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 behaviors. 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 1,982 genes. The greatest number of differentially expressed genes occurred at eight months of age, in the spring a full year before the obvious physiological transformation from stream-dwelling parr to seawater-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.

目前关于导致留居型与洄游型个体分化的个体发育变化的相关研究仍较为匮乏，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型虹鳟（Oncorhynchus mykiss）种群在早期发育阶段的基因表达情况，针对已知可整合环境信号以调控复杂发育过程与行为的组织展开研究。我们采集了洄游型亲本与留居型亲本所产生的后代样本：在初次摄食开始前收集全胚胎，在发育第一年的另外三个时间点采集脑组织样本。对32个个体开展RNA测序（RNA sequencing），最终构建了包含30177个符合计数阈值基因的参考转录组。研究共检测到1982个基因在洄游型与留居型后代中存在差异表达，其中差异表达基因的数量在8月龄时达到峰值，此时正值春季，距离洄游型个体从溪流栖息幼鲑向海水适应性银鲑的显著生理转变尚有一整年。性别与年龄对洄游型与留居型后代的差异基因表达均存在显著影响。差异表达基因既包含此前已被证实与洄游相关的基因，也包含此前未被发现与早期生活史分化相关的基因。通路分析显示，与光转导相关的基因呈现协同差异表达，这类基因可调控光周期响应性与昼夜节律的变异。光敏感性与生物节律的早期分化所发挥的作用，在解析调控洄游型与留居型生活史类型分化的早期脑发育过程中具有尤为重要的研究价值。