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portrait d'Alain Charcosset



Génétique Quantitative et Évolution - Le Moulon
INRA - Université Paris-Sud - CNRS - AgroParisTech
Ferme du Moulon
F-91190 Gif-sur-Yvette
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Tel +33 (0)1 69 33 23 35



> 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: Maize diversity, quantitative traits, breeding methods

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- )


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


> Selected recent publications

  1. Allier A, Teyssèdre S, Lehermeier C, Charcosset A, Moreau L (2019b) Genomic prediction with a maize collaborative panel: identification of genetic resources to enrich elite breeding programs. Theor Appl Genet,
  2. Negro S. S., Millet E. J., Madur D., Bauland C., Combes V., Welcker C., Tardieu F., Welcker C. Tardieu F., Charcosset A. and Nicolas S. D. (2019) Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies. BMC Plant Biol 19 (1), 318. doi:10.1186/s12870-019-1926-4
  3. Blein-Nicolas M., Negro S.S., Balliau T.,  Welcker C., Cabrera Bosquet L., Nicolas S.D., Charcosset A. and Zivy M. (2019) Integrating proteomics and genomics into systems genetics provides novel insights into the mechanisms of drought tolerance in maize. Under consideration at Nature Communications, available at bioRxiv
  4. Millet E. J., Kruijer W., Coupel-Ledru A., Alvarez Prado S., Cabrera-Bosquet L., Lacube S., Charcosset A., Welcker C., Eeuwijk F. van, Tardieu F. (2019) Genomic prediction of maize yield across European environmental conditions. Nature Genetics, 51 (6) 952-956. doi:10.1038/s41588-019-0414-y
  5. 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 (Bethesda, Md.), 9 (5) 1469–1479. doi:10.1534/g3.119.400129
  6. Allier A., Teyssedre S., Lehermeier C., Claustres B., Maltese S., Melkior S., Moreau L. and Charcosset A. (2019) Assessment of breeding programs sustainability: application of phenotypic and genomic indicators to a North European grain maize program. Theor Appl Genet, 132 (5) 1321–1334. doi:10.1007/s00122-019-03280-w
  7. Seye A. I., Bauland C., Giraud H., Mechin V., Reymond M., Charcosset A. and 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, 132 (5) 1523–1542. doi:10.1007/s00122-019-03296-2.
  8. Rio S., Mary-Huard T., Moreau L. and Charcosset A. (2018) Genomic selection efficiency and a priori estimation of accuracy in a structured dent maize panel. Theor Appl Genet, 132 (1) 81-96.
  9. Darracq A.*, Vitte C.*, Nicolas S., Duarte J., Pichon J. P., Mary-Huard T., Chevalier C., Berard A., Le Paslier M. C., 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, 19 (1) 119.  * Equal contributor
  10. 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 QTLs for General and Specific Combining Abilities in Hybrids Between Multiparental Populations from Two Maize (Zea mays L.) Heterotic Groups. Genetics, 207 (3) 1167-1180.
  11. 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 (Bethesda), 7 (11) 3649-3657.
  12. Gouesnard B., Negro S., Laffray A., Glaubitz J., Melchinger A., Revilla P., Moreno-Gonzalez J., Madur D., Combes V., Tollon-Cordet C., Laborde J., Kermarrec D., Bauland C., Moreau L., Charcosset A., Nicolas S. (2017) Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines, as compared to the maize USDA genebank. Theor Appl Genet, 130 (10) 2165-2189.
  13. 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, 130 (11) 2231-2247.
  14. 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), 118 (3) 249-259.
  15. Lariepe A., Moreau L., Laborde J., Bauland C., Mezmouk S., Decousset L., Mary-Huard T., Fievet J. B., 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, 130 (2) 403-417.
  16. Laporte F., Charcosset A., Mary-Huard T. (2017) Estimation of the relatedness coefficients from biallelic markers, application in plant mating designs. Biometrics, 73 (3) 885-894.
  17. Rousselle Y., Jones E., Charcosset A., Moreau P., Robbins K., Stich B., Knaak C., Flament P., Karaman Z., Martinant J. P., Fourneau M., Taillardat A., Romestant M., Tabel C., Bertran J., Ranc N., Lespinasse D., Blanchard P., Kahler A., Chen J. L., 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, 55 (3) 1170-1180.
  18. 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 A.E., Menz M., Moreno-González J., Ouzunova M., Charcosset A., Schön C.C., Moreau L. (2014) Two multi-line crosses of maize (Zea mays L.) evaluated for reciprocal hybrid performance reveal different multi-allelic QTL in the flint and dent heterotic groups.  Genetics, 198:1717-1734.
  19. Lehermeier C., Krämer N., Bauer E., Bauland C., Camisan C., Campo L., Flament P., Melchinger A.E., Menz M., Meyer N., Moreau L., Moreno-González J., Ouzunova M., Pausch H., Ranc N., Schipprack W., Schönleben M., Walter H., Charcosset A., Schön C. C. (2014) Usefulness of multi-parental populations of maize (Zea mays L.) for genome-based prediction. Genetics 198:3–16
  20. Rincent R., Moreau L. Monod H., Kuhn E., Melchinger A.E., Malvar R.A., 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, 197: 375-387
  21. Bauer E., Falque M., Walter H., Bauland C., Camisan C., Campo L., Meyer N., Ranc N., Rincent R., Schipprack W., Wimmer V., Altmann T., Flament P., Melchinger A.E., Menz M., Moreno-González J., Ouzunova M., Revilla P., Charcosset A., Martin O.C., Schön C.-C. (2013) Intraspecific variation of recombination rate in maize. Genome Biology 14:R103.
  22. Bouchet, S., Larièpe, A., Servin, B., Bertin, P., Madur, D., Combes, V., Dumas, F., Moreau, L., Laborde, J., Charcosset, A. and Nicolas, S. D. (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)
  23. Mir C., Zerjal T., Combes V., Dumas F., Madur D., Bedoya C., Dreisigacker S., Franco J., Grudloyma P., Hao P.X., Hearne S., Jampatong C., Laloë D., Muthamia Z., Nguyen T., Prasanna B.M., Taba S., Xie C.X., Yunus M., Zhang S., Warburton M. L., Charcosset A. (2013) Out of America: tracing the genetic footprints of the global diffusion of maize. Theor Appl Genet, 126: 2671-2682.
  24. Valente F., Gauthier F., Bardol N., Blanc G., Joets J., Charcosset., Moreau L. (2013) OptiMAS: A Decision Support Tool for Marker-Assisted Assembly of Diverse Alleles. J Heredity doi:10.1093/jhered/est020
  25. Larièpe A., Mangin B., Jasson S., Combes V., Dumas F., Jamin P., Lariagon C., Jolivot D., Madur D., Fiévet J., Gallais A., Dubreuil P. , Charcosset A., Moreau L. (2012) Heterosis in maize (Zea mays L.): Joint QTL mapping in hybrids between Recombinant Inbred Lines and their three diverse parental lines reveals contrasted levels of apparent overdominance among traits of agronomical interest.  Genetics 190:795–811
  26. Rincent R., Laloë D., Nicolas S., Altmann T., Brunel D., Revilla P., Rodríguez V.M., Moreno-Gonzalez  J., Melchinger A., Bauer E., Schoen C.C., 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 192: 715-72

> Selected text available on line

Le fait hybride, A. Charcosset, 2004 (pdf, French)