Discovery of high-confidence single nucleotide polymorphisms from large-scale de novo analysis of leaf transcripts of aegilops tauschii, a wild wheat progenitor

Julio Cesar Masaru Iehisa, Akifumi Shimizu, Kazuhiro Sato, Shuhei Nasuda, Shigeo Takumi

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Construction of high-resolution genetic maps is important for genetic and genomic research, as well as for molecular breeding. Single nucleotide polymorphisms (SNPs) are the predominant class of genetic variation and can be used as molecular markers. Aegilops tauschii, the D-genome donor of common wheat, is considered a valuable genetic resource for wheat improvement. Our previous study implied that Ae. tauschii accessions can be genealogically divided into two major lineages. In this study, the transcriptome of two Ae. tauschii accessions from each lineage, lineage 1 (L1) and 2 (L2), was sequenced, yielding 9435 SNPs and 739 insertion/deletion polymorphisms (indels) after de novo assembly of the reads. Based on 36 contig sequences, 31 SNPs and six indels were validated on 20 diverse Ae. tauschii accessions. Because almost all of the SNP markers were polymorphic between L1 and L2, and the D-genome donor of common wheat is presumed to belong to L2, these markers are available for D-genome typing in crosses between common wheat varieties and L1-derived synthetic wheat. Due to the conserved synteny between wheat and barley chromosomes, the high-density expressed sequence tag barley map and the hypothetical gene order in barley can be applied to develop markers on target chromosomal regions in wheat.

Original languageEnglish
Pages (from-to)487-497
Number of pages11
JournalDNA Research
Volume19
Issue number6
DOIs
Publication statusPublished - Dec 2012

Keywords

  • Aegilops tauschii
  • expression sequence tag
  • next generation sequencing
  • single nucleotide polymorphism
  • wheat

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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