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Génétique Quantitative et Évolution - Le Moulon


Junior Investigator, INRAE

Quantitative genetics and systems genetics of complex traits

  • Genome-Wide Association Mapping,
  • Genomic selection,
  • maize,
  • wheat,
  • omics,
  • genotype x environment interactions,
  • crop growth model



  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • 12 route 128
  • 91190 Gif-sur-Yvette

Education and Positions

  • 2020-Present: Paris Saclay University, INRAE Researcher, Quantitative Genetics and Evolution-Le Moulon, Gif-sur-Yvette, France. Integration of multi-omics data.
  • 2007-2009: Post-doctoratal Fellow Agreenskills+ (Pierre and Marie Curie) on the “prediction of genotype by environment interactions”, University of Wageningen, Wageningen, The Nethelands.
  • 2014-2020: INRAE Researcher, Genetics, Diversity, Ecophysiogy of cereals (GDEC), Clermont-Ferrand, France. Adaptation of Wheat to climate change.
  • 2011-2014: Phd student on the “Optimization of genomic selection and association mapping” with A. Charcosset and L. Moreau, INRAE-GQE Le Moulon, Gif-sur-Yvette, France.
  • 2011: MsC in Agricultural science (major Plant Genetics and Breeding), AgroCampus Ouest.
  • 2010: MsC in Agricultural and Environmetal science, AgroParisTech.
  • 2008: 6 months internship at KWS, Einbeck, Germany. Sugar Beet Molecular Breeding.
  • 2007: 6 months internship at Simon Fraser University, Vancouver, Canada. Ecophysiology of Bird Reproduction.

Research Interests

I am a quantitative geneticist interested in understanding and predicting the genotype/phenotype relationship. I am particularly involved in the modelling of genotype by environment interactions using association mapping and genomic prediction. I developed new approaches to improve association mapping detection power, and genomic prediction accuracy by optimizing the composition of the calibration set or by using crop-growth modelling. Recently I contributed to the development of a new approach for phenotype prediction (phenomic selection) based on Near Infrared Spectroscopy. I currently work on the integration of multi-omics data to refine our understanding of the genotype/phenotype relationship.

Main current collaborations

  • Lab’s: L. Moreau, A. Charcosset, T. Mary-Huard, S. Nicolas, J. Fievet (GQMS), C. Dillmann, J. Legrand (BASE), M. Zivy, M. Blein-Nicolas (PAPPSO)

  • France: P. Roumet, V. Segura (INRAE-AGAP) ; E. Kuhn, H. Monod, B. Mangin, M.-L. Martin-Magniette (INRAE-MIA) ; P. Martre, F. Tardieu, C. Welcker (INRAE-LEPSE) ; C. Salon, C. Jeudy, M. Lamboeuf (INRAE-4PMI) ; J. Le-Gouis, S. Bouchet, G. Charmet, E. Paux, C. Grand-Ravel (INRAE-GDEC) ; C. Giauffret (INRAE-AgroImpact) ; P. Dubreuil, A.-V. Dumas (Limagrain) ; K. Beauchene, M. Bogard (Arvalis) ; J. Auzanneau (Agri-Obtentions) ; E. Goudemand-Dugue, P. Lonnet (Florimond-Desprez) ; G. Touzy, P. Dufour (RAGT)

  • International: F. Van Eeuwick, D. Bustos-Kort, E. Millet (Wageningen University), J. Crossa (CIMMYT), X. Draye (UC Louvain), N. Pecchioni, G. Laido (CREA).

Teaching / Training

Phd Student / Postdoctoral Fellowship / CDD

  • Delphine Ly (INRAE GDEC 2013-2017)
  • Ali Zidi (INRAE GDEC 2014-2016)
  • Gaetan Touzy (CIFFRE Arvalis 2017-2019)
  • Pauline Robert (CIFRE Agri-Obtentions, Florimond-Desprez 2019-2022)

Teaching and training:

  • Supervisor of the module on quantitative genetics for the Plant Integrative Biology and Breeding Master (Clermont-Ferrand)
  • Genome-Wide Association Study (Master degree PIBB Clermont-Ferrand).
  • Genomic Selection (Master degree PIBB Clermont-Ferrand)..

