DiGEN (Diversity and Genome)

Research project

Characterization of bread wheat genetic diversity

  • Characterization of diversity, structural and functional variability of the genome
    • Development of methodologies for targeted sequencing/assembly of genomic regions of interest
    • Identification of structural variations
    • Construction of a wheat pangenome
  • Study the contribution of transposable elements to genomic variability
  • Impact of chromosomal introgressions from wild species

Exploiting diversity in wheat breeding programmes

  • Better understanding of Genotype x Environment interactions
    • Predict breeding value of lines in a given environment
    • Defining genotypes for the future
  • Methodologies of selection
    • Development of breeding programmes simulation tools
    • Modeling Genotype x Environment in GWAS and genomic selection
  • Methodologies of re-introduction of genetic diversity
    • Optimizing crossing plans for future breeding programmes
    • Development of SNP genotyping arrays for diagnostic markers (disease and quality)
    • Haplotyping (reconstruction pedigrees and ancestral genotypes)
  • Breeding and pre-breeding


Team members (2023)

  • Sophie BOUCHET, CR INRAE, co-leader
  • Frédéric CHOULET, IR INRAE, co-leader
  • François-Xavier OURY, IR INRAE
  • Jonathan KITT, TR INRAE
  • Gilles CHARMET, DR (early retirement)
  • Amandine ALBERT, intern

Former members

  • Claire OGET-EBRAD (postdoc 2021-23)
  • Ines ZARROUGUI (intern Master 2023)
  • Emma PUREUR (intern 2023)


Recent Publications (5 years)

As leader authors


Danguy des Déserts, A, Durand, N., Servin, B., Goudemand-Dugué, E., Alliot, J.M., Ruiz, D., Charmet, G., Elsen, J.M., and Bouchet, S. (2023). Comparison of genomic-enabled cross selection criteria for the improvement of inbred line breeding populations. G3 (Bethesda). 10.1093/g3journal/jkad195

Papon, N., Lasserre-Zuber, P., Rimbert, H., De Oliveira, R., Paux, E., and Choulet, F. (2023). All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity. Plant Genome 16, e20347. 10.1002/tpg2.20347


Paux, E., Lafarge, S., Balfourier, F., Derory, J., Charmet, G., Alaux, M., Perchet, G., Bondoux, M., Baret, F., Barillot, R., Ravel, C., Sourdille, P., Le Gouis, J., and On Behalf Of The Breedwheat Consortium. (2022). Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection. Biology (Basel) 11. 10.3390/biology11010149

Aury, J.M., Engelen, S., Istace, B., Monat, C., Lasserre-Zuber, P., Belser, C., Cruaud, C., Rimbert, H., Leroy, P., Arribat, S., Dufau, I., Bellec, A., Grimbichler, D., Papon, N., Paux, E., Ranoux, M., Alberti, A., Wincker, P., and Choulet, F. (2022). Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding. Gigascience 11. 10.1093/gigascience/giac034


Danguy des Déserts, A., Bouchet, S., Sourdille, P., and Servin, B. (2021). Evolution of Recombination Landscapes in Diverging Populations of Bread Wheat. Genome Biol Evol 13. 10.1093/gbe/evab152

Gimenez, K., Blanc, P., Argillier, O., Pierre, J.B., Le Gouis, J., and Paux, E. (2021). Dissecting Bread Wheat Heterosis through the Integration of Agronomic and Physiological Traits. Biology (Basel) 10. 10.3390/biology10090907

Juery, C., Concia, L., De Oliveira, R., Papon, N., Ramírez-González, R., Benhamed, M., Uauy, C., Choulet, F., and Paux, E. (2021). New insights into homoeologous copy number variations in the hexaploid wheat genome. Plant Genome 14, e20069. 10.1002/tpg2.20069


Ben-Sadoun, S., Rincent, R., Auzanneau, J., Oury, F.X., Rolland, B., Heumez, E., Ravel, C., Charmet, G., and 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 133, 2197-2212. 10.1007/s00122-020-03590-4

