Data from: Environmental and genetic determinants of transcriptional plasticity in Chinook salmon

Variation in gene transcription is widely believed to be the mechanistic basis of phenotypically plastic traits; however, comparatively little is known about the inheritance patterns of transcriptional variation that would allow us to predict its response to selection. In addition, acclimation to different environmental conditions influences acute transcriptional responses to stress and it is unclear if these effects are heritable. To address these gaps in knowledge, we assayed levels of messenger RNA for 14 candidate genes at rest and in response to a 24-hour confinement stress for 72 half-sib families of Chinook salmon reared in two different environments (hatchery and semi-natural stream channel). We observed extensive plasticity for mRNA levels of metabolic and stress response genes and demonstrated that mRNA-level plasticity due to rearing environment affects mRNA-level plasticity in response to stress. These effects have important implications for natural
populations experiencing multiple stressors. We identified genotype-by-environment interactions for mRNA levels that were dominated by maternal-effects; however, mRNA level response to challenge also exhibited a non-additive genetic basis. Our results indicate that while plasticity for mRNA-levels can evolve, predicting the outcome of selection will be difficult. The inconsistency in genetic architecture among treatment groups suggests there is considerable cryptic genetic variation for gene expression.

基因转录（gene transcription）的变异被普遍认为是表型可塑性性状（phenotypically plastic traits）的分子机制基础；但目前针对可用于预测其对选择响应的转录变异遗传模式的研究仍相对匮乏。此外，对不同环境条件的驯化会影响生物体对应激的急性转录应答，目前尚不清楚这些效应是否可遗传。为填补这些知识空白，我们针对在两种不同环境（孵化场（hatchery）与半自然溪流通道（semi-natural stream channel））中饲养的72个奇努克鲑（Chinook salmon）半同胞家系（half-sib families），分别检测了静息状态下以及经24小时束缚应激（24-hour confinement stress）处理后14个候选基因的信使RNA（messenger RNA，mRNA）水平。我们观察到代谢与应激应答基因的mRNA水平存在广泛的可塑性，并证实饲养环境带来的mRNA水平可塑性会影响生物体对应激的mRNA水平可塑性响应。这些效应对面临多重应激源的自然种群具有重要意义。我们鉴定出以母本效应（maternal-effects）为主导的mRNA水平基因型-环境互作（genotype-by-environment interactions）；不过，机体对应激刺激的mRNA水平响应也表现出非加性遗传基础（non-additive genetic basis）。我们的研究结果表明，尽管mRNA水平的可塑性可发生演化，但预测选择的结果将十分困难。不同处理组间遗传架构的不一致性提示，基因表达存在大量的隐性遗传变异（cryptic genetic variation）。