GQMS - Quantitative Genetics and Plant Breeding Methodology

Dominique Ahouanhode
Cyril Bauland
Sana Beji
Alain Charcosset
Bartschi Cédric
Annaig De Walsche
Augustin Desprez
Julie Fiévet
Agustin Galaretto
Romain Kadoumi
Tristan Mary-Huard
Laurence Moreau
Stéphane Nicolas
Renaud Rincent

1. Understand the organization of diversity in Maize

We aim at understanding the effect of historical and modern breeding on the evolution and adaptation of open pollinated and maize hybrid varieties, in terms of phenotypic variation, global organization of genetic diversity and polymorphism at the genome scale.

2. Decipher quantitative trait architecture

We aim to identify the genetic bases of complex traits for direct applications in marker-assisted and/or genomic selection, but also to better understand the nature of the genetic effects involved and the genotype-phenotype relationship using systems genetics approaches (integration of multi-omics data). We are paying specific attention to flowering time, biomass productivity under environmental constraints (particularly abiotic ones), performance stability and hybrid vigor in maize in relation to climate change and changes in agricultural practices (reduced inputs, agroecology, plant-mycorrhizae interactions, etc.).

3. Optimize breeding schemes

Our objectives are to optimize the breeding process, from genetic resources to variety development. We investigate more particularly the potential of genomic and phenomic predictions for improving diversity management in breeding schemes, for identifying and introgressing new sources of diversity in elite germplasm (issued from geneti resources or obtained by “New breeding Technologies”) and for optimizing breeding schemes in order to develop hybrids, improved populations or synthetics.

This research involves experimental and theoretical approaches, development of statistical methods and decision support tools.

Experimental approaches involve the assembly of diversity panels, the development of original genetic materials in maize, their genotyping in targeted chromosome segments or at the whole genome scale with different marker densities integrating also sequencing approaches and their phenotyping. These experiments are conducted by team members and also benefit to a large extent of the support of INRAE experimental structures and private partners involved in our research projects. Theoretical approaches aim more particularly at developing methods and optimizing experiments for QTL detection (using linkage or association mapping and meta-analysis), marker-assisted selection (with a specific focus on genomic selection), phenomic selection and systems genetics (multi-omics integration). These approaches being generic beyond maize, we collaborate to different projects on other species (beans andother legumes in the framework of INCREASE project, sugar beet, flax, cucumber, wheat, tomatoes, etc). We more particularly collaborate with the ABI group (now BiOSS) for the development of software (Biomercator, OptiMAS), database (ThaliaDB) and R packages (MM4LMM, Relatedness, metaGE, qch, fst4pg).

Beyond our research projects, we provide to researchers and technicians of INRAE working on maize knowledge sharing and we organize the circulation of genetic resources (coordination of the maize group and of the activities of Maize Biological Resources Center).

Most recent projects/network coordinated by team members (as PI or WP leaders):

Teaching:

Our teaching activities are focused on our main expertise domains such as population genetics, quantitative genetics, plant breeding, modern breeding methods (from QTL detection to genomic or phenomic selection), statistical modelling, adaptation of plants to abiotic stresses and genomics. We mostly contributed to different specialization of the engineer school AgroparisTech by co-organizing the PISTv specialization and the BIP master degree (M1 and M2) from the Univesity of Paris-Saclay. Researchers of our team also contribute more ponctually to other formations such as Institut Agro Rennes-Angers, Institut Agro Montpellier, ENS, Clermont-Auvergne University, Picardie Jules Verne University or the Reims-Champagne Ardennes University.

We also provide teaching to other researchers and breeders through the organization of (i) modules of the doctoral school ABIES on reproducible research and statistical modelling(ii) workshops organized in the framework of research projects or INRAE meta-programs (iii) (iii) training establishment such as ASFIS and (iii) training session defined specifically for breeding companies.

GQMS is attached to ABIES doctoral school.

