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

Heredity
Clare J VenneyDaniel D Heath

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 6 × 6 (North Carolina II) Chinook salmon breeding crosses and reared the offspring in two environments: uniform hatchery tanks and seminatural 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 nonadditive genetic variance in hatchery fish and greater mate...Continue Reading

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Citations

Apr 17, 2021·The Journal of Heredity·Rena M SchweizerGordon Luikart
Jun 15, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·W M TwardekS J Cooke
Oct 23, 2021·The Journal of Animal Ecology·Kara K S Layton, Ian R Bradbury

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Methods Mentioned

BETA
genotyping
PCR
Assay
Chip
transgenic
environmental stress

Software Mentioned

meth
Cervus
bwa
R package fullfact
R Development Core Team
R
lme4

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