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 maternal effects in seminatural 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.

中文翻译：

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饲养环境影响奇努克鲑鱼的遗传结构和 DNA 甲基化的可塑性

在研究群体内部和群体之间的性状变异时，遗传结构和表型可塑性是重要的考虑因素。由于环境变化可以引起遗传结构和性状可塑性的变化，因此考虑表型变异的遗传和环境来源非常重要。尽管有大量证据表明环境对表型的影响，但其潜在机制尚不清楚。DNA 甲基化变异是介导环境对表型影响的潜在机制，因为它对环境刺激、跨代遗传和转录影响敏感。为了表征环境对甲基化的影响，我们创建了两个 6 × 6（北卡罗莱纳州 II）奇努克鲑鱼繁殖杂交，并在两种环境中饲养后代：均匀的孵化池和半自然河道。我们在鱼的发育过程中，在鱼苗（幼鱼）和鱼苗（幼鱼）阶段对鱼进行了两次采样。我们使用基于 PCR 的亚硫酸氢盐测序方案测量了 13 个基因的 DNA 甲基化。DNA甲基化的遗传结构在不同的饲养环境中有所不同，孵化场鱼类的加性和非加性遗传差异更大，半自然斑点叉尾鱼的母体效应更大，尽管基因特异性变异很明显。我们观察到所有检测基因的甲基化可塑性，以及 alevin 中的两个基因和鱼苗中的 6 个基因的基因特异性效应，表明饲养环境对甲基化的发育阶段特异性影响。表征遗传和环境对甲基化的影响对于未来研究 DNA 甲基化作为适应和适应的潜在机制至关重要。