Exploiting barley genetic resources for genomewide association scans (GWAS)

We have been exploring the use of GWAS for trait analysis and gene isolation in cultivated barley. In this chapter we describe the approach we have taken and some of the hurdles that we have faced when attempting to establish the whole system. We discuss the way that we, but also others, have addressed the various issues that have arisen and provide guidance on how the can be avoided. These range from choosing the appropriate population for analysis, how to deal with inherent population structure, genetic marker discovery, application and the effect of ascertainment bias to the range of software currently available for conducting association analyses.We conclude by providing a series of successful examples from our laboratory that range from analysis of simple single gene traits through oligogenic to quantitative traits, and the detection of epistatic interactions. We conclude that appropriately designed and executed GWAS in barley is a powerful tool in our quest to identify the genes and alleles underlying key genetic traits.