Members

Former members

Alizarine Lorenzi, Doctorant (2019-2023); Dimitri Sanchez, Doctorant (2019-2023); Aurélien Beugnot, Doctorant (2019-2022) ; Pauline Robert, Doctorant (2020-2022); Capucine PONCE, DUT (2022); Antoine Roux, M2 (2022); Margaux Jullien, post-doctorante (2020-2021) ; Yacine DJABALI, M2 (1/2 PAPPSO)(2020); Alexis Vergne, M1 (2020); Antoine ALLIER, Doctorant (2017-2020); Clément MABIRE (2016-2019), Doctorant ; Simon RIO, Doctorant (2016-2019) ; Adama SEYE, Doctorant (2016-2019) ; Morgane Roth, Post-doc (3 mois en 2019); Romane Guilbaud (2018-2019); Camille Clipet, Ingénieur (2017-2018); Elodie Petitjean, M2(2018); Fabien Laporte, Doctorant (2015-2018); Alban Besnard, M2 (2017); Heloïse Giraud, Doctorante (2012-2016); Marie Gauvin, TR CDD (2017); Cecile Monteil, TR (2013-2017); Philippe Jamin, TR (1993-2017); Sandra Negro, Post-doc (2013-2016); Mariangela Arca, Post-doc (2012-2014); Franck Gauthier, Ingenieur (2011 puis 2013-2014); Fabio Valente, Ingenieur (2009-2013); Magali Joannin, TR (2011-2013); Denis Coubriche, TR ( ); Nicolas Bardol, Doctorant (2010-2013); Xiao Wang, Post-doc (2013); Amandine Larièpe, Doctorante (2008-2012); Ashwin Khobragade, Doctorant (2008-2012); Sophie Bouchet, Post-doc (2009-2012); Marion Trunztler, Doctorante (2008-2011); Yves Roussel, Post-doc (2011); Valerie Loywyck, Post-doc (2008-2010); Tatiana Zerjal, Post-doc (2009); Celine Mir, Post-doc (2006-2009); Yung-Fen Huang, M2 (2008)

Members

Former members

Alizarine Lorenzi PhD student (2020-2023), Dimitri Sanchez PhD student (2020-2023), Aurélien Beugnot PhD student (2020-2023), Pauline Robert PhD student (2020-2022), Margaux Julien Assistant Professor (2021-2020)

