logo umr
Génétique Quantitative et Évolution - Le Moulon

Alain CHARCOSSET

Alain CHARCOSSET

Directeur de Recherche, INRAE

maize, maize and maize

  • Maize diversity,
  • Quantitative traits,
  • Breeding methods

alain.charcosset@inrae.fr

01 69 33 23 35

orcid.org/0000-0001-6125-503X

Publications

  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • Ferme du Moulon
  • F-91190 Gif-sur-Yvette

Education and Positions

  • Senior Researcher (DR1) Institut National de la Recherche Agronomique (INRA)
  • Deputy director of UMR Quantitative Genetics & Evolution - Le Moulon
  • Head of GQMS team (Quantitative Genetics and Selection Methods)
  • 1990: PhD thesis INA-PG
  • 1986: ingénieur Agronome and MS in Plant Breeding INA-PG (present AgroParisTech)

Research interests

My current research aims at

  • understanding how maize genetic European diversity is organized and shaped by past and ongoing selection programs, in order to facilitate the identification of original diversity sources to be used in genetics studies and breeding programs.
  • determining genetic effects involved in the variation of quantitative traits of agronomical interest. To do so, we develop(ed) QTL meta-analysis methods, association mapping panels, and original multiparental QTL mapping populations to rank multiple alleles and address non additive effects.
  • developing marker assisted breeding methods, based on the assembly of favorable alleles at detected QTLs or global genomic prediction, with a specific focus on population optimization.

These research involve dense genotyping of genetic resources or newly created materials and their phenotyping, conducted within our group and by collaborators. I am also involved in the development of informatics tools to facilitate data management / analysis.

Main ongoing / recent external collaborators

  • Brigitte Gouesnard (INRA, AGAP Montpellier) - François Tardieu and Claude Welcker (INRA LEPSE Montpellier) - Catherine Giauffret (INRA Mons), INRA EPGV Evry - J. Laborde, C. Palaffre and colleagues (INRA Saint-Martin de Hinx)
  • Fred van Eeuwijk (WUR, Netherlands) - Chris-Carolyn Schoen (TUM, Germany) - Albrecht Melchinger (Univ. Hohenheim, Germany) - Pedro Revilla (CSIS, Spain) - Jesus Moreno-Gonzalez (CIAM, Spain)
  • CIMMYT - Integrated Breeding Platform Consortium
  • Biogemma - Euralis - Syngenta - RAGT - Limagrain - KWS, Maïsadour - Caussade - Promaïs association.

Main ongoing / recent project responsibilities and community implication

  • Coordinator of Amaizing Project (ANR investment for the Future, 2011- )
  • Coordinator of CornFed Project (2009-2014, Germany, France, Spain), WP leader in UE DROPS project (2011-2015)
  • Coordinator of Promaïs projects related to maize diversity analysis and exploitation
  • Coordinator of INRA Maize Genetics and Breeding program (1994- )
  • Member of the scientific council of INRA “Plant Biology and Improvement” department (2011-2016)
  • Associate editor for Theoretical and Applied Genetics (2004 -) and Genetics (2010- )
  • President of Eucarpia Maize and Sorghum section (2015- ), organization of 2015 section conference
  • Vice-Chair of Maize Steering Committee (2016- )

Awards

  • Prix Jean Dufrenoy (main award of French Agricultural Academy, 2003),
  • Chevalier du Mérite Agricole (national distinction for contribution to French agriculture, 2013)