Main responsibilities in recent projects

  • 2021-2023: GPS4Pea, expertise for the implementation of phenomic selection for pea
  • 2019-2024: H2020 Invite, in charge of methological development for the integration of crop growth model and genomic prediction
  • 2018-2023: H2020 SolACE, in charge of genomic prediction and analysis of root architecture traits for durum and bread wheat
  • 2017-2020: Principal Investigator of FSOV project on the genetic analysis of root architecture for durum and bread wheat
  • 2018-2019: Principal Investigator of SelGen project OptiGBM : Methodology of “Gene-based modelling”
  • 2016-2017: Principal Investigator of SelGen project PredIGE : Genomic prediction of genotype x environment interactions
  • 2011-2020: Projet Investissement d’avenir BreedWheat Responsible of the genetic analysis of the genotype x environment interactions in the multi-environment trials


  • De Walsche A., Vergne A., Rincent R. , Roux F., Nicolas S., Welcker C., Mezmouk S., Charcosset A., Mary-Huard T.. (2023) metaGE: Investigating Genotype × Environment interactions through meta-analysis. Plant Biology,
  • Raffo MA., Cuyabano BCD., Rincent R. , Sarup P., Moreau L., Mary-Huard T., Jensen J.. (2023) Genomic prediction for grain yield and micro-environmental sensitivity in winter wheat. Front. Plant Sci., (13) 1075077
  • Revilla P., Butrón A., Rodriguez VM., Rincent R. , Charcosset A., Giauffret C., Melchinger AE., Schön CC., Bauer E., Altmann T., Brunel D., Moreno-González J., Campo L., Ouzunova M., Álvarez Ángel., Ruíz de Galarreta JI., Laborde J., Malvar RA.. (2023) Genetic Variation for Cold Tolerance in Two Nested Association Mapping Populations. Agronomy, 1 (13) 195
  • Ahmadi N., Bartholomé J., Rio S., Charcosset A., Mary-Huard T., Moreau L., Rincent R. . (2022) Building a Calibration Set for Genomic Prediction, Characteristics to Be Considered, and Optimization Approaches. DOI.org (Crossref), (2467) 77-112
  • Ahmadi N., Bartholomé J., Crossa J., Montesinos-López OA., Pérez-Rodríguez P., Costa-Neto G., Fritsche-Neto R., Ortiz R., Martini JWR., Lillemo M., Montesinos-López A., Jarquin D., Breseghello F., Cuevas J., Rincent R. . (2022) Genome and Environment Based Prediction Models and Methods of Complex Traits Incorporating Genotype × Environment Interaction. DOI.org (Crossref), (2467) 245-283
  • Ahmadi N., Bartholomé J., Robert P., Brault C., Rincent R. , Segura V.. (2022) Phenomic Selection: A New and Efficient Alternative to Genomic Selection. DOI.org (Crossref), (2467) 397-420
  • Colombo M., Roumet P., Salon C., Jeudy C., Lamboeuf M., Lafarge S., Dumas AV., Dubreuil P., Ngo W., Derepas B., Beauchêne K., Allard V., Le Gouis J., Rincent R. . (2022) Genetic Analysis of Platform-Phenotyped Root System Architecture of Bread and Durum Wheat in Relation to Agronomic Traits. Front. Plant Sci., (13) 853601
  • Lemeunier P., Paux E., Babi S., Auzanneau J., Goudemand-Dugué E., Ravel C., Rincent R. . (2022) Training population optimization for genomic selection improves the predictive ability of a costly measure in bread wheat, the gliadin to glutenin ratio. Euphytica, 8 (218) 111
  • Robert P., Auzanneau J., Goudemand E., Oury FX., Rolland B., Heumez E., Bouchet S., Le Gouis J., Rincent R. . (2022) Phenomic selection in wheat breeding: identification and optimisation of factors influencing prediction accuracy and comparison to genomic selection. Theor Appl Genet, 3 (135) 895-914
