利用单碱基分辨率甲基化图谱鉴定家猪驯化的DNA甲基化标记

The significant phenotypic variation between domestic pig and wild boar could, to a large extent, be attributed to strong artificial selection during domestication. Relevant research so far has been focusing on the DNA sequence level. However, in recent years ceaseless reports demonstrated that, epigenetic mechanism, especially variation in DNA methylation level was also an important factor contributing to animal phenotypic variation in evolution. To solve this frontier and popular scientific problem, we proposed to employ domestic pig and wild boar as study material, construct their single-base resolution genomic DNA methylation map, analyze that together with their coding and non-coding gene expression profiles, and comprehensively elucidate the DNA methylation variation underlying the phenotypic variation during domestication. We further proposed to identify the epigenetic marks closely related to economic traits that are fixed in the domestic pig genome during the long-term artificial selection process, shed new light on deep understanding of epigenetic variation underlying pig economic traits, and provide valuable reference data for pig economic trait improvement by molecular breeding approaches. This project is also novel in utilizing the domestication of wild boar as “special evolution model under artificial selection” to reveal the DNA methylation variation patterns during species/sub-species differentiation.

家猪和野猪在表型上的显著差异在很大程度上可归因于驯化过程中的强烈人工选择。目前相关研究主要集中在DNA序列水平。然而近年来不断有报道表明，表观遗传机制，特别是DNA甲基化水平的变异也是进化过程中动物表型发生显著改变的重要原因。本课题针对这一前沿热点科学问题，以家猪和野猪为研究对象，旨在构建家猪和野猪单碱基分辨率水平的全基因组DNA甲基化图谱，与编码和非编码基因的表达谱进行关联性分析，进而全面解析驯化过程中表型变异下的DNA甲基化变异，特别是鉴定长期人工选择过程中，家猪基因组中固定的与经济性状密切相关的表观标记，为深刻理解猪经济性状的表观基因组变异提供新思路和视野，并为后续利用分子育种手段改良猪经济性状提供宝贵参考数据。另外，本课题的创新之处还在于以野猪到家猪的驯化过程作为一种“人工选择下的特殊进化模型”，来模拟刻画物种/亚种分化过程中DNA甲基化图谱的变异规律 。

家猪和野猪在表型上的显著差异在很大程度上可归因于驯化过程中的强烈人工选择。目前相关研究主要集中在DNA序列水平。然而近年来不断有报道表明，表观遗传机制，特别是DNA甲基化水平的变异也是进化过程中动物表型发生显著改变的重要原因。本研究以家猪和野猪为研究对象，构建家猪和野猪单碱基分辨率水平的全基因组DNA甲基化图谱，并与编码和非编码基因的表达谱进行关联性分析；检测了与驯化性状变异相关的差异甲基化候选基因，发现DNA甲基化能抑制mRNA和miRNA的表达，不同的组学数据间具有复杂的直接或间接相互作用，且与不同的生长、抗病及能量代谢性状相关。本研究全面解析了驯化过程中表型变异下的表观变异, 为深刻理解猪经济性状的表观基因组变异提供新思路和视野，并为后续利用分子育种手段改良猪经济性状提供宝贵参考数据。