Whole-genome association mapping in elite inbred crop varieties

Robbie Waugh, David Marshall, Bill Thomas, Jordi Comadran, Joanne Russell, Tim Close, Nils Stein, Pat Hayes, Gary Muehlbauer, James Cockram, Donal O'Sullivan, Ian MacKay, Andrew Flavell, Luke Ramsay, AGOUEB, BarleyCAP

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    18 Citations (Scopus)

    Abstract

    We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley ( Hordeum vulgare) gene pool extends, on average, for <1-5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism ( SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.

    Original languageEnglish
    Pages (from-to)967-972
    Number of pages6
    JournalGenome Biology
    Volume53
    Issue number11
    DOIs
    Publication statusPublished - Nov 2010

    Keywords

    • barley
    • SNP
    • linkage disequilibrium
    • association mapping
    • LINKAGE DISEQUILIBRIUM
    • RESISTANCE GENES
    • HORDEUM-VULGARE
    • FLOWERING TIME
    • BARLEY
    • MAIZE
    • POPULATION

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