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PMID: 16244872 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Molecular genetics and genomics : MGG ·Vol. 274 ·No. 5 ·2005-12-00 ·Pages 515-27

Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R

Abstract

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.

MeSH Terms
Expressed Sequence Tags Genes, Plant Genetic Linkage Hordeum/genetics Polymorphism, Single Nucleotide
Authors & Affiliations
16 authors, click to expand affiliations / ORCID
Rostoks Nils
Genome Dynamics, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK. Nils.Rostoks@scri.ac.uk
Mudie Sharon
Cardle Linda
Russell Joanne
Ramsay Luke
Booth Allan
Svensson Jan T
Wanamaker Steve I
Walia Harkamal
Rodriguez Edmundo M
Hedley Peter E
Liu Hui
Morris Jenny
Close Timothy J
Marshall David F
Waugh Robbie
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Article Info
Journal
Molecular genetics and genomics : MGG
Abbr.
Mol Genet Genomics
ISSN
1617-4615
DOI
10.1007/s00438-005-0046-z
Email
nils.rostoks@scri.ac.uk
Published
2005-12-00
Epub
2005-00-22
Pages
515-27
Language
English
Region
Germany
NLM ID
101093320
Subset
IM
External Links
PubMed source DOI: 10.1007/s00438-005-0046-z View journal details
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