title: Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress.
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.
authors.affiliation: Genome Dynamics, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK. Nils.Rostoks@scri.ac.uk
authors.forename: Nils
authors.initials: N
authors.lastname: Rostoks
authors.forename: Sharon
authors.initials: S
authors.lastname: Mudie
authors.forename: Linda
authors.initials: L
authors.lastname: Cardle
authors.forename: Joanne
authors.initials: J
authors.lastname: Russell
authors.forename: Luke
authors.initials: L
authors.lastname: Ramsay
authors.forename: Allan
authors.initials: A
authors.lastname: Booth
authors.forename: Jan T
authors.initials: JT
authors.lastname: Svensson
authors.forename: Steve I
authors.initials: SI
authors.lastname: Wanamaker
authors.forename: Harkamal
authors.initials: H
authors.lastname: Walia
authors.forename: Edmundo M
authors.initials: EM
authors.lastname: Rodriguez
authors.forename: Peter E
authors.initials: PE
authors.lastname: Hedley
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.forename: Jenny
authors.initials: J
authors.lastname: Morris
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Close
authors.forename: David F
authors.initials: DF
authors.lastname: Marshall
authors.forename: Robbie
authors.initials: R
authors.lastname: Waugh
mesh_terms: D020224:Expressed Sequence Tags; D017343:Genes, Plant; D008040:Genetic Linkage; D001467:Hordeum / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide