Molecular Breeding

, Volume 23, Issue 1, pp 23–33

Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars

  • Shiaoman Chao
  • Wenjun Zhang
  • Eduard Akhunov
  • Jamie Sherman
  • Yaqin Ma
  • Ming-Cheng Luo
  • Jorge Dubcovsky

DOI: 10.1007/s11032-008-9210-6

Cite this article as:
Chao, S., Zhang, W., Akhunov, E. et al. Mol Breeding (2009) 23: 23. doi:10.1007/s11032-008-9210-6


In this study, we developed 359 detection primers for single nucleotide polymorphisms (SNPs) previously discovered within intron sequences of wheat genes and used them to evaluate SNP polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 US elite wheat cultivars, representing seven market classes. This value increased to 0.23 when SNPs were pre-selected for polymorphisms among a diverse set of 13 hexaploid wheat accessions (excluding synthetic wheats) used in the wheat SNP discovery project ( PIC values for SNP markers in the D genome were approximately half of those for the A and B genomes. D genome SNPs also showed a larger PIC reduction relative to the other genomes (P < 0.05) when US cultivars were compared with the more diverse set of 13 wheat accessions. Within those accessions, D genome SNPs show a higher proportion of alleles with low minor allele frequencies (<0.125) than found in the other two genomes. These data suggest that the reduction of PIC values in the D genome was caused by differential loss of low frequency alleles during the population size bottleneck that accompanied the development of modern commercial cultivars. Additional SNP discovery efforts targeted to the D genome in elite wheat germplasm will likely be required to offset the lower diversity of this genome. With increasing SNP discovery projects and the development of high-throughput SNP assay technologies, it is anticipated that SNP markers will play an increasingly important role in wheat genetics and breeding applications.





Expressed sequence tag


Fluorescence polarization


Hard red spring


Hard white spring


Hard red winter


Hard White Winter


Polymorphism information content


Simple sequence repeat


Single nucleotide polymorphism


Soft red winter


Soft white spring


Soft white winter

Supplementary material

11032_2008_9210_MOESM1_ESM.doc (512 kb)
(DOC 511 kb)

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Shiaoman Chao
    • 1
  • Wenjun Zhang
    • 2
  • Eduard Akhunov
    • 3
  • Jamie Sherman
    • 4
  • Yaqin Ma
    • 2
  • Ming-Cheng Luo
    • 2
  • Jorge Dubcovsky
    • 2
  1. 1.USDA-ARS Biosciences Research LabFargoUSA
  2. 2.Department of Plant SciencesUniversity of California, DavisDavisUSA
  3. 3.Department of Plant PathologyKansas State UniversityManhattanUSA
  4. 4.Department of Plant and Soil SciencesMontana State UniversityBozemanUSA