Identifying Quantitative Trait Loci in Oat: Lessons from Human Population-Based GWAS

In recent years, resources have become available to enable genome-wide genotype-phenotype association analyses in cereal crops using thousands of genetic markers measured on hundreds of lines. One open question is whether these resources are sufficient to identify the loci influencing quantitative trait variation more effectively and efficiently than through linkage analyses in bi-parental populations. Quantitative geneticists have been performing genome-wide association analyses (GWAS) in human population-based samples for nearly a decade. A look at these studies can illustrate issues likely to be encountered in oat GWAS; including the impacts of population structure, marker density, recombination hotspots, the allele frequency distribution, and estimated effect size.  This presentation discusses these issues with specific examples drawn from human and plant studies of genotype-phenotype association.