Abstract
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 www.wheatgenome.info.
Highlights
Wheat is a major food crop, ranked within the top four agricultural commodities globally by production and value according to the Food and Agricultural Organization of the United Nations (FAO; http://www.fao.org/home/en/), and used widely for making products including breads, pastries, noodles and dumplings
We have discovered more than 4 million candidate intervarietal Single nucleotide polymorphisms (SNPs) across the wheat group 7 chromosomes from these data, using the SGSautoSNP pipeline (Lorenc et al, 2012)
Our results demonstrate the impact of evolution and breeding on bread wheat genome diversity and provide a valuable resource for the further characterization and improvement of this important crop
Summary
Wheat is a major food crop, ranked within the top four agricultural commodities globally by production and value according to the Food and Agricultural Organization of the United Nations (FAO; http://www.fao.org/home/en/), and used widely for making products including breads, pastries, noodles and dumplings. Substantial cultivation of tetraploid wheat occurs, primarily ‘durum’ wheat (Triticum durum). Greater than 90% of the world’s cultivated wheat is the hexaploid species Triticum aestivum (Shewry, 2009), known as ‘common’ or ‘bread’ wheat. Between 0.5 and 3 MYA, the diploid genomes of Triticum urartu (AuAu) and an unidentified species (BB) similar to Aegilops speltoides combined to produce the allotetraploid genome of wild emmer wheat or Triticum turgidum (AuAuBB) (Chantret et al, 2005; Eckardt, 2001; Huang et al, 2002). 8000 years ago, probably in a region close to the Caspian Sea, a second event combined the genomes of T. turgidum (AuAuBB) and Aegilops tauschii (DD), producing the allohexaploid T. aestivum genome (AuAuBBDD) (McFadden and Sears, 1946). Genome analysis in bread wheat poses substantial challenges; in addition to the complexity associated with its hexaploid structure, the bread wheat genome is very large (~17 Gb; around 40 times the size of rice or nearly six times larger than the human genome) and consists of about 80–90% repetitive sequence (Safar et al, 2010; Wanjugi et al, 2009)
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