Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

Migration traits are presumed to be complex and to involve interaction among multiple genes, thus we employed both univariate analyses and multivariate Random Forest (RF) machine learning algorithm to conduct association mapping of 15,239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead (Oncorhynchus mykiss). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer- and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration-timing (p < 0.000005) that explained 46% of trait variation. Alignment to the annotated S. salar genome provided evidence that all three SNPs localize within a 46 kb region overlapping GREB1-like (an estrogen target gene) on chromos...