Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome

James Cockram (Lead / Corresponding author), Jon White, Diana L. Zuluaga, David Smith, Jordi Comadran, Malcolm Macaulay, Zewei Luo, Mike J. Kearsey, Peter Werner, David Harrap, Chris Tapsell, Hui Liu, Peter E. Hedley, Nils Stein, Daniela Schulte, Burkhard Steuernagel, David F. Marshall, William T. B. Thomas, Luke Ramsay, Ian MacKayDavid J. Balding, , Robbie Waugh, Donal M. O'Sullivan (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

227 Citations (Scopus)


Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.

Original languageEnglish
Pages (from-to)21611-21616
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number50
Early online date29 Nov 2010
Publication statusPublished - 14 Dec 2010


  • Colinearity
  • Genetic variation
  • Small grain cereals

ASJC Scopus subject areas

  • General


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