Domestication is the process by which organisms become adapted to the human-controlled environment. Since the selection pressures that act upon cultured and natural populations differ, adaptations that favour life in the domesticated environment are unlikely to be advantageous in the wild. Elucidation of the differences between wild and domesticated Atlantic salmon may provide insights into some of the genomic changes occurring during domestication, and, help to predict the evolutionary consequences of farmed salmon escapees interbreeding with wild conspecifics. In this study the transcriptome of the offspring of wild and domesticated Atlantic salmon were compared using a common-garden experiment under standard hatchery conditions and in response to an applied crowding stressor. Transcriptomic differences between wild and domesticated crosses were largely consistent between the control and stress conditions, and included down-regulation of environmental information processing, immune and nervous system pathways and up-regulation of genetic information processing, carbohydrate metabolism, lipid metabolism and digestive and endocrine system pathways in the domesticated fish relative to their wild counterparts, likely reflective of different selection pressures acting in wild and cultured populations. Many stress responsive functions were also shared between crosses and included down-regulation of cellular processes and genetic information processing and up-regulation of some metabolic pathways, lipid and energy in particular. The latter may be indicative of mobilization and reallocation of energy resources in response to stress. However, functional analysis indicated that a number of pathways behave differently between domesticated and wild salmon in response to stress. Reciprocal F1 hybrids permitted investigation of inheritance patterns that govern transcriptomic differences between these genetically divergent crosses. Additivity and maternal dominance accounted for approximately 42 and 25% of all differences under control conditions for both hybrids respectively. However, the inheritance of genes differentially expressed between crosses under stress was less consistent between reciprocal hybrids, potentially reflecting maternal environmental effects. We conclude that there are transcriptomic differences between the domesticated and wild salmon strains studied here, reflecting the different selection pressures operating on them. Our results indicate that stress may affect certain biological functions differently in wild, domesticated and hybrid crosses and these should be further investigated.

中文翻译：

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在应激和控制条件下共同饲养的野生、驯化和杂交大西洋鲑鱼苗的转录组比较。

驯化是生物体适应人类控制环境的过程。由于作用于养殖种群和自然种群的选择压力不同，有利于驯化环境中生活的适应在野外不太可能有利。阐明野生和驯化大西洋鲑鱼之间的差异可能有助于了解驯化过程中发生的一些基因组变化，并有助于预测养殖鲑鱼逃逸者与野生同种杂交的进化后果。在这项研究中，使用标准孵化场条件下的普通花园实验以及对所施加的拥挤应激源的反应，对野生和驯化大西洋鲑鱼后代的转录组进行了比较。野生和驯化杂交之间的转录组差异在对照和胁迫条件下基本一致，包括环境信息处理、免疫和神经系统途径的下调以及遗传信息处理、碳水化合物代谢、脂质代谢以及消化和内分泌的上调驯化鱼类相对于野生鱼类的系统途径，可能反映了野生和养殖种群中不同的选择压力。许多应激反应功能也在杂交之间共享，包括细胞过程和遗传信息处理的下调以及某些代谢途径（特别是脂质和能量）的上调。后者可能表明能源资源的动员和重新分配以应对压力。然而，功能分析表明，驯化鲑鱼和野生鲑鱼在应对压力时的许多途径表现不同。互惠 F1 杂交允许研究控制这些遗传上不同的杂交之间转录组差异的遗传模式。对于两个杂种来说，加性性和母本优势分别占对照条件下所有差异的约 42% 和 25%。然而，在胁迫下杂交之间差异表达的基因的遗传在互交杂交之间不太一致，这可能反映了母体环境的影响。我们的结论是，这里研究的驯化和野生鲑鱼品系之间存在转录组差异，反映了对它们施加的不同选择压力。我们的结果表明，应激可能对野生、驯化和杂交杂交中的某些生物学功能产生不同的影响，这些应该进一步研究。