FrancaisEnglish (United Kingdom)


Portrait de Stéphane Nicolas

Stéphane NICOLAS


Genomics of the maize genetic diversity

Génétique Quantitative et Évolution - Le Moulon
INRA - Université Paris-Sud - CNRS – AgroParisTech
Ferme du Moulon
F-91190 Gif-sur-Yvette
e-mail : Cette adresse email est protégée contre les robots des spammeurs, vous devez activer Javascript pour la voir.
Phone: + 33 1 69 33 23 69
Google scholar
- Research Gate - ORCID


> Educations and Positions

2009-Present: INRA Researcher, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
2007-2009: Post-doctoratal Fellow on “Fine mapping of linkage disequilibrium in grapevine”, AGAP, Montpelier, France
2007: Phd in Biology and Agriculture Plant Breeding and Genetics, Université Rennes 1 and Agrocampus Ouest, Rennes, France
2003-2007: Phd student on “Genetic control of homeologous recombination in haploid Oilseed Rape (Brassica napus L.)”, IGEPP (formely UMR Amélioration des Plantes et Biotechnologies Végétales), Rennes, France
2003: MsC in Agricultural science (major Plant Genetics and Breeding), AgroCampus Ouest, (formerly École Nationale Supérieure Agronomique de Rennes) and Master Degree in Plant Biology (Seeds and Plants), Université Rennes 1.

> Research Interests

Broadening the genetic diversity of the breeding programs by mining interesting allelic variation from the genetic resources is a key issue to speed up the genetic progress, to face the challenge of climate changes, and to decrease the use of fertilizers and pesticides. However, the exploitation of the genetic diversity in breeding programs is currently limited by the poor characterization of germplasms and by the difficulties to identify favorable alleles to improve agronomic traits of elite material. My research aims at overcoming these bottlenecks by better understanding (i) how the DNA polymorphisms contributed to agronomic trait variation, (ii) how the complex interplay between human/environmental selection and other evolutionary forces shaped the genetic diversity along the genome. Maize is a particularly good model to address these questions. Domesticated in Mexico around 9000 years ago, this tropical annual allogamous cereal with high degree of polymorphisms has been selected by humans to grown in various agro-climatic conditions and for various uses until becoming one of the largest cultivated cereal in the world playing an essential role in the food safety.

In this context, I am more particularly interested in:

  1. Deciphering the organization of the genetic diversity within the maize germplasm at the genome scale level and identifying interesting sources of genetic diversity for pre-breeding. My research are focusing on (i) the effect of the modern selection on the genetic diversity and linkage disequilibrium (transition from open pollinated varieties (landraces) to F1 hybrids...) by developing and implementing high-throughput sequencing and genotyping technologies and methods for studying landraces and inbred lines collection [1,2, 5, 7, 10], (ii) the detection of genomic regions involved in the adaptation of maize to contrasted environments by integrating selective footprints detection with association studies [1,2].
  2. Identifying the allelic variation involved in the variation of agronomic traits and in adaptation to different stress within inbred lines collection representing large genetic diversity using genome-wide association studies (GWAS). My research are focusing on (i) the development and implementation of high-throughput genotyping technologies, methods, and bio-informatics tools for performing GWAS [4,7,8,11], (ii) the effect of different biological parameters on the power of GWAS for detecting Quantitative Trait Loci [5,6,7], (iii) the development of integrative approaches coupling eco-physiology, GWAS, and functional genomics for identifying allelic variation involved in genotype by environment interaction [3].
  3. Studying the contribution of the Copy Number Variations (CNV), e.g changes in gene content and order between inbred lines, to the genetic diversity, the variation of agronomic traits, the adaptation to environment and heterosis. To this end, I develop high-throughput genotyping approaches of these polymorphisms and appropriate statistical methods for genome-wide association studies.

Key words: Genome-Wide Association Mapping, Genetic diversity, Copy Number Variation, High-Throughput Genotyping, Linkage Disequilibrium, Haplotype, Pre-breeding.

Main current collaborations

· Lab’s: M. Tenaillon, J. Joets & C. Vitte (DyGAP) ; D. Steinbach, Y. De Oliviera & P. Montalent (ABI) ; M. Zivy & M. Blein-Nicolas (PAPPSO)
· France: F. Tardieu and C. Welcker (LEPSE) ; D. Brunel & M-C Le Paslier (EPGV), B. Gouesnard and A. Doligez (AGAP) ; S. Robin, E. Lebarbier and J. Aubert (MIA) ; P. Dubreuil, J-P Pichon, S. Praud, M-H Tixier and J. Duarte (Biogemma) ; B. Hirel, M. Raymond and S. Coursol (IJPB) ; C. Giauffret (UR AgroImpact), B. Mangin (Toulouse)
· International: F. Van Eeuwick, W. Kruijer (Wageningen University), F. Chaumont (UCL).


> Teaching / Training

Phd Student / Postdoctoral Fellowship / CDD

· Camille Clipet (2017-Present)
· Clément Mabire (Phd Student 2016-Present)
· Sandra Negro (Drops and Amaizing Post-doctoral fellow : 2013-2017)
· Mariangela Arca (Diversity Zea and Amaizing Post-doctocal fellow : 2012-2014).

