Molecular Genetics and Genomics

, Volume 274, Issue 5, pp 515–527 | Cite as

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

  • Nils Rostoks
  • Sharon Mudie
  • Linda Cardle
  • Joanne Russell
  • Luke Ramsay
  • Allan Booth
  • Jan T. Svensson
  • Steve I. Wanamaker
  • Harkamal Walia
  • Edmundo M. Rodriguez
  • Peter E. Hedley
  • Hui Liu
  • Jenny Morris
  • Timothy J. Close
  • David F. Marshall
  • Robbie Waugh
Original Paper

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.

Keywords

Barley SNP discovery Haplotype Integrated linkage map Rice synteny 

Supplementary material

438_2005_46_MOESM1_ESM.pdf (39 kb)
Supplementary material 1 (PDF)
438_2005_46_MOESM2_ESM.xls (142 kb)
Supplementary material 2 (XLS)
438_2005_46_MOESM3_ESM.txt (16 kb)
Supplementary material 3 (TXT)
438_2005_46_MOESM4_ESM.txt (39 kb)
Supplementary material 4 (TXT)

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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Nils Rostoks
    • 1
  • Sharon Mudie
    • 1
  • Linda Cardle
    • 1
  • Joanne Russell
    • 1
  • Luke Ramsay
    • 1
  • Allan Booth
    • 1
  • Jan T. Svensson
    • 2
  • Steve I. Wanamaker
    • 2
  • Harkamal Walia
    • 2
  • Edmundo M. Rodriguez
    • 2
  • Peter E. Hedley
    • 1
  • Hui Liu
    • 1
  • Jenny Morris
    • 1
  • Timothy J. Close
    • 2
  • David F. Marshall
    • 1
  • Robbie Waugh
    • 1
  1. 1.Genome DynamicsScottish Crop Research InstituteDundeeUK
  2. 2.Department of Botany and Plant SciencesUniversity of CaliforniaRiversideUSA

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