Publications

Allier A, Teyssèdre S, Lehermeier C, Charcosset A, Moreau L. (2020) Genomic prediction with a maize collaborative panel: identification of genetic resources to enrich elite breeding programs. Theor Appl Genet, 1 (133) 201-215
Allier A, Teyssèdre S, Lehermeier C, Moreau L, Charcosset A. (2020) Optimized breeding strategies to harness genetic resources with different performance levels. BMC Genomics, 1 (21) 349
Allier A, 20 janvier 2020, Contributions to genetic diversity management in maize breeding programs using genomic selection
Arca M, Mary-Huard T, Gouesnard B, Bérard A, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD. (2020) Deciphering the genetic diversity of landraces with high-throughput SNP genotyping of DNA bulks: methodology and application to the maize 50k array. bioRxiv,
Rio S, Mary-Huard T, Moreau L, Bauland C, Palaffre C, Madur D, Combes V, Charcosset A, Springer NM. (2020) Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering. PLoS Genet, 3 (16) e1008241
Rio S, Moreau L, Charcosset A, Mary-Huard T. (2020) Accounting for Group-Specific Allele Effects and Admixture in Genomic Predictions: Theory and Experimental Evaluation in Maize. Genetics, genetics.303278.2020
Seye AI, Bauland C, Charcosset A, Moreau L. (2020) Revisiting hybrid breeding designs using genomic predictions: simulations highlight the superiority of incomplete factorials between segregating families over topcross designs. Theor Appl Genet, 6 (133) 1995-2010
Allier A, Moreau L, Charcosset A, Teyssèdre S, Lehermeier C. (2019) Usefulness Criterion and Post-selection Parental Contributions in Multi-parental Crosses: Application to Polygenic Trait Introgression. G3: Genes, Genomes, Genetics, 5 (9) 1469-1479
Allier A, Teyssèdre S, Lehermeier C, Claustres B, Maltese S, Melkior S, Moreau L, Charcosset A. (2019) Assessment of breeding programs sustainability: application of phenotypic and genomic indicators to a North European grain maize program. Theor Appl Genet, 5 (132) 1321-1334
Allier A, Lehermeier C, Charcosset A, Moreau L, Teyssèdre S. (2019) Improving Short- and Long-Term Genetic Gain by Accounting for Within-Family Variance in Optimal Cross-Selection. Front. Genet., (10) 1006
Mabire C, 2019-04-23 23/04/19, Contribution des variations structurales de type insertions/délétions à l'adaptation, la variation des caractères et les performances hybrides chez le maïs
Millet EJ, Kruijer W, Coupel-Ledru A, Prado SA, Cabrera-Bosquet L, Lacube S, Charcosset A, Welcker C, Eeuwijk F, Tardieu F. (2019) Genomic prediction of maize yield across European environmental conditions. Nat Genet, 6 (51) 952-956
Negro SS, Millet EJ, Madur D, Bauland C, Combes V, Welcker C, Tardieu F, Charcosset A, Nicolas SD. (2019) Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies. BMC Plant Biol., 1 (19) 318
Rio S, 2019-04-26 26/04/19, Contributions to genomic selection and association mapping in structured and admixed populations : application to maize
Rio S, Mary-Huard T, Moreau L, Charcosset A. (2019) Genomic selection efficiency and a priori estimation of accuracy in a structured dent maize panel. Theor Appl Genet, 1 (132) 81-96
Seye A, 2019-03-21 21/03/19, Prédiction assistée par marqueurs de la performance hybride dans un schéma de sélection réciproque : simulations et évaluation expérimentale pour le maïs ensilage
Seye AI, Bauland C, Giraud H, Mechin V, Reymond M, Charcosset A, Moreau L. (2019) Quantitative trait loci mapping in hybrids between Dent and Flint maize multiparental populations reveals group-specific QTL for silage quality traits with variable pleiotropic effects on yield. Theor Appl Genet, 5 (132) 1523-1542
Darracq A, Vitte C, Nicolas S, Duarte J, Pichon JP, Mary-Huard T, Chevalier C, Bérard A, Le Paslier MC, Rogowsky P, Charcosset A, Joets J. (2018) Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics, 1 (19) 119
Joets J, Vitte C, Charcosset A, Bennetzen J, Flint-Garcia S, Hirsch C, Tuberosa R. (2018) Draft assembly of the F2 European maize genome sequence and its comparison to the B73 genome sequence: a characterization of genotype-specific regions.. , In Press
Laporte F, 2018-03-13 13/03/18, Développement de méthodes statistiques pour l’identification de gènes d’intérêt en présence d’apparentement et de dominance, application à la génétique du maïs
Bedoya CA, Dreisigacker S, Hearne S, Franco J, Mir C, Prasanna BM, Taba S, Charcosset A, Warburton ML. (2017) Genetic diversity and population structure of native maize populations in Latin America and the Caribbean. PLoS One, 4 (12)
Bouchet S, Bertin P, Presterl T, Jamin P, Coubriche D, Gouesnard B, Laborde J, Charcosset A. (2017) Association mapping for phenology and plant architecture in maize shows higher power for developmental traits compared with growth influenced traits. Heredity (Edinb), 3 (118) 249-259
Brandenburg JT, Mary-Huard T, Rigaill G, Hearne SJ, Corti H, Joets J, Vitte C, Charcosset A, Nicolas SD, Tenaillon MI. (2017) Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLOS Genetics, 3 (13) e1006666
Giraud H, Bauland C, Falque M, Madur D, Combes V, Jamin P, Monteil C, Laborde J, Palaffre C, Gaillard A, Blanchard P, Charcosset A, Moreau L. (2017) Reciprocal Genetics: Identifying QTL for General and Specific Combining Abilities in Hybrids Between Multiparental Populations from Two Maize (Zea mays L.) Heterotic Groups. Genetics, 3 (207) 1167-1180
Giraud H, Bauland C, Falque M, Madur D, Combes V, Jamin P, Monteil C, Laborde J, Palaffre C, Gaillard A, Blanchard P, Charcosset A, Moreau L. (2017) Linkage Analysis and Association Mapping QTL Detection Models for Hybrids Between Multiparental Populations from Two Heterotic Groups: Application to Biomass Production in Maize (Zea mays L.). G3: Genes, Genomes, Genetics, g3.300121.2017
Laporte F, Charcosset A, Mary‐Huard T. (2017) Estimation of the relatedness coefficients from biallelic markers, application in plant mating designs. Biometrics, 3 (73) 885-894
Larièpe A, Moreau L, Laborde J, Bauland C, Mezmouk S, Décousset L, Mary-Huard T, Fiévet JB, Gallais A, Dubreuil P, Charcosset A. (2017) General and specific combining abilities in a maize (Zea mays L.) test-cross hybrid panel: relative importance of population structure and genetic divergence between parents. Theor. Appl. Genet., 2 (130) 403-417
Rincent R, Charcosset A, Moreau L. (2017) Predicting genomic selection efficiency to optimize calibration set and to assess prediction accuracy in highly structured populations. Theor Appl Genet, 11 (130) 2231-2247
Fernandez O, Urrutia M, Bernillon S, Giauffret C, Tardieu F, Le Gouis J, Langlade N, Charcosset A, Moing A, Gibon Y. (2016) Fortune telling: metabolic markers of plant performance. Metabolomics, 10 (12) 158
Giraud H, 2016-01-22 22/01/16, Genetic analysis of hybrid value for silage maize in multiparental designs : QTL detection and genomic selection
Millet E, Welcker C, Kruijer W, Negro S, Nicolas S, Coupel-Ledru A, Bauland C, Praud S, Ranc N, Presterl T, Tuberosa R, Bedo Z, Draye X, Usadel B, Charcosset A, van Eeuwijk F, Tardieu F. (2016) Genome-wide analysis of yield in Europe: allelic effects as functions of drought and heat scenarios. Plant physiology, 2 (172) 749-764
Moreau L, Charmet G, Charcosset A, Le Gouis J, Deretz S. (2016) Quelle place pour la selection génomique chez les espèces de grande culture ?. ,
Revilla P, Rodriguez VM, Ordas A, Rincent R, Charcosset A, Giauffret C, Melchinger AE, Schon CC, Bauer E, Altmann T, Brunel D, Moreno-Gonzalez J, Campo L, Ouzunova M, Alvarez A, Ruiz de Galarreta JI, Laborde J, Malvar RA. (2016) Association mapping for cold tolerance in two large maize inbred panels. BMC plant biology, 1 (16) 127
Rousselle Y, Jones E, Charcosset A, Moreau P, Robbins K, Stich B, Knaak C, Flament P, Karaman Z, Martinant JP, Fourneau M, Taillardat A, Romestant M, Tabel C, Bertran J, Ranc N, Lespinasse D, Blanchard P, Kahler A, Chen J, Kahler J, Dobrin S, Warner T, Ferris R, Smith S. (2015) Study on Essential Derivation in Maize: III. Selection and Evaluation of a Panel of Single Nucleotide Polymorphism Loci for Use in European and North American Germplasm. Crop Science, 3 (55) 1170-1180
