Table3_Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish (Siniperca chuatsi).XLSX

Mandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individuals could accept dead prey fish and artificial diets. The genetic basis of individual difference in artificial diet feeding habit is still unknown. In the present study, the resequencing was performed between 10 individuals which could be domesticated to accept artificial diets and 10 individuals which could not. Through the selective sweep analysis based on heterozygosity (Hp) and population differentiation coefficient (Fst), 57 candidate windows were identified as the putative selected regions for feeding habit domestication of mandarin fish, involved in 149 genes. These genes were related to memory, vision and olfaction function, which could be potential targets of molecular marker assistant breeding of artificial diet feeding trait. Beside of the DNA sequence, we also explored the potential role of DNA methylation in feeding habit domestication in mandarin fish. Whole-genome bisulfite sequencing was performed between the individuals which could be domesticated to accept artificial diets and those could not. 5,976 differentially methylated regions were identified, referring to 3,522 genes, such as the genes involved in cAMP signaling pathway. The DNA methylation changes of these genes might contribute to the adaption of artificial diets in mandarin fish. In conclusion, the putative selected regions and the differentially methylated regions were identified in the whole genome, providing new insights into the feeding habit domestication from live prey fish to artificial diets in mandarin fish. And the involved genes were identified as the candidate genes for molecular breeding of artificial diet utilization in mandarin fish.

鳜（Siniperca chuatsi）是我国经济价值极高的淡水鱼类之一。但其具有独特的摄食习性：自开口摄食起便仅以活饵为食，完全拒绝死饵或人工配合饲料。经特定驯化流程后，部分个体可接受死饵与人工配合饲料。目前，鳜鱼人工饲料摄食习性的个体差异的遗传基础仍未明确。本研究对10尾可驯化摄食人工饲料的个体与10尾无法驯化的个体开展全基因组重测序。基于杂合度（Hp）与群体分化系数（Fst）进行选择性清除分析，共鉴定得到57个候选窗口，被认定为鳜鱼摄食习性驯化的潜在受选择区域，涉及149个功能基因。这些基因与记忆、视觉及嗅觉功能密切相关，可作为鳜鱼人工饲料摄食性状分子标记辅助育种的潜在靶点。
除DNA序列层面外，本研究还探讨了DNA甲基化在鳜鱼摄食习性驯化中的潜在作用。对可驯化摄食人工饲料的个体与无法驯化的个体开展全基因组亚硫酸氢盐测序后，共鉴定到5976个差异甲基化区域，涉及3522个基因，其中包括参与环腺苷酸（cAMP）信号通路的相关基因。这些基因的DNA甲基化变化可能参与调控鳜鱼对人工饲料的适应性过程。
综上，本研究在全基因组范围内鉴定到潜在受选择区域与差异甲基化区域，为解析鳜鱼从活饵摄食到人工饲料摄食的驯化机制提供了全新视角。同时鉴定得到的相关基因可作为鳜鱼人工饲料利用性状分子育种的候选基因。