RRC ID 25669
Author Iehisa JC, Shimizu A, Sato K, Nasuda S, Takumi S.
Title Discovery of high-confidence single nucleotide polymorphisms from large-scale de novo analysis of leaf transcripts of Aegilops tauschii, a wild wheat progenitor.
Journal DNA Res.
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.
Volume 19(6)
Pages 487-97
Published 2012-12
DOI 10.1093/dnares/dss028
PII dss028
PMID 23125207
PMC PMC3514859
MeSH Base Sequence Chromosome Mapping Chromosomes, Plant / genetics* Contig Mapping DNA, Complementary / chemistry DNA, Complementary / genetics DNA, Plant / chemistry DNA, Plant / genetics Expressed Sequence Tags Gene Library Genetic Linkage Genome, Plant / genetics* High-Throughput Nucleotide Sequencing INDEL Mutation Microsatellite Repeats / genetics Molecular Sequence Annotation Nucleotide Motifs Plant Leaves / genetics Poaceae / genetics* Polymorphism, Single Nucleotide / genetics* RNA, Plant / genetics Sequence Analysis, DNA Synteny Transcriptome
IF 5.415
Wheat KU-2627 KU-2826 KU-2087 KU-2144 KU-2069 KU-2811 KU-2100 KU-2159 KU-2093