Berthet E, Charcosset A, Lemarié S, Moreau L, Segrestin B, Debaeke P, Quilot-Turion B. (2014) Nouvelles questions pour la conception.. ,
Giraud H, Lehermeier C, Bauer E, Falque M, Segura V, Bauland C, Camisan C, Campo L, Meyer N, Ranc N, Schipprack W, Flament P, Melchinger AE, Menz M, Moreno-Gonzalez J, Ouzunova M, Charcosset A, Schon CC, Moreau L. (2014) Linkage disequilibrium with linkage analysis of multiline crosses reveals different multiallelic QTL for hybrid performance in the flint and dent heterotic groups of maize. Genetics, 4 (198) 1717-34
Lehermeier C, Kramer N, Bauer E, Bauland C, Camisan C, Campo L, Flament P, Melchinger AE, Menz M, Meyer N, Moreau L, Moreno-Gonzalez J, Ouzunova M, Pausch H, Ranc N, Schipprack W, Schonleben M, Walter H, Charcosset A, Schon CC. (2014) Usefulness of multiparental populations of maize (Zea mays L.) for genome-based prediction. Genetics, 1 (198) 3-16
Revilla P, Rodriguez VM, Ordas A, Rincent R, Charcosset A, Giauffret C, Melchinger AE, Schon CC, Bauer E, Altmann T, Brunel D, Moreno-Gonzalez J, Campo L, Ouzunova M, Laborde J, Alvarez A, de Galarreta JIR, Malvar RA. (2014) Cold Tolerance in Two Large Maize Inbred Panels Adapted to European Climates. Crop Sci., 5 (54) 1981-1991
Rincent R, Moreau L, Monod H, Kuhn E, Melchinger AE, Malvar RA, Moreno-Gonzalez J, Nicolas S, Madur D, Combes V, Dumas F, Altmann T, Brunel D, Ouzunova M, Flament P, Dubreuil P, Charcosset A, Mary-Huard T. (2014) Recovering power in association mapping panels with variable levels of linkage disequilibrium. Genetics, 1 (197) 375-87
Rincent R, Nicolas S, Bouchet S, Altmann T, Brunel D, Revilla P, Malvar RA, Moreno-Gonzalez J, Campo L, Melchinger AE, Schipprack W, Bauer E, Schoen CC, Meyer N, Ouzunova M, Dubreuil P, Giauffret C, Madur D, Combes V, Dumas F, Bauland C, Jamin P, Laborde J, Flament P, Moreau L, Charcosset A. (2014) Dent and Flint maize diversity panels reveal important genetic potential for increasing biomass production. Theor Appl Genet, 11 (127) 2313-31
Rincent R, 2014-11-04 11/04/14, Optimization of association genetics and genomic selection strategies for populations of different diversity levels. Application in maize (Zea mays L.)
Valente F, Gauthier F, Bardol N, Blanc G, Joets J, Charcosset A, Moreau L, Fleury D, Whitford R. (2014) OptiMAS: A Decision Support Tool to Conduct Marker-Assisted Selection Programs. , (1145) 97-116
Bardol N, Ventelon M, Mangin B, Jasson S, Loywick V, Couton F, Derue C, Blanchard P, Charcosset A, Moreau L. (2013) Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 11 (126) 2717-36
Bardol N, 2013-08-03 08/03/13, Interest of dense genotyping for selection in multi-parental designs. Comparison of two marker-assisted selection approaches: Genomewide selection and QTL-LDLA based selection. Application in maize (Zea mays L.)
Bauer E, Falque M, Walter H, Bauland C, Camisan C, Campo L, Meyer N, Ranc N, Rincent R, Schipprack W, Altmann T, Flament P, Melchinger AE, Menz M, Moreno-Gonzalez J, Ouzunova M, Revilla P, Charcosset A, Martin OC, Schon CC. (2013) Intraspecific variation of recombination rate in maize. Genome biology, 9 (14) R103
Bouchet S, Servin B, Bertin P, Madur D, Combes V, Dumas F, Brunel D, Laborde J, Charcosset A, Nicolas S. (2013) Adaptation of maize to temperate climates: mid-density genome-wide association genetics and diversity patterns reveal key genomic regions, with a major contribution of the Vgt2 (ZCN8) locus. PloS one, 8 (8) e71377
Mir C, Zerjal T, Combes V, Dumas F, Madur D, Bedoya C, Dreisigacker S, Franco J, Grudloyma P, Hao PX, Hearne S, Jampatong C, Laloe D, Muthamia Z, Nguyen T, Prasanna BM, Taba S, Xie CX, Yunus M, Zhang S, Warburton ML, Charcosset A. (2013) Out of America: tracing the genetic footprints of the global diffusion of maize. Theor Appl Genet, 11 (126) 2671-82
