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 |
2012-12-1
|
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 |
4.009
|
Times Cited |
25
|
Resource |
Wheat |
KU-2627
KU-2826
KU-2087
KU-2144
KU-2069
KU-2811
KU-2100
KU-2159
KU-2093 |