Charmet, G., Tran, L.G., Auzanneau, J., Rincent, R., and Bouchet, S. (2020). BWGS: A R package for genomic selection and its application to a wheat breeding programme. PLoS One 15, e0222733. 10.1371/journal.pone.0222733

De Oliveira, R., Rimbert, H., Balfourier, F., Kitt, J., Dynomant, E., Vrána, J., Doležel, J., Cattonaro, F., Paux, E., and Choulet, F. (2020). Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats. Front Genet 11, 891. 10.3389/fgene.2020.00891


Balfourier, F., Bouchet, S., Robert, S., De Oliveira, R., Rimbert, H., Kitt, J., Choulet, F., Paux, E., Consortium, I.W.G.S., and Consortium, B. (2019). Worldwide phylogeography and history of wheat genetic diversity. Sci Adv 5, eaav0536. 10.1126/sciadv.aav0536

Blancon, J., Dutartre, D., Tixier, M.H., Weiss, M., Comar, A., Praud, S., and Baret, F. (2019). A High-Throughput Model-Assisted Method for Phenotyping Maize Green Leaf Area Index Dynamics Using Unmanned Aerial Vehicle Imagery. Front Plant Sci 10, 685. 10.3389/fpls.2019.00685


As collaborators


Banouh, M., Armisen, D., Bouguennec, A., Huneau, C., Sow, M.D., Pont, C., Salse, J., and Civáň, P. (2023). Low impact of polyploidization on the transcriptome of synthetic allohexaploid wheat. BMC Genomics 24, 255. 10.1186/s12864-023-09324-2

Zhang, J., Debernardi, J.M., Burguener, G.F., Choulet, F., Paux, E., O'Connor, L., Enk, J., and Dubcovsky, J. (2023). A second-generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives. Plant Genome 16, e20296. 10.1002/tpg2.20296

Mishina, K., Suzuki, T., Oono, Y., Yamashita, Y., Zhu, H., Ogawa, T., Ohta, M., Doman, K., Xu, W., Takahashi, D., Miyazaki, T., Tagiri, A., Soma, C., Horita, H., Nasuda, S., De Oliveira, R., Paux, E., Chen, G., Pourkheirandish, M., Wu, J., Liu, C., and Komatsuda, T. (2023). Wheat Ym2 originated from Aegilops sharonensis and confers resistance to soil-borne Wheat yellow mosaic virus infection to the roots. Proc Natl Acad Sci U S A 120, e2214968120. 10.1073/pnas.2214968120


Fugeray-Scarbel, A., Ben-Sadoun, S., Bouchet, S., and Lemarié, S. (2022). Analyzing the Economic Effectiveness of Genomic Selection Relative to Conventional Breeding Approaches. Methods Mol Biol 2467, 619-644. 10.1007/978-1-0716-2205-6_22

Robert, P., Auzanneau, J., Goudemand, E., Oury, F.X., Rolland, B., Heumez, E., Bouchet, S., Le Gouis, J., and Rincent, R. (2022a). Phenomic selection in wheat breeding: identification and optimisation of factors influencing prediction accuracy and comparison to genomic selection. Theor Appl Genet 135, 895-914. 10.1007/s00122-021-04005-8

Robert, P., Goudemand, E., Auzanneau, J., Oury, F.X., Rolland, B., Heumez, E., Bouchet, S., Caillebotte, A., Mary-Huard, T., Le Gouis, J., and Rincent, R. (2022b). Phenomic selection in wheat breeding: prediction of the genotype-by-environment interaction in multi-environment breeding trials. Theor Appl Genet 135, 3337-3356. 10.1007/s00122-022-04170-4

