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 from the Methow River, Washington USA. Our main objectives were to determine if hatchery and natural-origin fish from this stock could be distinguished genetically by examining SNPs across the genome, and whether differences in epigenetic programming (DNA methylation) in somatic and germ cells could be detected between the two groups. Although genetic analysis using RAD-Seq did not reveal differences between the hatchery and natural fish, we found significant differences in epigenetic programming in both somatic (red blood cells) and germ cells (sperm). Because hatchery fish experience similar environmental conditions as their wild conspecifics once they leave the hatchery, our results raise the possibility that these DNA methylation changes occurred during the first year in the hatchery and persisted into adulthood in the form of an ‘epigenetic memory’ of the hatchery environment.