Valente F, Gauthier F, Bardol N, Blanc G, Joets J, Charcosset A, Moreau L. (2013) OptiMAS: a decision support tool for marker-assisted assembly of diverse alleles. The Journal of heredity, 4 (104) 586-90
Durand E, Bouchet S, Bertin P, Ressayre A, Jamin P, Charcosset A, Dillmann C, Tenaillon MI. (2012) Flowering time in maize: linkage and epistasis at a major effect locus. Genetics, 4 (190) 1547-62
Khobragade A, 2012-03-23 23/03/12, Combining linkage analysis and association genetics to finely map loci involved in maize grain production and maturation -- Cartographie fine de locus impliqués dans la production et la maturation du grain chez le maïs par une approche conjointe de linkage et de génétique d’association
Larièpe A, Mangin B, Jasson S, Combes V, Dumas F, Jamin P, Lariagon C, Jolivot D, Madur D, Fievet J, Gallais A, Dubreuil P, Charcosset A, Moreau L. (2012) The genetic basis of heterosis: multiparental quantitative trait loci mapping reveals contrasted levels of apparent overdominance among traits of agronomical interest in maize (Zea mays L.). Genetics, 2 (190) 795-811
Rincent R, Laloe D, Nicolas S, Altmann T, Brunel D, Revilla P, Rodriguez VM, Moreno-Gonzalez J, Melchinger A, Bauer E, Schoen CC, Meyer N, Giauffret C, Bauland C, Jamin P, Laborde J, Monod H, Flament P, Charcosset A, Moreau L. (2012) Maximizing the reliability of genomic selection by optimizing the calibration set of reference individuals: comparison of methods in two diverse groups of maize inbreds (Zea mays L.). Genetics, 2 (192) 715-28
Sosnowski O, Charcosset A, Joets J. (2012) BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms. Bioinformatics, 15 (28) 2082-3
Truntzler M, Ranc N, Sawkins MC, Nicolas S, Manicacci D, Lespinasse D, Ribiere V, Galaup P, Servant F, Muller C, Madur D, Betran J, Charcosset A, Moreau L. (2012) Diversity and linkage disequilibrium features in a composite public/private dent maize panel: consequences for association genetics as evaluated from a case study using flowering time. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 4 (125) 731-47
Zerjal T, Rousselet A, Mhiri C, Combes V, Madur D, Grandbastien MA, Charcosset A, Tenaillon MI. (2012) Maize genetic diversity and association mapping using transposable element insertion polymorphisms. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 8 (124) 1521-37
Charcosset A, Moreau L, Ricroch A, Dattée Y, Fellous M. (2011) Cartographie de QTL, génétique d’association et application en sélection. , 112-125
Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, Charcosset A, Clarke JD, Graner EM, Hansen M, Joets J, Le Paslier MC, McMullen MD, Montalent P, Rose M, Schön CC, Sun Q, Walter H, Martin OC, Falque M, Lukens L. (2011) A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome. PLoS ONE, 12 (6) e28334
Manicacci D, Moreau L, Charcosset A, Prioul JL, Thévenot C, Molnar T, Mike Burrel . (2011) QTL cartography, meta-analysis and association genetics. , 37-66
Mezmouk S, Dubreuil P, Bosio M, Decousset L, Charcosset A, Praud S, Mangin B. (2011) Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels. Theor Appl Genet, 6 (122) 1149-60
Moreau L, Charcosset A, Prioul JL, Thévenot C, Molnar T, Mike Burrel . (2011) Marker-assisted selection in maize. , 411-434
Tenaillon MI, Charcosset A. (2011) A European perspective on maize history. Comptes rendus biologies, 3 (334) 221-8
Warburton M, Wilkes G, Taba S, Charcosset A, Mir C, Dumas F, Madur D, Dreisigacker S, Bedoya C, Prasanna B, Xie C, Hearne S, Franco J. (2011) Gene flow among different teosinte taxa and into the domesticated maize gene pool. Genet Resour Crop Ev, 8 (57) 1243-1261
Welcker C, Sadok W, Dignat G, Renault M, Salvi S, Charcosset A, Tardieu F. (2011) A common genetic determinism for sensitivities to soil water deficit and evaporative demand: meta-analysis of quantitative trait Loci and introgression lines of maize. Plant physiology, 2 (157) 718-29