title: Identification and characterization of more than 4 million intervarietal SNPs across the group 7 chromosomes of bread wheat.
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.
authors.affiliation: School of Agriculture and Food Sciences, University of Queensland, Brisbane, Qld, Australia; Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, Qld, Australia.
authors.forename: Kaitao
authors.initials: K
authors.lastname: Lai
authors.forename: Michał T
authors.initials: MT
authors.lastname: Lorenc
authors.forename: Hong Ching
authors.initials: HC
authors.lastname: Lee
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Berkman
authors.forename: Philipp Emanuel
authors.initials: PE
authors.lastname: Bayer
authors.forename: Paul
authors.initials: P
authors.lastname: Visendi
authors.forename: Pradeep
authors.initials: P
authors.lastname: Ruperao
authors.forename: Timothy L
authors.initials: TL
authors.lastname: Fitzgerald
authors.forename: Manuel
authors.initials: M
authors.lastname: Zander
authors.forename: Chon-Kit Kenneth
authors.initials: CK
authors.lastname: Chan
authors.forename: Sahana
authors.initials: S
authors.lastname: Manoli
authors.forename: Jiri
authors.initials: J
authors.lastname: Stiller
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.forename: David
authors.initials: D
authors.lastname: Edwards
mesh_terms: D001315:Australia; D001939:Bread; D032461:Chromosomes, Plant / Q000235:genetics*; D018745:Genome, Plant; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D014908:Triticum / Q000235:genetics*
keywords: Triticum aestivum; diversity; evolution; single nucleotide polymorphisms