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


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.


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.



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)


  1. Akbari M, Wenzl P, Caig V, Carling J, Xia L et al (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420PubMedCrossRefGoogle Scholar
  2. Allan RE, Vogel OA, Peterson CJ (1968) Inheritance and differentiation of semi-dwarf culm length of wheat. Crop Sci 8:701–704CrossRefGoogle Scholar
  3. Allan RE (1983) Yield performance of lines isogenic for semi-dwarf genes doses in several wheat populations. In: Sakamoto S (ed) Proceedings of 6th international wheat genetics symposium, Kyoto, Japan, pp 265–270Google Scholar
  4. Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-Wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1:531–539CrossRefGoogle Scholar
  5. Balding DJ (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7(10):781–791PubMedCrossRefGoogle Scholar
  6. Balfourier F, Roussel V, Strelchenko, Exbrayat-Vinson F, Sourdille P, Boutet G, Koenig J, Ravel C, Mitrofanova O, Beckert M, Charmet G (2007) A worldwide bread wheat core collection arrayed in a 384-well plate. Theor Appl Genet 114:1265–1275PubMedCrossRefGoogle Scholar
  7. Beales J, Turner A, Griffiths S, Snape JW, Laurie DA (2007) A Pseudo-Response Regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet 115:721–733PubMedCrossRefGoogle Scholar
  8. Borlaug NE (1968) Wheat breeding and its impact on world food supply. In: Finlay KW, Shepherd KW (eds) Proceedings of 3rd international wheat genetics symposium. Australian Academy of Science, Canberra, Australia, pp 1–36Google Scholar
  9. Börner A, Worland AJ, Plaschke J, Schumann E, Law CN (1993) Pleiotropic effects of genes for reduced height (Rht) and day-length insensitivity (Ppd) on yield and its components for wheat grown in middle Europe. Plant Breed 111:204–216CrossRefGoogle Scholar
  10. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177PubMedCrossRefGoogle Scholar
  11. Camus-Kulandaivelu L, Veyrieras J-B, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A (2006) Maize adaptation to temperate climate: relationship between population structure and polymorphism in the dwarf8 gene. Genetics 172:2449–2463PubMedCrossRefGoogle Scholar
  12. Camus-Kulandaivelu L, Veyrieras J-B, Gouesnard B, Charcosset A, Manicacci D (2007) Evaluating the reliability of structure outputs in case of relatedness between individuals. Crop Sci 47:887–892CrossRefGoogle Scholar
  13. Cockram J, Jones H, Leigh FJ, O’Sullivan D, Powell W, Laurie DA, Greenland AJ (2007) Control of flowering time in temperate cereals: genes, domestication and sustainable productivity. J Exp Bot 58:1231–1244PubMedCrossRefGoogle Scholar
  14. Crossa J, Burgueño J, Dreisigacker S, Vargas M, Herrera-Foessel SA, Lillemo M, Singh RP, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch JH, Ortiz R (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913PubMedCrossRefGoogle Scholar
  15. Donini P, Law JR, Koebner RM, Reeves JC, Cooke RJ (2000) Temporal trends in the diversity of UK wheat. Theor Appl Genet 100:912–917CrossRefGoogle Scholar
  16. Ellis MH, Spielmeyer W, Gale KR, Rebetzke GJ, Richards RA (2002) “Perfect” markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theor Appl Genet 105:1038–1042PubMedCrossRefGoogle Scholar
  17. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMedGoogle Scholar
  18. Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, Patterson N, Gabriel SB, Topol EJ, Smoller JW, Pato CN, Pato MT, Petryshen TL, Kolonel LN, Lander ES, Sklar P, Henderson B, Hirschhorn JN, Altshuler D (2004) Assessing the impact of population stratification on genetic association studies. Nat Genet 36:388–393PubMedCrossRefGoogle Scholar
