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

Citation

Venney, Clare; Wellband, Kyle; Heath, Daniel (2020), Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon, Dryad, Dataset, https://doi.org/10.5061/dryad.0k6djh9xf

Abstract

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.

Usage Notes

This Dryad entry contains bisulfite sequencing data for Chinook salmon reared in the semi-natural channel. For hatchery-reared fish data, see https://doi.org/10.5061/dryad.5x69p8d07.

Funding

Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada, Award: 814014