, Volume 197, Issue 3, pp 447–462 | Cite as

Changes in allelic frequency over time in European bread wheat (Triticum aestivum L.) varieties revealed using DArT and SSR markers

  • Jihad Orabi
  • Ahmed Jahoor
  • Gunter Backes


A collection of 189 bread wheat landraces and cultivars, primarily of European origin, released between 1886 and 2009, was analyzed using two DNA marker systems. A set of 76 SSR markers and ~7,000 DArT markers distributed across the wheat genome were employed in these analyses. All of the SSR markers were found to be polymorphic, whereas only 2,532 of the ~7,000 DArT markers were polymorphic. A Mantel test between the genetic distances calculated based on the SSR and DArT data showed a strong positive correlation between the two marker types, with a Pearson’s value (r) of 0.66. We assessed the genetic diversity and allelic frequencies among the accessions based on spring- versus winter-wheat type as well as between landraces and cultivars. We also analyzed the changes in genetic diversity and allelic frequencies in these samples over time. We observed separation based on both vernalization type and release date. Interestingly, we detected a decrease in genetic diversity in wheat accessions released over the period from 1960 to 1980. However, our results also showed that modern plant breeding have succeeded in maintaining genetic diversity in modern wheat cultivars. Studying allelic frequencies using SSR and DArT markers over time revealed changes in allelic frequencies for a number of markers that are known to be linked to important traits, which should be useful for genomic screening efforts. Monitoring changes in the frequency of molecular DNA markers over time in wheat cultivars may yield insight into alleles linked to important traits that have been the subject of positive or negative selection in the past and that may be useful for marker-assisted breeding programs in the future.


Molecular markers Allelic frequency Plant breeding Genetic diversity 



We thank NordGen ( and IPK ( for providing the seeds used in this study. The project was conducted within a larger project (3304-FVFP-07-771-0) funded by the Ministry of Food, Agriculture and Fisheries of Denmark.

Supplementary material

10681_2014_1080_MOESM1_ESM.pdf (367 kb)
Supplementary material 1 (PDF 367 kb)