  19. Fu YB, Peterson GW, Scoles G, Rossnagel B, Schoen DJ, Richards KW (2003) Allelic diversity changes in 96 Canadian oat cultivars released from 1886 to 2001. Crop Sci 43:1989–1995CrossRefGoogle Scholar
  20. Garris AJ, McCough SR, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759–769PubMedGoogle Scholar
  21. Hai L, Wagner C, Friedt W (2007) Quantitative structure analysis of genetic diversity among spring bread wheats (Triticum aestivum L.) from different geographical regions. Genetica 130:213–225PubMedCrossRefGoogle Scholar
  22. Jagathesan D, Bhatia C, Swaminathan S (1961) Effects of induced awn mutations on yield in wheat. Nature 190:468CrossRefGoogle Scholar
  23. Kennedy BW, Quinton M, Van Arendonk JAM (1992) Estimation of effects of single genes on quantitative traits. J Anim Sci 70:2000–2012PubMedGoogle Scholar
  24. Koebner RMD, Donini P, Reeves JC, Cooke RJ, Law JR (2003) Temporal flux in the morphological and molecular diversity of UK barley. Theor Appl Genet 106:550–558PubMedGoogle Scholar
  25. Lander ES, Green P, Abrahamson J, Barlow A, Daly M, Lincoln SE, Newberg LA, Newburg L (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1(2):174–181PubMedCrossRefGoogle Scholar
  26. Law CN (1966) The location of genetic factors affecting a quantitative character in wheat. Genetics 53:487–498PubMedGoogle Scholar
  27. Law CN, Sutka J, Worland AJ (1978) A genetic study of day-length response in wheat. Heredity 41:185–191CrossRefGoogle Scholar
  28. Marchini J, Cardon LR, Phillips MS, Donnelly P (2004) The effects of human population structure on large genetic association studies. Nat. Genet. 36:512–517PubMedCrossRefGoogle Scholar
  29. McIntosh RA, Hart GE, Devos KM, Gale MD, Rogers WJ (1998) Catalogue of gene symbols for wheat. In: Slinkard AE (ed) Proceedings of 9th international wheat genetics symposium, Saskatoon, vol 5. University Extension Press, Saskatoon, Canada, pp 1–235Google Scholar
  30. McIntosh RA, Devos KM, Dubcovsky J, Morris CF, Rogers WJ (2003) “Catalogue of gene symbols for wheat”.
  31. Melchinger AE, Messmer MM, Lee M, Woodman WL, Lamkey KR (1991) Diversity and relationships among U.S. maize inbreds revealed by restriction fragment length polymorphisms. Crop Sci 31:669–678CrossRefGoogle Scholar
  32. Miedaner T, Würschum T, Maurer HP, Korzun V, Ebmeyer E, Reif JC (2010) Association mapping for Fusarium head blight resistance in European soft winter wheat. Mol breed. doi: 10.1007/s11032-010-9516
  33. Nei M (1973) Analysis of gene diversity in subdivided populations. In: Proceedings of the National Academy of Sciences of the United States of America, vol 70, pp 3321–3323Google Scholar
  34. Plaschke J, Ganal MW, Röder MS (1995) Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor Appl Genet 91:1001–1007CrossRefGoogle Scholar
  35. Prasad M, Varshney RK, Roy JK, Balyan HS, Gupta PK (2000) The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theor Appl Genet 100:584–592Google Scholar
  36. Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65:220–228PubMedCrossRefGoogle Scholar
  37. Pritchard JK, Stephens M, Donnelly P (2000a) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  38. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000b) Association mapping in structured populations. Am J Hum Genet 67:170–181PubMedCrossRefGoogle Scholar
  39. R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
  40. Röder M, Wendehake K, Korzun V, Bredemeijer G, Laborie D, Bertrand L, Isaac P, Rendell S, Jackson J, Cooke RJ, Vosman B, Ganal M (2002) Construction and analysis of a microsatellite-based database of European wheat varieties. Theor Appl Genet 106:67–73PubMedGoogle Scholar
  41. Roussel V, Koenig J, Beckert M, Balfourier F (2004) Molecular diversity in French bread wheat accessions related to temporal trends and breeding programmes. Theor Appl Genet 108:920–930PubMedCrossRefGoogle Scholar
