Data from: Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss

Little information has been gathered regarding the ontogenetic changes that contribute to differentiation between resident and migrant individuals, particularly before the onset of gross morphological and physiological changes in migratory individuals. The aim of this study was to evaluate gene expression during early development in Oncorhynchus mykiss populations with different life histories, in a tissue known to integrate environmental cues to regulate complex developmental processes and behaviours. We sampled offspring produced from migrant and resident parents, collecting whole embryos prior to the beginning of first feeding, and brain tissue at three additional time points over the first year of development. RNA sequencing for 32 individuals generated a reference transcriptome of 30 177 genes that passed count thresholds. Differential gene expression between migrant and resident offspring was observed for 1982 genes. The greatest number of differentially expressed genes occurred at 8 months of age, in the spring a full year before the obvious physiological transformation from stream-dwelling parr to sea water-adaptable smolts begins for migrant individuals. Sex and age exhibited considerable effects on differential gene expression between migrants and resident offspring. Differential gene expression was observed in genes previously associated with migration, but also in genes previously unassociated with early life history divergence. Pathway analysis revealed coordinated differential expression in genes related to phototransduction, which could modulate photoperiod responsiveness and variation in circadian rhythms. The role for early differentiation in light sensitivity and biological rhythms is particularly intriguing in understanding early brain processes involved in differentiation of migratory and resident life history types.目前关于导致定居型与洄游型个体分化的个体发育变化的相关研究信息仍较为匮乏，尤其是在洄游个体出现显著形态与生理变化之前的阶段。本研究旨在探究不同生活史类型的虹鳟（Oncorhynchus mykiss）种群在早期发育阶段的基因表达情况，所选组织已知可整合环境信号以调控复杂的发育过程与行为模式。我们采集了洄游型与定居型亲本所产的子代样本：在首次摄食开始前收集完整胚胎，并在发育第一年的另外三个时间点采集脑组织样本。对32个个体进行RNA测序（RNA sequencing）后，构建得到包含30177个符合计数阈值基因的参考转录组。共检测到1982个基因在洄游型与定居型子代间存在差异表达。差异表达基因的数量峰值出现在发育至8月龄的春季，此时距离洄游个体从溪流栖居幼鳟向适应海水的降海幼鳟发生显著生理转变尚有一整年时间。性别与发育年龄对洄游型与定居型子代间的差异基因表达均存在显著影响。研究不仅在既往与洄游行为相关的基因中检测到差异表达，还在此前未被发现与早期生活史分化相关的基因中同样发现了差异表达现象。通路分析结果显示，与光转导（phototransduction）相关的基因存在协同差异表达，这类基因可调控光周期响应性与昼夜节律的变异。在探究调控定居型与洄游型生活史类型分化的早期脑发育机制时，早期光敏感性与生物节律分化的相关作用尤为值得关注。