Differential DNA Methylation in Somatic and Sperm cells of Hatchery versus Wild (Natural-Origin) Steelhead Trout Populations

The study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) versus the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth and fast growth hatchery trout were investigated. The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery versus wild steelhead trout populations. Interestingly, the DMRs were cell type specific with negligible overlap. Slow growth compared to fast growth steelhead also had a larger number of DMRs in the RBC samples. Observations demonstrate a major epigenetic programming difference between the hatchery and wild fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth rate can alter the epigenetic developmental programming of the steelhead trout, which may correlate to the phenotypic variations observed. Overall design: The sperm and red blood cells (RBC) from adult male slow growth hatchery steelhead, fast-growth hatchery steelhead, and wild (natural-origin) steelhead were collected for DNA preparation to investigate potential alterations in differential DNA methylation regions (DMRs). An MeDIP-seq procedure was used to identify the DMR.