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

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...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2010-12, Vol.107 (50), p.21611-21616
Main Authors: Cockram, James, White, Jon, Zuluaga, Diana L., Smith, David, Comadran, Jordi, Macaulay, Malcolm, Luo, Zewei, Kearsey, Mike J., Werner, Peter, Harrap, David, Tapsell, Chris, Liu, Hui, Hedley, Peter E., Stein, Nils, Schulte, Daniela, Steuernagel, Burkhard, Marshall, David F., Thomas, William T. B., Ramsay, Luke, Mackay, Ian, Balding, David J., Waugh, Robbie, O'Sullivan, Donal M., Doebley, John
Format: Article
Language:English
Subjects:
Alleles
Arabidopsis Proteins - genetics
Barley
Biological Sciences
Chromosome Mapping
Chromosomes
Cultivars
Genes
Genetic loci
Genetic mapping
Genetic Markers
Genome, Plant
Genome-Wide Association Study
Genomes
Genomics
Genotype
Genotype & phenotype
Grain
Homeodomain Proteins - genetics
Hordeum - genetics
Humans
Molecular Sequence Data
Morphology
Phenotype
Phenotypic traits
Plants
Polymorphism
Polymorphism, Genetic
Principal Component Analysis
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1010179107