Publications

  • Ali B. , Huguenin-Bizot B., Laurent M., Chaumont F., Maistriaux LC., Nicolas S. , Duborjal H., Welcker C., Tardieu F., Mary-Huard T. , Moreau L. , Charcosset A. , Runcie D., Rincent R. . (2024) High-dimensional multi-omics measured in controlled conditions are useful for maize platform and field trait predictions. Theor Appl Genet, 7 (137) 175
  • Balconi C., Galaretto A. , Malvar RA., Nicolas S. , Redaelli R., Andjelkovic V., Revilla P., Bauland C. , Gouesnard B., Butron A., Torri A., Barata AM., Kravic N., Combes V. , Mendes-Moreira P., Murariu D., Šarčević H., Schierscher-Viret B., Vincent M., Zanetto A., Kessel B., Madur D. , Mary-Huard T. , Pereira A., Placinta DD., Strigens A., Charcosset A. , Goritschnig S.. (2024) Genetic and Phenotypic Evaluation of European Maize Landraces as a Tool for Conservation and Valorization of Agrobiodiversity. Biology, 6 (13) 454
  • De Walsche A. , Gauthier F., Charcosset A. , Mary-Huard T. . (2024) Large-scale composite hypothesis testing for omics analyses. ,
  • Lorenzi A., Bauland C. , Pin S., Madur D. , Combes V. , Palaffre C., Guillaume C., Touzy G., Mary-Huard T. , Charcosset A. , Moreau L. . (2024) Portability of genomic predictions trained on sparse factorial designs across two maize silage breeding cycles. Theor Appl Genet, 3 (137) 75
  • Maistriaux LC., Laurent MJ., Jeanguenin L., Prado SA., Nader J., Welcker C., Charcosset A. , Tardieu F., Nicolas S. , Chaumont F.. (2024) Genetic variability of aquaporin expression in maize: From eQTLs to a MITE insertion regulating PIP2;5 expression. Plant Physiology, kiae326
  • Arca M., Gouesnard B., Mary‐Huard T., Le Paslier MC., Bauland C. , Combes V. , Madur D. , Charcosset A. , Nicolas S. . (2023) Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next‐generation varieties. Plant Biotechnology Journal, 6 (21) 1123-1139
  • Beugnot A., 07/02/2023, Hybrid performance in maize: from study of complementary between heterotic groups to genomic prediction, PhD, Université Paris-Saclay
  • Bouidghaghen J., Moreau L. , Beauchêne K., Chapuis R., Mangel N., Cabrera‐Bosquet L., Welcker C., Bogard M., Tardieu F.. (2023) Robotized indoor phenotyping allows genomic prediction of adaptive traits in the field. Nat Commun, 1 (14) 6603
  • 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. ,
  • Fraunhoffer NA., Moreno Vega AI., Abuelafia AM., Morvan M., Lebarbier E., Mary-Huard T. , Zimmermann MT., Lomberk G., Urrutia R., Dusetti N., Blum Y., Nicolle R., Iovanna J.. (2023) Priming therapy by targeting enhancer-initiated pathways in patient-derived pancreatic cancer cells. eBioMedicine, (92) 104602
  • Galić V., Anđelković V., Kravić N., Grčić N., Ledenčan T., Jambrović A., Zdunić Z., Nicolas S. , Charcosset A. , Šatović Z., Šimić D.. (2023) Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels. BMC Plant Biol, 1 (23) 315
  • Haug B., Messmer MM., Enjalbert J., Goldringer I., Flutre T., Mary-Huard T. , Hohmann P.. (2023) New insights towards breeding for mixed cropping of spring pea and barley to increase yield and yield stability. Field Crops Research, (297) 108923
  • Legarra A., Gonzalez-Dieguez DO., Charcosset A. , Vitezica ZG.. (2023) Impact of interpopulation distance on dominance variance and average heterosis in hybrid populations within species. GENETICS, 2 (224)
  • Lorenzi A., 08/11/2023, Optimization of genomic selection for hybrids in a reciprocal selection program: Experimental evaluation in maize and simulations, PhD, Université Paris-Saclay
  • Mary-Huard T. , Balding D., Weir BS.. (2023) Fast and accurate joint inference of coancestry parameters for populations and/or individuals. PLoS Genet, 1 (19) e1010054
  • 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
  • Rio S., Charcosset A. , Moreau L. , Mary-Huard T. , Endelman J.. (2023) Detecting directional and non-directional epistasis in bi-parental populations using genomic data. GENETICS, 3 (224) iyad089
  • Rishmawi L., Bauget F., Protto V., Bauland C. , Nacry P., Maurel C.. (2023) Natural variation of maize root hydraulic architecture underlies highly diverse water uptake capacities. Plant Physiology, 3 (192) 2404-2418
  • Sanane I., Nicolas S. , Bauland C. , Marion-Poll F., Noûs C., Legrand J., Dillmann C.. (2023) Large genetic variability of maize leaf palatability to european corn borer : metabolic insights. bioRxiv,
  • Sanchez D., Sadoun SB., Mary-Huard T. , Allier A., Moreau L. , Charcosset A. . (2023) Improving the use of plant genetic resources to sustain breeding programs’ efficiency. Proc. Natl. Acad. Sci. U.S.A., 14 (120) e2205780119
  • Sanchez D., 29/09/2023, Incorporation of genetic resources in breeding programs: theoretical analysis and experimental evaluation of a pre-breeding multiparental maize population, PhD, Université Paris-Saclay
