The design of mapping populations: Impacts of geographic scale on genetic architecture and mapping efficacy for defense and immunity

Genome-wide association studies (GWAS) have yielded tremendous insight into the genetic architecture of trait variation. However, the collections of loci they uncover are far from exhaustive. As many of the complicating factors that confound or limit the efficacy of GWAS are exaggerated over broad geographic scales, a shift toward more analyses using mapping panels sampled from narrow geographic localities (“local” populations) could provide novel, complementary insights. Here, we present an overview of the major complicating factors, review mounting evidence from genomic analyses that these factors are pervasive, and synthesize theoretical and empirical evidence for the power of GWAS in local populations.