressed by synthesizing a total of 313 quantitative trait loci (QTL) available for this trait. These were analyzed first with an overview statistic that highlighted regions of key importance and then with a meta-analysis method that yielded a synthetic genetic model with 62 consensus QTL. Six of these displayed a major effect. Meta-analysis led in this case to a twofold increase in the precision in QTL position estimation, when compared to the most precise initial QTL position within the corresponding region. The 62 consensus QTL were compared first to the positions of the few flowering-time candidate genes that have been mapped in maize. We then projected rice candidate genes onto the maize genome using a synteny conservation approach based on comparative mapping between the maize genetic map and japonica rice physical map. This yielded 19 associations between maize QTL and genes involved in flowering time in rice and in Arabidopsis. Results suggest that the combination of meta-analysis within a species of interest and synteny-based projections fiom a related model plant can be an efficient strategy for identifying new candidate genes for trait variation.

Published
2004

87. Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines

Author

Bouchez, Agnes, Hospital, Frederic, Causse, Mathilde, Gallais, Andre, and Charcosset, Alain

Subjects
Corn -- Genetic aspects, Genetic research, Biological sciences
Abstract

This article reports the marker-assisted introgression of favorable alleles at three quantitative trait loci (QTL) for earliness and grain yield among maize elite lines. The QTL were originally detected in 1992 by means of ANOVA in a population of 96 recombinant inbred lines (RILs). Introgression started from a selected RIL, which was crossed three times to one of the original parents and then self-fertilized, leading to B[C.sub.3][S.sub.1] progenies. Markers were used to assist both foreground and background selection at each generation. At the end of the program, the effect of introgression was assessed phenotypically in agronomic trials, and QTL detection was performed by composite interval mapping among B[C.sub.3][S.sub.1] progenies. The marker-assisted introgression proved successful at the genotypic level, as analyzed by precision graphical genotypes, although no emphasis was put on the reduction of linkage drag around QTL. Also, QTL positions were generally sustained in the introgression background. For earliness, the magnitude and sign of the QTL effects were in good agreement with those expected from initial RIL analyses. Conversely, for yield, important discrepancies were observed in the magnitude and sign of the QTL effects observed after introgression, when compared to those expected from initial RIL analyses. These discrepancies are probably due to important genotype-by-environment interactions.

Published
2002

97. Les mélanges de variétés ont contribué à l’expansion géographique mondiale d’une espèce cultivée, le maïs

Author

Tenaillon, Maud, Charcosset, Alain, 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), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID]Life Sciences [q-bio]/Biodiversity, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

98. Responses to selection for adaptation to temperate conditions in tropical drought tolerant maize production

Author

Gouesnard, Brigitte, Zanetto, Anne, Palaffre, Carine, Chapuis, Romain, Arca, Mariangela, Nicolas, Stephane, Charcosset, Alain, Welcker, Claude, 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), Unité expérimentale du maïs (BORDX ST-MARTIN UE), Institut National de la Recherche Agronomique (INRA), Domaine expérimental de Melgueil (MONTP MELGUEIL UE), 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), and Agropolis International. Montpellier, FRA.

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

National audience

Published
2019

99. Diversity analysis within a collection of 1191 flint maize inbred lines using genotyping-by-sequencing

Author

Gouesnard, Brigitte, Negro, Sandra Silvia, LAFFRAY, Amélie, Glaubitz, Jeff, Melchinger, A.E., Revilla, Pedro, Moreno-Gonzalez, Jesus, Madur, Delphine, Tollon-Cordet, Christine, Laborde, Jacques, Kermarrec, Dominique, Bauland, Cyril, Moreau, Laurence, Charcosset, Alain, Nicolas, Stephane, 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), 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), Cornell University [New York], University of Hohenheim, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Centro de Investigaciones Agrarias de Mabegondo (CIAM), Unité expérimentale du maïs (BORDX ST-MARTIN UE), Institut National de la Recherche Agronomique (INRA), Ressources Génétiques Végétales en Conditions Océaniques (RGCO), and Agropolis International. Montpellier, FRA.

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

National audience

Published
2019

100. A proteomics-based systems genetics approach reveals environment-specific loci modulating protein co-expression and drought-related traits in maize

Author

Blein-Nicolas, Mélisande, Negro, Sandra Sylvia, Balliau, Thierry, Welcker, Claude, Bosquet, Llorenç Cabrera, Nicolas, Stéphane Dimitri, Charcosset, Alain, and Zivy, Michel

Subjects
fungi, food and beverages
Abstract

The evolution of maize yields under drought is of particular concern in the context of climate change and human population growth. To better understand the mechanisms associated with the genetic polymorphisms underlying the variations of traits related to drought tolerance, we used a systems genetics approach integrating high-throughput phenotypic, proteomics and genomics data acquired on 254 maize hybrids grown under two watering conditions. We show that water deficit, even mild, induced a strong proteome remodeling and a reprogramming of the genetic control of the abundance of many proteins. We identify close co-localizations between QTLs and pQTLs, thus highlighting environment-specific pleiotropic loci associated to the co-expression of drought-responsive proteins and to the variations of phenotypic traits. These findings bring several lines of evidence supporting candidate genes at many loci and provide novel insight into the molecular mechanisms of drought tolerance.

Published
2019
Full Text
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