Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat

Plant Biotechnol J. 2015 Jan;13(1):97-104. doi: 10.1111/pbi.12240. Epub 2014 Aug 22.


Despite being a major international crop, our understanding of the wheat genome is relatively poor due to its large size and complexity. To gain a greater understanding of wheat genome diversity, we have identified single nucleotide polymorphisms between 16 Australian bread wheat varieties. Whole-genome shotgun Illumina paired read sequence data were mapped to the draft assemblies of chromosomes 7A, 7B and 7D to identify more than 4 million intervarietal SNPs. SNP density varied between the three genomes, with much greater density observed on the A and B genomes than the D genome. This variation may be a result of substantial gene flow from the tetraploid Triticum turgidum, which possesses A and B genomes, during early co-cultivation of tetraploid and hexaploid wheat. In addition, we examined SNP density variation along the chromosome syntenic builds and identified genes in low-density regions which may have been selected during domestication and breeding. This study highlights the impact of evolution and breeding on the bread wheat genome and provides a substantial resource for trait association and crop improvement. All SNP data are publically available on a generic genome browser GBrowse at

Keywords: Triticum aestivum; diversity; evolution; single nucleotide polymorphisms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Australia
  • Bread*
  • Chromosomes, Plant / genetics*
  • Genome, Plant
  • Phylogeny
  • Polymorphism, Single Nucleotide / genetics*
  • Reproducibility of Results
  • Triticum / genetics*