Data from: Environmental associations with gene transcription in Babine Lake rainbow trout: evidence for local adaptation

The molecular genetic mechanisms facilitating local adaptation in salmonids continue to be poorly characterized. Gene transcription is a highly regulated step in the expression of a phenotype and it has been shown to respond to selection and thus may be one mechanism that facilitates the development of local adaptation. Advances in molecular genetic tools and an increased understanding of the functional roles of specific genes allow us to test hypotheses concerning the role of variable environments in shaping transcription at known-function candidate loci. To address these hypotheses, wild rainbow trout were collected in their first summer and subjected to metabolic and immune challenges. We assayed gene transcription at candidate loci that play a role in the molecular genetic response to these stresses, and correlated transcription with temperature data from the streams and the abundance and diversity of bacteria as characterized by massively parallel pyrosequencing. Patterns of transcriptional regulation from resting to induced levels varied among populations for both treatments. Co-inertia analysis demonstrated significant associations between resting levels of metabolic gene transcription and thermal regime (R2 = 0.19, P = 0.013) as well as in response to challenge (R2 = 0.39, P = 0.001) and resting state and challenged levels of cytokine gene transcription with relative abundances of bacteria (resting: R2 = 0.25, P = 0.009, challenged: R2 = 0.65, P = 0.001). These results show that variable environments, even within a small geographic range (<250 km), can drive divergent selection among populations for transcription of genes related to surviving stress.

鲑科鱼类（salmonids）局部适应的分子遗传机制，迄今仍未得到充分解析。基因转录是表型表达过程中受到严格调控的关键步骤，已有研究表明其可响应选择压力，因此可能是推动种群局部适应形成的核心机制之一。随着分子遗传工具的发展进步，以及对特定基因功能角色的认知不断深化，我们得以验证相关假说：多变环境如何对已知功能的候选基因位点的转录水平产生塑造作用。为验证上述假说，研究人员在野生虹鳟（rainbow trout）的首个夏季进行采样，并对其开展代谢应激与免疫应激处理。我们针对参与上述应激分子遗传响应的候选基因位点开展转录水平检测，并将转录数据与溪流温度数据、通过大规模并行焦磷酸测序（massively parallel pyrosequencing）表征的细菌丰度与多样性进行关联分析。两种应激处理下，种群间从基础转录水平到诱导转录水平的调控模式均存在显著差异。共惯量分析（Co-inertia analysis）结果显示，代谢基因的基础转录水平与溪流热制度之间存在显著关联（R²=0.19，P=0.013）；应激诱导后的代谢基因转录水平同样与热制度显著相关（R²=0.39，P=0.001）。此外，细胞因子基因的基础转录水平与应激后转录水平均与细菌相对丰度存在显著关联（基础状态：R²=0.25，P=0.009；应激状态：R²=0.65，P=0.001）。本研究结果证实，即便地理分布范围狭小（<250 km），多变的环境仍可驱动不同种群间与应激耐受相关基因的转录水平发生适应性分化。