Data from: Genetics of gene expression responses to temperature stress in a sea urchin gene network

Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress. We found that an increase from 12 °C to 18 °C caused widespread alterations in gene expression including in genes involved in protein folding, RNA processing, and development. To understand the quantitative genetic architecture of this response, we then focused on a well-characterized gene network involved in endomesoderm and ectoderm specification. Using a breeding design with wild-caught individuals, we measured genetic and gene-environment interaction effects on 72 genes within this network. We found genetic or maternal effects in 33 of these genes, and that the genetic effects were correlated in the network. 14 network genes also responded to higher temperatures, but we found no significant genotype-environment interactions in any of the genes. This absence may be due to an effective buffering of the temperature perturbations within the network. In support of this hypothesis, perturbations to regulatory genes did not affect the expression of the genes that they regulate. Together, these results provide novel insights into the relationship between environmental change and developmental evolution and suggest that climate change may not expose large amounts of cryptic genetic variation to selection in this species.应激反应在塑造物种分布范围及其应对气候变化的鲁棒性方面发挥着关键作用。本研究以紫海胆（Strongylocentrotus purpuratus）为研究对象，探究在模拟真实气候变化情景的升温条件下，应激反应如何改变紫海胆发育过程中加性遗传变异对基因表达的贡献。我们首先通过RNA测序（RNA-seq）技术检测胚胎的基因表达响应，以表征轻度慢性温度胁迫的分子特征。研究发现，将培养温度从12℃提升至18℃会引发全基因组范围的基因表达改变，涉及蛋白质折叠、RNA加工及发育相关的诸多基因。为解析该响应的数量遗传结构，我们后续聚焦于一个已得到充分研究的、参与内中胚层与外胚层特化的基因调控网络。我们利用野生捕获个体构建繁育设计方案，对该网络内的72个基因的遗传效应以及基因-环境互作效应进行了量化检测。结果显示，其中33个基因存在遗传效应或母源效应，且该网络内的遗传效应呈现显著相关性。另有14个网络基因对升温处理产生了响应，但未在任何基因中检测到显著的基因型-环境互作效应。这种无显著互作的现象可能源于该基因网络内部对温度扰动的有效缓冲作用。为佐证该假说，我们观察到调控基因的扰动并不会影响其所调控基因的表达，这一结果为假说提供了有力支撑。综上，本研究结果为理解环境变化与发育演化之间的关联提供了全新视角，同时表明在该海胆物种中，气候变化可能并不会暴露大量的隐蔽遗传变异以供自然选择作用。