Hussain, B., Akpınar, B.A., Alaux, M., Algharib, A.M., Sehgal, D., Ali, Z., Aradottir, G.I., Batley, J., Bellec, A., Bentley, A.R., Cagirici, H.B., Cattivelli, L., Choulet, F., Cockram, J., Desiderio, F., Devaux, P., Dogramaci, M., Dorado, G., Dreisigacker, S., Edwards, D., El-Hassouni, K., Eversole, K., Fahima, T., Figueroa, M., Gálvez, S., Gill, K.S., Govta, L., Gul, A., Hensel, G., Hernandez, P., Crespo-Herrera, L.A., Ibrahim, A., Kilian, B., Korzun, V., Krugman, T., Li, Y., Liu, S., Mahmoud, A.F., Morgounov, A., Muslu, T., Naseer, F., Ordon, F., Paux, E., Perovic, D., Reddy, G.V.P., Reif, J.C., Reynolds, M., Roychowdhury, R., Rudd, J., Sen, T.Z., Sukumaran, S., Ozdemir, B.S., Tiwari, V.K., Ullah, N., Unver, T., Yazar, S., Appels, R., and Budak, H. (2022). Capturing Wheat Phenotypes at the Genome Level. Front Plant Sci 13, 851079. 10.3389/fpls.2022.851079

Darrier, B., Colas, I., Rimbert, H., Choulet, F., Bazile, J., Sortais, A., Jenczewski, E., and Sourdille, P. (2022). Location and Identification on Chromosome 3B of Bread Wheat of Genes Affecting Chiasma Number. Plants (Basel) 11. 10.3390/plants11172281


Zhu, T., Wang, L., Rimbert, H., Rodriguez, J.C., Deal, K.R., De Oliveira, R., Choulet, F., Keeble-Gagnère, G., Tibbits, J., Rogers, J., Eversole, K., Appels, R., Gu, Y.Q., Mascher, M., Dvorak, J., and Luo, M.C. (2021). Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. Plant J 107, 303-314. 10.1111/tpj.15289

Budak, H., Appels, R., and Paux, E. (2021). Insights on decoding wheat and barley genomes. Funct Integr Genomics 21, 157-159. 10.1007/s10142-021-00774-z

Nurit, E., Bordes, J., Balfourier, F., Paux, E., Piquet, A., Fossati, D., and Branlard, G. (2021). Association between SNP Markers and 11 Vitamin Contents in Grains of a Worldwide Bread Wheat Core Collection. J Agric Food Chem 69, 4307-4318. 10.1021/acs.jafc.0c07763


Concia, L., Veluchamy, A., Ramirez-Prado, J.S., Martin-Ramirez, A., Huang, Y., Perez, M., Domenichini, S., Rodriguez Granados, N.Y., Kim, S., Blein, T., Duncan, S., Pichot, C., Manza-Mianza, D., Juery, C., Paux, E., Moore, G., Hirt, H., Bergounioux, C., Crespi, M., Mahfouz, M.M., Bendahmane, A., Liu, C., Hall, A., Raynaud, C., Latrasse, D., and Benhamed, M. (2020). Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol 21, 104. 10.1186/s13059-020-01998-1

Falque, M., Jebreen, K., Paux, E., Knaak, C., Mezmouk, S., and Martin, O.C. (2020). CNVmap: A Method and Software To Detect and Map Copy Number Variants from Segregation Data. Genetics 214, 561-576. 10.1534/genetics.119.302881


Tulpová, Z., Luo, M.C., Toegelová, H., Visendi, P., Hayashi, S., Vojta, P., Paux, E., Kilian, A., Abrouk, M., Bartoš, J., Hajdúch, M., Batley, J., Edwards, D., Doležel, J., and Šimková, H. (2019). Integrated physical map of bread wheat chromosome arm 7DS to facilitate gene cloning and comparative studies. N Biotechnol 48, 12-19. 10.1016/j.nbt.2018.03.003

Modification date: 22 April 2024 | Publication date: 29 May 2020 | By: Frédéric CHOULET