The historically recent domestication of fishes has been essential to meet the protein demands of a growing human population. Selection for traits of interest during domestication is a complex process whose epigenetic basis is poorly understood. Cytosine hydroxymethylation is increasingly recognized as an important DNA modification involved in epigenetic regulation. In the present study, we investigated if hydroxymethylation plays a role in fish domestication and demonstrated for the first time at a genome-wide level and single nucleotide resolution that the muscle hydroxymethylome changes after a single generation of Nile tilapia (Oreochromis niloticus, Linnaeus) domestication. The overall decrease in hydroxymethylcytosine levels was accompanied by the downregulation of 2015 genes in fish reared in captivity compared to their wild progenitors. In contrast, several myogenic and metabolic genes that can affect growth potential were upregulated. There were 126 differentially hydroxymethylated cytosines between groups, which were not due to genetic variation; they were associated with genes involved in immune-, growth- and neuronal-related pathways. Taken together, our data unveil a new role for DNA hydroxymethylation in epigenetic regulation of fish domestication with impact in aquaculture and implications in artificial selection, environmental adaptation and genome evolution.

历史上最近的鱼类驯化对于满足不断增长的人口的蛋白质需求至关重要。在驯化过程中选择感兴趣的性状是一个复杂的过程，其表观遗传基础知之甚少。胞嘧啶羟甲基化越来越被认为是参与表观遗传调控的重要 DNA 修饰。在本研究中，我们研究了羟甲基化是否在鱼类驯化中发挥作用，并首次在全基因组水平和单核苷酸分辨率上证明了尼罗罗非鱼（ Oreochromis niloticus ，Linnaeus）驯化后单代肌肉羟甲基化发生了变化。与野生鱼类相比，圈养鱼类中羟甲基胞嘧啶水平的总体下降伴随着 2015 年基因的下调。相比之下，一些可以影响生长潜力的生肌和代谢基因被上调。组间有 126 个差异羟甲基化胞嘧啶，这不是由于遗传变异所致；它们与涉及免疫、生长和神经元相关途径的基因有关。总而言之，我们的数据揭示了 DNA 羟甲基化在鱼类驯化的表观遗传调控中的新作用，对水产养殖产生影响，并对人工选择、环境适应和基因组进化产生影响。