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Theoretical and Applied Genetics

, Volume 123, Issue 5, pp 715–727 | Cite as

Analysis of genetic structure in a panel of elite wheat varieties and relevance for association mapping

  • Fabien Le Couviour
  • Sebastien Faure
  • Bruno Poupard
  • Yann Flodrops
  • Pierre Dubreuil
  • Sebastien PraudEmail author
Original Paper

Abstract

During the last decades, with the intensification of selection and breeding using crosses between varieties, a very complex genetic structure was shaped in the elite wheat germplasm. However, precise description of this structure with panels and collections is becoming more and more crucial with the development of resource management and new statistical tools for mapping genetic determinants (e.g. association studies). In this study, we investigated the genetic structure of 195 Western European elite wheat varieties using the recent development of high throughput screening methods for molecular markers. After observing that both microsatellites and Diversity Array Technology markers are efficient to estimate the structure of the panel, we used different complementary approaches (Genetic distances, principal component analysis) that showed that the varieties are separated by geographical origin (France, Germany and UK) and also by breeding history, confirming the impact of plant breeding on the wheat germplasm structure. Moreover, by analysing three phenotypic traits presenting significant average differences across groups (plant height, heading date and awnedness), and by using markers linked to major genes for these traits (Ppd-D1, Rht-B1, Rht-D1 and B1), we showed that for each trait, there is a specific optimal Q matrix to use as a covariate in association tests.

Keywords

Double Haploid Single Nucleotide Polymorphism Marker DArT Marker Head Date Diversity Array Technology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The authors gratefully acknowledge Nadine Duranton for genotyping work and Jean-Bruno Beaufumé for information on genetic structure. We thank Philippe Brabant and Wyatt Paul for revision of the manuscript. We are grateful to Delphine Girardi for her help with growing and phenotyping wheat varieties. F. Le Couviour was supported by a joint grant from ANRT (Association Nationale de la Recherche et de la Technologie) and Biogemma.

Supplementary material

122_2011_1621_MOESM1_ESM.xls (34 kb)
Table S1 List of the names, origin and breeder of the 195 elite wheat varieties of the panel. (XLS 34 kb)
122_2011_1621_MOESM2_ESM.xls (36 kb)
Table S2 Chromosomal location, number of alleles amplified, number of alleles with a frequency above 0.05 (excluding rare alleles) and Nei’s diversity values for the 159 SSR loci used in the genetic analysis of the 195 wheat genotypes. (XLS 36 kb)
122_2011_1621_MOESM3_ESM.xls (40 kb)
Table S3 Chromosomal location and Nei’s diversity values for the 252 DArT loci used in the genetic analysis of the 195 wheat genotypes. (XLS 39 kb)
122_2011_1621_MOESM4_ESM.xls (24 kb)
Table S4 List of the pedigree record for 32 varieties of the panel. (XLS 23 kb)

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Fabien Le Couviour
    • 1
  • Sebastien Faure
    • 1
  • Bruno Poupard
    • 2
  • Yann Flodrops
    • 3
  • Pierre Dubreuil
    • 1
  • Sebastien Praud
    • 1
    Email author
  1. 1.Biogemma, Site de la GarenneChappesFrance
  2. 2.Limagrain EuropeVerneuil L’EtangFrance
  3. 3.ARVALIS Institut du végétalParisFrance

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