An Epigenetics Pilot Study to Evaluate Effects of Rearing Density on Methylation Patterns in Chinook Salmon
Abstract
Fitness differences between fish born in nature (natural-origin) versus in the hatchery setting (hatchery-origin) are well documented, yet strong genomic differences between these phenotypes have not been consistently found. On the contrary, parallel epigenetic differences between hatchery- and natural-origin salmonids have recently emerged from the literature. However, the specific environmental triggers that shape epigenetic differences remain largely unknown. We present plans for an upcoming experiment that is designed to test the hypothesis that hatchery rearing density influences methylation patterns in Chinook salmon. Offspring from 8 half-sib families will be divided in a controlled experiment into three different study groups including low density treatment, high density treatment, and a density level mimicking conservation hatchery targets. Multiple tissue types will be collected from parents and offspring (during parr and smolt life stages) from each family to further determine the heritability of epigenetic signals. Using whole genome bisulfite sequencing, we will explore the functional regions of the genome that are differentially methylated in response to density treatments. Results from this study are expected to provide insight into the relationship between environmental triggers, methylation patterns, and subsequent fitness differences between hatchery- and natural-origin fish that could ideally be incorporated into future hatchery management protocols.
Authors
Citation
Koch, I., H. Nuetzel, and S. Narum. 2025. An epigenetics pilot study to evaluate effects of rearing density on methylation patterns in Chinook Salmon. Idaho Chapter of American Fisheries Society Meeting, April 1-4, 2025. Boise, ID.