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；然而，学界对转录变异的遗传模式所知甚少，而此类模式本可助力我们预判其对选择的响应。此外，不同环境条件下的驯化过程会影响生物对胁迫的急性转录响应，目前尚不清楚此类效应是否具备可遗传性。为填补这一研究空白，我们针对两种饲养环境（孵化场与半天然溪流通道）中的72个奇努克鲑（Chinook salmon）半同胞家系（half-sib families），分别测定了静息状态下以及经24小时监禁胁迫后14个候选基因的信使RNA（messenger RNA, mRNA）水平。我们观测到代谢基因与胁迫响应基因的mRNA水平存在广泛的可塑性，并证实：饲养环境所诱导的mRNA水平可塑性，会影响生物应对胁迫时的mRNA水平可塑性。此类效应对于面临多重胁迫的自然种群具有重要的研究意义。我们鉴定出了以母体效应（maternal effects）为主导的mRNA水平基因型-环境互作（genotype-by-environment interactions）；此外，生物对胁迫挑战的mRNA水平响应同样表现出非加性遗传基础（non-additive genetic basis）。本研究结果表明，尽管mRNA水平的可塑性可发生演化，但要预判选择的结果仍颇具难度。各处理组间遗传架构的不一致性表明，基因表达存在大量的隐秘遗传变异（cryptic genetic variation）。