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

Research output: Contribution to journalArticle

18 Scopus citations

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 (US)
Pages (from-to)967-972
Number of pages6
JournalGenome
Volume53
Issue number11
DOIs
StatePublished - 2010

Keywords

  • SNP
  • association mapping
  • barley
  • linkage disequilibrium

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    Waugh, R., Marshall, D., Thomas, B., Comadran, J., Russell, J., Close, T., Stein, N., Hayes, P., Muehlbauer, G., Cockram, J., O'Sullivan, D., MacKay, I., Flavell, A., & Ramsay, L. (2010). Whole-genome association mapping in elite inbred crop varieties. Genome, 53(11), 967-972. https://doi.org/10.1139/G10-078