  • 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
  • Laporte F., Charcosset A. , Mary-Huard T. . (2022) Efficient ReML inference in variance component mixed models using a Min-Max algorithm. PLoS Comput Biol, 1 (18) e1009659
  • 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
  • Lorenzi A., Bauland C. , Mary-Huard T. , Pin S., Palaffre C., Guillaume C., Lehermeier C., Charcosset A. , Moreau L. . (2022) Genomic prediction of hybrid performance: comparison of the efficiency of factorial and tester designs used as training sets in a multiparental connected reciprocal design for maize silage. Theor Appl Genet,
  • Monnot S., Cantet M., Mary-Huard T. , Moreau L. , Lowdon R., Van Haesendonck M., Ricard A., Boissot N.. (2022) Unravelling cucumber resistance to several viruses via genome-wide association studies highlighted resistance hotspots and new QTLs. Horticulture Research, uhac184
  • 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
  • Roth M., Beugnot A., Mary-Huard T. , Moreau L. , Charcosset A. , Fievet JB.. (2022) Improving genomic predictions with inbreeding and non-additive effects in two admixed maize hybrid populations in single and multi-environment contexts. Genetics, iyac018
  • Speck A., Trouvé JP., Enjalbert J., Geffroy V., Joets J., Moreau L. . (2022) Genetic Architecture of Powdery Mildew Resistance Revealed by a Genome-Wide Association Study of a Worldwide Collection of Flax (Linum usitatissimum L.). Front. Plant Sci., (13) 871633
  • Welcker C., Spencer NA., Turc O., Granato I., Chapuis R., Madur D. , Beauchene K., Gouesnard B., Draye X., Palaffre C., Lorgeou J., Melkior S., Guillaume C., Presterl T., Murigneux A., Wisser RJ., Millet EJ., van Eeuwijk F., Charcosset A. , Tardieu F.. (2022) Physiological adaptive traits are a potential allele reservoir for maize genetic progress under challenging conditions. Nat Commun, 1 (13) 3225
  • Arca M., Mary-Huard T. , Gouesnard B., Bérard A., Bauland C. , Combes V. , Madur D. , Charcosset A. , Nicolas S. . (2021) Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array. Front. Plant Sci., (11) 568699
  • 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
  • Diaw Y., Tollon-Cordet C., Charcosset A. , Nicolas S. , Madur D. , Ronfort J., David J., Gouesnard B., Chiang TY.. (2021) Genetic diversity of maize landraces from the South-West of France. PLoS ONE, 2 (16) e0238334
  • Gonzàlez-Diéguez D., Legarra A., Charcosset A. , Moreau L. , Lehermeier C., Teyssèdre S., Vitezica ZG.. (2021) Genomic Prediction of Hybrid Crops Allows Disentangling Dominance and Epistasis. Genetics, iyab026
  • Haug B., Messmer MM., Enjalbert J., Goldringer I., Forst E., Flutre T., Mary-Huard T. , Hohmann P.. (2021) Advances in Breeding for Mixed Cropping – Incomplete Factorials and the Producer/Associate Concept. Front. Plant Sci., (11) 620400
  • Mary-Huard T. , Perduca V., Martin-Magniette ML., Blanchard G.. (2021) Error rate control for classification rules in multiclass mixture models. The International Journal of Biostatistics, 0 (0)
  • Mary-Huard T. , Das S., Mukhopadhyay I., Robin S., Birol I.. (2021) Querying multiple sets of P -values through composed hypothesis testing. Bioinformatics, 1 (38) 141-148
  • Monnot S., Desaint H., Mary-Huard T. , Moreau L. , Schurdi-Levraud V., Boissot N.. (2021) Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances. Cells, 11 (10) 3080
  • Allier A., 2020-01, Contributions to Genetic Diversity Management in Maize Breeding Programs using Genomic Selection, Theses, Université Paris-Saclay
  • 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
  • Arca M., Gouesnard B., Mary-Huard T. , Le Paslier MC., Bauland C. , Combes V. , Madur D. , Charcosset A. , Nicolas S. . (2020) Genome-wide SNP genotyping of DNA pools identifies untapped landraces and genomic regions that could enrich the maize breeding pool. DOI.org (Crossref),
  • Benoist R., Capdevielle‐Dulac C., Chantre C., Jeannette R., Calatayud PA., Drezen JM., Dupas S., Le Rouzic A., Le Ru B., Moreau L. , Van Dijk E., Kaiser L., Mougel F.. (2020) Quantitative Trait Loci involved in the reproductive success of a parasitoid wasp. Mol Ecol, mec.15567
  • Blein-Nicolas M., Negro SS., Balliau T., Welcker C., Cabrera-Bosquet L., Nicolas S. , Charcosset A. , Zivy M.. (2020) A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Res., 11 (30) 1593-1604
  • Castelletti S., Coupel-Ledru A., Granato I., Palaffre C., Cabrera-Bosquet L., Tonelli C., Nicolas S. , Tardieu F., Welcker C., Conti L., de Meaux J.. (2020) Maize adaptation across temperate climates was obtained via expression of two florigen genes. PLoS Genet, 7 (16) e1008882