  1. Akbari M, Wenzl P, Caig V et al (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420. doi: 10.1007/s00122-006-0365-4 PubMedCrossRefGoogle Scholar
  2. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedCentralPubMedGoogle Scholar
  3. Dreisigacker S (2011) CGIAR Generation Challenge Programme, 2011. 2011 Project updates (incorporating projects completed in 2010 and 2009. pp 88–91Google Scholar
  4. Elouafi I, Nachit MM, Martin LM (2001) Identification of a microsatellite on chromosome 7B showing a strong linkage with yellow pigment in durum wheat (Triticum turgidum L. var. durum). Hereditas 135:255–261. doi: 10.1111/j.1601-5223.2001.t01-1-00255.x PubMedCrossRefGoogle Scholar
  5. Fu YB, Peterson GW, Yu JK et al (2006) Impact of plant breeding on genetic diversity of the Canadian hard red spring wheat germplasm as revealed by EST-derived SSR markers. Theor Appl Genet 112:1239–1247. doi: 10.1007/s00122-006-0225-2 PubMedCrossRefGoogle Scholar
  6. Herrera-Foessel SA, Djurle A, Yuen J et al (2008) Identification and molecular characterization of leaf rust resistance gene Lr14a in durum wheat. Plant Dis 92:469–473. doi: 10.1094/pdis-92-3-0469 CrossRefGoogle Scholar
  7. Huang XQ, Wolf M, Ganal MW et al (2007) Did modern plant breeding lead to genetic erosion in European winter wheat varieties? Crop Sci 47:343–349. doi: 10.2135/cropsci2006.04.0261 CrossRefGoogle Scholar
  8. Hurtado P, Olsen KM, Buitrago C et al (2008) Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava (Manihot esculenta Crantz). Plant Genet Resour 6:208–214. doi: 10.1017/S1479262108994181 CrossRefGoogle Scholar
  9. Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:e25. doi: 10.1093/nar/29.4.e25 PubMedCentralPubMedCrossRefGoogle Scholar
  10. Jing HC, Bayon C, Kanyuka K et al (2009) DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum. BMC Genome 10:458. doi: 10.1186/1471-2164-10-458 CrossRefGoogle Scholar
  11. Knopf C, Becker H, Ebmeyer E, Korzun V (2008) Occurrence of three dwarfing Rht genes in german winter wheat varieties. Cereal Res Commun 36:553–560. doi: 10.1556/crc.36.2008.4.4 CrossRefGoogle Scholar
  12. Korzun V, Röder MS, Ganal MW et al (1998) Genetic analysis of the dwarfing gene (Rht8) in wheat. Part I. Molecular mapping of Rht8 on the short arm of chromosome 2D of bread wheat (Triticum aestivum L.). Theor Appl Genet 96:1104–1109. doi: 10.1007/s001220050845 CrossRefGoogle Scholar
  13. Liu Y, Liu D, Zhang H et al (2005) Allelic variation, sequence determination and microsatellite screening at the XGWM261 locus in Chinese hexaploid wheat (Triticum aestivum) varieties. Euphytica 145:103–112. doi: 10.1007/s10681-005-0549-z CrossRefGoogle Scholar
  14. Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323PubMedCentralPubMedCrossRefGoogle Scholar
  15. Peng JR, Richards DE, Hartley NM et al (1999) “Green revolution” genes encode mutant gibberellin response modulators. Nature 400:256–261PubMedCrossRefGoogle Scholar
  16. Raman H, Stodart BJ, Cavanagh C et al (2010) Molecular diversity and genetic structure of modern and traditional landrace cultivars of wheat (Triticum aestivum L.). Crop Pasture Sci 61:222–229. doi: 10.1071/cp09093 CrossRefGoogle Scholar
  17. Reif JC, Zhang P, Dreisigacker S et al (2005) Wheat genetic diversity trends during domestication and breeding. Theor Appl Genet 110:859–864. doi: 10.1007/s00122-004-1881-8 PubMedCrossRefGoogle Scholar
  18. Roussel V, Leisova L, Exbrayat F et al (2005) SSR allelic diversity changes in 480 European bread wheat varieties released from 1840 to 2000. Theor Appl Genet 111:162–170. doi: 10.1007/s00122-005-2014-8 PubMedCrossRefGoogle Scholar
  19. 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 81:8014–8018PubMedCentralPubMedCrossRefGoogle Scholar
  20. Sambasivam PK, Bansal UK, Hayden MJ et al. (2008) Identification of markers linked with stem rust resistance genes Sr33 and Sr45. In: Russell A, Eastwood E, Lagudah P, et al. (eds) 11th international wheat genetics symposium, vol 2. Sydney University Press, Sydney, pp 351–353Google Scholar
  21. Sherman JD, Weaver DK, Hofland ML et al (2010) Identification of novel QTL for Sawfly resistance in wheat. Crop Sci 50:73. doi: 10.2135/cropsci2009.03.0145 CrossRefGoogle Scholar
