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

Research output: Contribution to journalArticle

186 Citations (Scopus)

Abstract

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
Volume107
Issue number50
Early online date29 Nov 2010
DOIs
Publication statusPublished - 14 Dec 2010

Keywords

  • Colinearity
  • Genetic variation
  • Small grain cereals

Fingerprint Dive into the research topics of 'Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome'. Together they form a unique fingerprint.

  • Cite this