Oncorhynchus mykiss Raw sequence reads

The genetic underpinnings associated with the earliest stages of plant and animal domestication have remained elusive. Because a genome-wide response to selection can take many generations, the earliest detectable changes associated with domestication may first manifest as heritable changes to global patterns of gene expression. To test this hypothesis, we measured differential gene expression in the offspring of wild and first-generation hatchery steelhead trout (Oncorhynchus mykiss) reared in a common environment. Remarkably, we find that there were 723 genes differentially expressed between the two groups of offspring. Reciprocal crosses reveal that the differentially expressed genes could not be explained by maternal effects or by chance differences in the background levels of gene expression among unrelated families. Gene enrichment analyses reveal that adaptation to the novel hatchery environment involved responses in wound healing, immunity, and metabolism. These findings suggest that the earliest stages of domestication may involve adaptation to highly crowded conditions.与动植物驯化早期阶段相关的遗传基础，迄今仍未得到清晰阐释。由于全基因组层面的选择响应往往需要历经多代方可显现，因此与驯化相关的最早可检测到的变化，或许最初会以全基因组基因表达模式的可遗传改变形式出现。为验证这一假说，本研究在统一饲养环境下，对野生种群与第一代孵化场繁育硬头鳟（Oncorhynchus mykiss）的子代开展了差异基因表达量检测。值得注意的是，本研究在两组子代中鉴定出723个存在差异表达的基因。正反交实验结果显示，上述差异表达基因无法通过母体效应，或是无亲缘关系家系间基因表达本底水平的随机差异予以解释。基因富集分析结果表明，对新型孵化场环境的适应涉及伤口愈合、免疫与代谢通路的响应。上述研究结果表明，驯化的早期阶段或许涉及对高密度饲养环境的适应。