  42. Roussel V, Leisova L, Exbrayat F, Stehno Z, Balfourier F (2005) SSR allelic diversity changes in 480 European bread wheat varieties released from 1840 to 2000. Theor Appl Genet 111:162–170PubMedCrossRefGoogle Scholar
  43. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018PubMedCrossRefGoogle Scholar
  44. Sears ER (1954) The aneuploids of common wheat. Univ Missouri Res Bull 572:1–58Google Scholar
  45. Semagn K, Skinnes H, Bjørnstad Å, Marøy A-G, Tarkegne Y (2007) Quantitative Trait loci controlling Fusarium head blight resistance and low deoxynivalenol content in hexaploid wheat population from “Arina” and NK93604. Crop Sci 47:294–303CrossRefGoogle Scholar
  46. Somers DJ, Banks T, DePauw R, Fox S, Clarke J, Pozniak C, McCartney C (2007) Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 50:557–567PubMedCrossRefGoogle Scholar
  47. Sourdille P, Charmet G, Trottet M, Tixier MH, Boeuf C, Nègre S, Barloy D, Bernard M (1998) Linkage between RFLP molecular markers and the dwarfing genes Rht-B1 and Rht-D1 in wheat. Hereditas 128:41–46CrossRefGoogle Scholar
  48. Sourdille P, Cadalen T, Gay G, Gill B, Bernard M (2002) Molecular and physical mapping of genes affecting awning in wheat. Plant Breed 121:320–324CrossRefGoogle Scholar
  49. Stachel M, Lelley T, Grausgruber H, Vollmann J (2000) Application of microsatellites in wheat (Triticum aestivum L.) for studying genetic differentiation caused by selection for adaptation and use. Theor Appl Genet 100:242–248CrossRefGoogle Scholar
  50. Strampelli N (1932) Early ripening wheats and the advance of Italian wheat production. Tipographia Failli, Rome, pp 5–7Google Scholar
  51. Tommasini L, Schnurbusch T, Fossati D, Mascher F, Keller B (2007) Association mapping of Stagonaspora nodorum blotch resistance in modern European winter wheat varieties. Theor Appl Genet 115:697–708PubMedCrossRefGoogle Scholar
  52. Van Inghelandt D, Melchinger AE, Lebreton C, Stich B (2010) Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theor Appl Genet 120:1289–1299PubMedCrossRefGoogle Scholar
  53. Wenzl P, Li H, Carling J, Zhou M, Raman H, Paul E, Hearnden P, Maier C, Xia L, Caig V, Ovesná J, Cakir M, Poulsen D, Wang J, Raman R, Smith KP, Muehlbauer GJ, Chalmers KJ, Kleinhofs A, Huttner E, Killian A (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 7:206PubMedCrossRefGoogle Scholar
  54. White J, Law JR, MacKay I, Chalmers KJ, Smith JSC, Kilian A, Powell W (2007) The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. Theor Appl Genet 116:439–453PubMedCrossRefGoogle Scholar
  55. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl Acids Res 18:6531–6535PubMedCrossRefGoogle Scholar
  56. Worland AJ, Appendino ML, Sayers EJ (1994) The distribution, in European winter wheats, of genes that influence ecoclimatic adaptability whilst determining photoperiod insensitivity and plant height. Euphytica 80:219–228CrossRefGoogle Scholar
  57. Worland AJ (1996) The influence of flowering time genes on environmental adaptability in European wheats. Euphytica 89:49–57CrossRefGoogle Scholar
  58. Worland AJ, Börner A, Korzun V, Li WM, Petrovic S, Sayers EJ (1998) The influence of photoperiod genes on the adaptability of European winter wheats. Euphytica 100:385–394CrossRefGoogle Scholar
  59. Yu J, Pressoir G, Briggs WH, Vroh Bi, Yamasaki M, Doebley JF et al (2005) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208PubMedCrossRefGoogle Scholar
  60. Zhang LY, Marchand S, Tinker NA, Belzile F (2009) Population structure and linkage disequilibrium in barley assessed by DArT markers. Theor Appl Genet 119:43–52PubMedCrossRefGoogle Scholar
  61. Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:71–82CrossRefGoogle Scholar
  62. Zwart RS, Muylle H, Van Bockstaele E, Roldán-Ruiz I (2008) Evaluation of genetic diversity of Fusarium head blight resistance in European winter wheat. Theor Appl Genet 117:813–828PubMedCrossRefGoogle Scholar

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

Personalised recommendations