  22. Siedler H, Messmer MM, Schachermayr GM et al (1994) Genetic diversity in European wheat and spelt breeding material based on RFLP data. Theor Appl Genet 88:994–1003PubMedCrossRefGoogle Scholar
  23. Singh RP, Hodson DP, Jin Y et al (2006) Current status, likely migration and strategies to mitigate the threat to wheat production from race Ug99 (TTKS) of stem rust pathogen. CAB Rev Perspect Agric Vet Sci Nutr Nat Resour 1:13. doi: 10.1079/PAVSNNR20061054 Google Scholar
  24. Singrün C, Hsam SLK, Hartl L et al (2003) Powdery mildew resistance gene Pm22 in cultivar Virest is a member of the complex Pm1 locus in common wheat (Triticum aestivum L. em Thell.). Theor Appl Genet 106:1420–1424. doi: 10.1007/s00122-002-1187-7 PubMedGoogle Scholar
  25. Stodart BJ, Mackay M, Raman H (2005) AFLP and SSR analysis of genetic diversity among landraces of bread wheat (Triticum aestivum L. em. Thell) from different geographic regions. Aust J Agric Res 56:691–697. doi: 10.1071/ar05015 CrossRefGoogle Scholar
  26. Stodart BJ, Mackay MC, Raman H (2007) Assessment of molecular diversity in landraces of bread wheat (Triticum aestivum L.) held in an ex situ collection with diversity arrays technology (DArTTM). Aust J Agric Res 58:1174–1182. doi: 10.1071/ar07010 CrossRefGoogle Scholar
  27. Van de Wouw M, van Hintum T, Kik C et al (2010) Genetic diversity trends in twentieth century crop cultivars: a meta analysis. Theor Appl Genet 120:1241–1252. doi: 10.1007/s00122-009-1252-6 PubMedCentralPubMedCrossRefGoogle Scholar
  28. Venables W, Ripley BD (2002) Modern applied statistics with S, 4th edn. Springer, New York, p 495CrossRefGoogle Scholar
  29. Villareal RL, Rajaram S, Mujeebkazi A, Deltoro E (1991) The effect of chromosome 1B/1R translocation on the yield potential of certain spring wheats (Triticum aestivum L.). Plant Breed 106:77–81. doi: 10.1111/j.1439-0523.1991.tb00482.x CrossRefGoogle Scholar
  30. Wenzl P, Li HB, Carling J et al (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genome 7:206. doi: 10.1186/1471-2164-7-206 CrossRefGoogle Scholar
  31. White J, Law JR, MacKay I et al (2008) 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
  32. Worland AJ, Korzun V, Roder MS et al (1998) Genetic analysis of the dwarfing gene Rht8 in wheat. Part II. The distribution and adaptive significance of allelic variants at the Rht8 locus of wheat as revealed by microsatellite screening. Theor Appl Genet 96:1110–1120CrossRefGoogle Scholar
  33. Wright S (1978) Evolution and the genetics of populations, variability within and among natural populations. vol. 4. University of Chicago Press, ChicagoGoogle Scholar
  34. Xia L, Peng KM, Yang SY et al (2005) DArT for high-throughput genotyping of Cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet 110:1092–1098. doi: 10.1007/s00122-005-1937-4 PubMedCrossRefGoogle Scholar
  35. Yamasaki M, Tenaillon MI, Bi IV et al (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17:2859–2872. doi: 10.1105/tpc.105.037242 PubMedCentralPubMedCrossRefGoogle Scholar
  36. Yamasaki M, Wright SI, McMullen MD (2007) Genomic screening for artificial selection during domestication and improvement in maize. Ann Bot 100:967–973. doi: 10.1093/aob/mcm173 PubMedCentralPubMedCrossRefGoogle Scholar
  37. Yang SY, Pang W, Ash G et al (2006) Low level of genetic diversity in cultivated pigeonpea compared to its wild relatives is revealed by diversity arrays technology. Theor Appl Genet 113:585–595. doi: 10.1007/s00122-006-0317-z PubMedCrossRefGoogle Scholar
  38. Zhang LY, Marchand S, Tinker N, Belzile F (2009) Population structure and linkage disequilibrium in barley assessed by DArT markers. Theor Appl Genet 119:43–52. doi: 10.1007/s00122-009-1015-4 PubMedCrossRefGoogle Scholar
  39. Zhang LY, Liu D, Guo X et al (2011) Investigation of genetic diversity and population structure of common wheat cultivars in northern China using DArT markers. BMC Genet 12:42. doi: 10.1186/1471-2156-12-42 PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Department of Plant Science and Environment, Faculty of ScienceCopenhagen UniversityFrederiksbergDenmark
  2. 2.Nordic Seed A/SHolebyDenmark
  3. 3.Department of Plant BreedingSwedish University of Agricultural SciencesAlnarpSweden
  4. 4.Faculty of Organic Agricultural SciencesUniversity of KasselWitzenhausenGermany

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