Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress

More than 2,000 genome-wide barley single nucleotide polymorphisms (SNPs) were developed by resequencing unigene fragments from eight diverse accessions. The average genome-wide SNP frequency observed in 877 unigenes was 1 SNP per 200 bp. However, SNP frequency was highly variable with the least num...

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Bibliographic Details
Published in:Molecular genetics and genomics : MGG 2005-12, Vol.274 (5), p.515-527
Main Authors: Rostoks, N, Mudie, S, Cardle, L, Russell, J, Ramsay, L, Booth, A, Svensson, J.T, Wanamaker, S.I, Walia, H, Rodriguez, E.M
Format: Article
Language:English
Subjects:
Abiotic stress
amplified fragment length polymorphism
barley
chromosome mapping
Expressed Sequence Tags
flooded conditions
Gene expression
Genes, Plant
Genetic diversity
Genetic Linkage
genetic markers
genome
Genomics
haplotypes
Hordeum - genetics
Hordeum vulgare
microsatellite repeats
nitrate nitrogen
nutrient deficiencies
Oryza sativa
Polymorphism, Single Nucleotide
quantitative trait loci
restriction fragment length polymorphism
salt tolerance
single nucleotide polymorphism
stress tolerance
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Summary:More than 2,000 genome-wide barley single nucleotide polymorphisms (SNPs) were developed by resequencing unigene fragments from eight diverse accessions. The average genome-wide SNP frequency observed in 877 unigenes was 1 SNP per 200 bp. However, SNP frequency was highly variable with the least number of SNP and SNP haplotypes observed within European cultivated germplasm reflecting effects of breeding history on genetic diversity. More than 300 SNP loci were mapped genetically in three experimental mapping populations which allowed the construction of an integrated SNP map incorporating a large number of RFLP, AFLP and SSR markers (1,237 loci in total). The genes used for SNP discovery were selected based on their transcriptional response to a variety of abiotic stresses. A set of known barley abiotic stress QTL was positioned on the linkage map, while the available sequence and gene expression information facilitated the identification of genes potentially associated with these traits. Comparison of the sequenced SNP loci to the rice genome sequence identified several regions of highly conserved gene order providing a framework for marker saturation in barley genomic regions of interest. The integration of genome-wide SNP and expression data with available genetic and phenotypic information will facilitate the identification of gene function in barley and other non-model organisms.
ISSN:1617-4615
1617-4623
DOI:10.1007/s00438-005-0046-z