Characterization of genetic and epigenetic variation in hatchery and natural-origin steelhead, Oncorhynchus mykiss

Relative reproductive success studies have documented substantial fitness loss for wild steelhead after a single generation of rearing in the hatchery, but the relative contribution of genetic selection and/or environmentally-induced heritable epigenetic changes passed through the germline are unknown. Here, as a step toward understanding mechanisms of fitness loss, we describe genetic and epigenetic variation in adult hatchery and natural-origin steelhead. Our main objectives were to determine if hatchery and natural-origin fish from this stock could be distinguished genetically by examining SNPs across the entire genome, and whether differences in epigenetic programming (DNA methylation) in somatic and germ cells could be detected between the two groups.