  • Diouf I., Derivot L., Koussevitzky S., Carretero Y., Bitton F., Moreau L. , Causse M., Rebetzke G.. (2020) Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population. Journal of Experimental Botany, eraa265
  • Goldringer I., van Frank G., Bouvier d’Yvoire C., Forst E., Galic N., Garnault M., Locqueville J., Pin S., Bailly J., Baltassat R., Berthellot JF., Caizergues F., Dalmasso C., de Kochko P., Gascuel JS., Hyacinthe A., Lacanette J., Mercier F., Montaz H., Ronot B., Rivière P.. (2020) Agronomic Evaluation of Bread Wheat Varieties from Participatory Breeding: A Combination of Performance and Robustness. Sustainability, 1 (12) 128
  • 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, 1 (216) 27-41
  • 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
  • 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
  • de Vienne D., Fiévet J. . (2020) The Pitfalls of Heterosis Coefficients. Plants, 7 (9) 875
  • 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
  • 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
  • Boussardon C., Martin-Magniette ML., Godin B., Benamar A., Vittrant B., Citerne S., Mary-Huard T. , Macherel D., Rajjou L., Budar F.. (2019) Novel Cytonuclear Combinations Modify Arabidopsis thaliana Seed Physiology and Vigor. Front Plant Sci, (10) 32
  • Courret C., Gérard PR., Ogereau D., Falque M., Moreau L. , Montchamp-Moreau C.. (2019) X-chromosome meiotic drive in Drosophila simulans: a QTL approach reveals the complex polygenic determinism of Paris drive suppression. Heredity, 6 (122) 906-915
  • Forst E., Enjalbert J., Allard V., Ambroise C., Krissaane I., Mary-Huard T. , Robin S., Goldringer I.. (2019) A generalized statistical framework to assess mixing ability from incomplete mixing designs using binary or higher order variety mixtures and application to wheat. Field Crops Research, (242) 107571
  • Fustier MA., Martínez-Ainsworth NE., Aguirre-Liguori JA., Venon A., Corti H., Rousselet A., Dumas F., Dittberner H., Camarena MG., Grimanelli D., Ovaskainen O., Falque M., Moreau L. , Meaux J., Montes-Hernández S., Eguiarte LE., Vigouroux Y., Manicacci D., Tenaillon MI.. (2019) Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude. PLOS Genetics, 12 (15) e1008512
  • Mabire C., 2019-04, Contribution des variations structurales de type insertions/délétions à l'adaptation, la variation des caractères et les performances hybrides chez le maïs, Theses, Université Paris Saclay (COmUE)
  • Mabire C., Duarte J., Darracq A., Pirani A., Rimbert H., Madur D. , Combes V. , Vitte C., Praud S., Rivière N., Joets J., Pichon JP., Nicolas S. . (2019) High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array. BMC Genomics, 1 (20) 848
  • 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
  • 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 S. . (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, Contributions to genomic selection and association mapping in structured and admixed populations : application to maize, Theses, Université Paris Saclay (COmUE)
  • 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 AI., 2019-03, Prédiction assistée par marqueurs de la performance hybride dans un schéma de sélection réciproque : simulations et évaluation expérimentale pour le maïs ensilage, Theses, Université Paris Saclay (COmUE)
  • 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
  • Virlouvet L., El Hage F., Griveau Y., Jacquemot MP., Gineau E., Baldy A., Legay S., Horlow C., Combes V. , Bauland C. , Palafre C., Falque M., Moreau L. , Coursol S., Méchin V., Reymond M.. (2019) Water Deficit-Responsive QTLs for Cell Wall Degradability and Composition in Maize at Silage Stage. Front. Plant Sci., (10) 488
  • Bennetzen J., Flint-Garcia S., Hirsch C., Tuberosa R., Joets J., Vitte C., Charcosset A. . (2018) Draft Assembly of the F2 European Maize Genome Sequence and Its Comparison to the B73 Genome Sequence: A Characterization of Genotype-Specific Regions. DOI.org (Crossref), 3-12
  • 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
  • Fiévet J. , Nidelet T., Dillmann C., de Vienne D.. (2018) Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations. Front. Genet., (9)
  • 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, PhD thesis, Université Paris-Saclay
  • Baldy A., Jacquemot MP., Griveau Y., Bauland C. , Reymond M., Mechin V.. (2017) Energy Values of Registered Corn Forage Hybrids in France over the Last 20 Years Rose in a Context of Maintained Yield Increase. American Journal of Plant Sciences, (08) 1449
  • 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)
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