Teaching and training:

· Genome-Wide Association Mapping (Msc / Master degree in Plant Breeding and Genetics at AgroCampus Ouest, Master 2 at Université Paris Sud, Breeder’s training)
· Linkage disequilibrium (Master degree GCDE & Doctoral School GGC.


> Main responsibilities in recent projects

2016-Present: Co-Principal Investigator with D. Rocha of CNV4Sel INRA Project in the framework of “Métaprogramme SelGen”: "Strategies for CNV discovery in animal and plant species and their use in breeding"
2010-Present: Investissement d’avenir Amaizing (PI: A. Charcosset): Task leader of “high density genotyping and imputation” in WP4 (Lead by L. Moreau)
2010-2015: European project F7P Drops (PI: F. Tardieu): In charge of high-throughput genotyping of maize association panel, diversity analysis and development of single environment GWAS approach
2011-2015: PLANT-KBBE European project CornFed (PI: A. Charcosset): In charge of genotyping, GWAS and LD analysis
2011-2015: ANR project GNPasso (PI. D. Steinbach): "Sofware to visualize GWAS results and connect with genome-browser"
2010-2014: Principal Investigator of ANR project CNV-Maize: "Genome wide association study between structural variation, agronomic traits variation and heterosis in maize"
2009-2013: Project Promais Diversity Zea (PI: A. Charcosset), In charge of analysis of genetic diversity landraces using 50K high-troughput genotyping array.


> Selected Publication

  1. Mabire C., Duarte J., Darracq A., Pirani A., Rimbert H., Madur D., Combes V., Vitte C., Praud S., Rivière N., Joets J., Pichon J.-P., Nicolas S.D. (2019) High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array. BMC Genomics, 20 (1) 848.
  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. 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
  5. Gouesnard B., Negro S. 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. Theoretical and Applied Genetics, 130 (10) 2165-2189. DOI : 10.1007/s00122-017-2949-6
  6. Brandenburg J.-T., Mary-Huard T., Rigaill G., Hearne S. J., Corti H., Joets J., Vitte C., Charcosset A., Nicolas S., Tenaillon M. I. (2017) Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. Plos Genetics, 13 (3) e1006666. DOI : 10.1371/journal.pgen.1006666
  7. Canas-Pendon R., Yesbergenova-Cuny Z., Simons M., Chardon F., Armengaud P., Quillere I., Cukier C., Gibon Y., Limami A.-M., Nicolas S., Brule L., Lea P. J., Maranas CD., Hirel B. (2017) Exploiting the Genetic Diversity of Maize Using a Combined Metabolomic, Enzyme Activity Profiling, and Metabolic Modeling Approach to Link Leaf Physiology to Kernel Yield. Plant Cell, 29 (5) 919-943. DOI : 10.1105/tpc.16.00613
  8. Millet E., Welcker C., Kruijer W., Negro S., Coupel-Ledru A., Nicolas S., Laborde J., 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, 172 (2) 749-764. DOI : 10.1104/pp.16.00621
  9. Nicolas S., Peros J.-P., Lacombe T., Launay A., Le Paslier M.-C., Berard A., Mangin B., Valiere S., Martins F., Le Cunff L., Laucou V., Bacilieri R., Dereeper A., Chatelet P., This D., Doligez A. (2016) Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L.) diversity panel newly designed for association studies. BMC Plant Biology, 16 (1). DOI : 10.1186/s12870-016-0754-z
  10. Rincent R., Nicolas S., Bouchet S., Altmann T., Brunel D., Revilla P., Malvar R. A., Moreno-Gonzalez J., Campo L., Melchinger A. E., Schipprack W., Bauer E., Schoen C. -C., Meyer N., Ouzunova M., Dubreuil P., Giauffret C., Madur D., Combes V., Dumas F., Bauland C., Jamin P., Laborde J., D., Flament P., Moreau L., Charcosset A. (2014) Dent and flint maize diversity panels reveal important genetic potential for increasing biomass production. Theoretical and Applied Genetics, 127 (11) 2313-2331. DOI : 10.1007/s00122-014-2379-7
  11. 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 (1) 375-87. DOI : 10.1534/genetics.113.
  12. 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.
  13. Nicolas S., Monod H., Eber F., Chèvre A.M., Jenczewski E. (2012) Non-random distribution of extensive chromosome rearrangements in Brassica napus depends on genome organization. Plant Journal, 70 (4) 691-703.
  14. Mangin B., Siberchicot A., Nicolas S., Doligez A., This P., Cierco-Ayrolles C. (2012) Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity, 108 (3) 285-291. DOI : 10.1038/hdy.2011.73
  15. Dereeper A., Nicolas S.D., Le Cunff L., Bacilieri R., Doligez A., Peros J.P., Ruiz M. and This P. (2011) SNiPlay: a Web-based tool for detection, management and analysis of SNP. Application to grapevine diversity projects, BMC Bioinformatics, 12 134.

All my publications are available here.