  • Robert P., Goudemand E., Auzanneau J., Oury FX., Rolland B., Heumez E., Bouchet S., Caillebotte A., Mary-Huard T., Le Gouis J., Rincent R. . (2022) Phenomic selection in wheat breeding: prediction of the genotype-by-environment interaction in multi-environment breeding trials. Theor Appl Genet, 10 (135) 3337-3356
  • Atanda SA., Olsen M., Crossa J., Burgueño J., Rincent R. , Dzidzienyo D., Beyene Y., Gowda M., Dreher K., Boddupalli PM., Tongoona P., Danquah EY., Olaoye G., Robbins KR.. (2021) Scalable Sparse Testing Genomic Selection Strategy for Early Yield Testing Stage. Front. Plant Sci., (12) 658978
  • Ben-Sadoun S., Rincent R. , Auzanneau J., Oury FX., Rolland B., Heumez E., Ravel C., Charmet G., Bouchet S.. (2020) Economical optimization of a breeding scheme by selective phenotyping of the calibration set in a multi-trait context: application to bread making quality. Theor Appl Genet, 7 (133) 2197-2212
  • Beral A., Rincent R. , Le Gouis J., Girousse C., Allard V., Zhang A.. (2020) Wheat individual grain-size variance originates from crop development and from specific genetic determinism. PLoS ONE, 3 (15) e0230689
  • Charmet G., Tran LG., Auzanneau J., Rincent R. , Bouchet S., Lukens L.. (2020) BWGS: A R package for genomic selection and its application to a wheat breeding programme. PLoS ONE, 4 (15) e0222733
  • Robert P., Le Gouis J., The BreedWheat Consortium, Rincent R. . (2020) Combining Crop Growth Modeling With Trait-Assisted Prediction Improved the Prediction of Genotype by Environment Interactions. Front. Plant Sci., (11) 827
  • Mangin B., Rincent R. , Rabier CE., Moreau L., Goudemand-Dugue E.. (2019) Training set optimization of genomic prediction by means of EthAcc. PLOS ONE, 2 (14) e0205629
  • Rincent R. , Malosetti M., Ababaei B., Touzy G., Mini A., Bogard M., Martre P., Le Gouis J., van Eeuwijk F.. (2019) Using crop growth model stress covariates and AMMI decomposition to better predict genotype-by-environment interactions. Theor Appl Genet, 12 (132) 3399-3411
  • Touzy G., Rincent R. , Bogard M., Lafarge S., Dubreuil P., Mini A., Deswarte JC., Beauchêne K., Le Gouis J., Praud S.. (2019) Using environmental clustering to identify specific drought tolerance QTLs in bread wheat (T. aestivum L.). Theor Appl Genet, 10 (132) 2859-2880
  • Ly D., Huet S., Gauffreteau A., Rincent R. , Touzy G., Mini A., Jannink JL., Cormier F., Paux E., Lafarge S., Le Gouis J., Charmet G.. (2018) Whole-genome prediction of reaction norms to environmental stress in bread wheat (Triticum aestivum L.) by genomic random regression. Field Crops Research, (216) 32-41
  • Rincent R. , Charpentier JP., Faivre-Rampant P., Paux E., Le Gouis J., Bastien C., Segura V.. (2018) Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar. G3, g3.200760.2018
  • Ly D., Chenu K., Gauffreteau A., Rincent R. , Huet S., Gouache D., Martre P., Bordes J., Charmet G.. (2017) Nitrogen nutrition index predicted by a crop model improves the genomic prediction of grain number for a bread wheat core collection. Field Crops Research, (214) 331-340
  • Rincent R. , Kuhn E., Monod H., Oury FX., Rousset M., Allard V., Le Gouis J.. (2017) Optimization of multi-environment trials for genomic selection based on crop models. Theor Appl Genet, 8 (130) 1735-1752
  • 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
  • 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
  • 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. , 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. , 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
  • 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
  • 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