Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon

Genetic architecture and phenotypic plasticity are important
considerations when studying trait variation within and among populations.
Since environmental change can induce shifts in the genetic architecture
and plasticity of traits, it is important to consider both genetic and
environmental sources of phenotypic variation. While there is overwhelming
evidence for environmental effects on phenotype, the underlying mechanisms
are less clear. Variation in DNA methylation is a potential mechanism
mediating environmental effects on phenotype due to its sensitivity to
environmental stimuli, transgenerational inheritance, and influences on
transcription. To characterize the effect of environment on methylation,
we created two 6x6 (North Carolina II) Chinook salmon breeding crosses and
reared the offspring in two environments: uniform hatchery tanks and
semi-natural stream channels. We sampled the fish twice during
development, at the alevin (larval) and fry (juvenile) stages. We measured
DNA methylation at 13 genes using a PCR-based bisulfite sequencing
protocol. The genetic architecture of DNA methylation differed between
rearing environments, with greater additive and non-additive genetic
variance in hatchery fish and greater maternal effects in semi-natural
channel fish, though gene-specific variation was evident. We observed
plasticity in methylation across all assayed genes, as well as
gene-specific effects at two genes in alevin and six genes in fry,
indicating developmental stage-specific effects of rearing environment on
methylation. Characterizing genetic and environmental influences on
methylation is critical for future studies on DNA methylation as a
potential mechanism for acclimation and adaptation.