太湖流域地方猪种遗传结构评估和体重体尺性状差异相关选择位点鉴定

旨在解析太湖流域地方猪品种内部遗传结构,鉴定梅山猪亚群间、二花脸群体间和米猪群体间体重体尺性状差异的候选基因。试验采集440头猪样本(代表太湖流域地方猪最全面血统)进行基因芯片分型,并使用该基因分型数据集进行多种群体遗传学分析,明确太湖流域地方猪品种内部的遗传结构,并鉴定梅山猪亚群间、以及二花脸和米猪群体间体重体尺性状差异的候选SNP位点和候选基因。结果显示:在太湖流域地方猪种内部,二花脸猪与米猪间的亲缘关系最接近,其遗传距离小于梅山猪两个亚群间的遗传距离,并且拥有最为一致的进化路线。太湖流域地方猪各品种及梅山猪品种内两个亚群间都达到高度分化水平,Fst值均大于0.25,ADMIXTURE分析表明,包括梅山猪两个亚群在内的8个群体的群体结构不完全一致,在K=8时,各自展现出完全不同的祖先血统组成。通过梅山猪亚群间Fst分析、以及米猪和二花脸猪间Fst分析,在猪1、3和6号等染色体上,共鉴定到24个位点在两个分析中都表现出受选择状态,并在这些位点上下游50 kb范围注释到20个基因,其中有8个基因被报道与体重体尺性状相关。此外,受选择位点形成的选择区域与多个猪体重体尺相关QTLs重叠。试...

Internal population structure and selected loci associated with body weight and body size traits of indigenous pig breeds in the Taihu Lake region

This research was to analyze the internal genetic structure of the indigenous pig breeds in the Taihu Lake region and to identify the candidate genes accounting for the body size differentiation between the Meishan pig subgroups,and Erhualian versus Mi pig populations.440 pig samples representing the most comprehensive consanguinities of Taihu Lake indigenous pigs were selected in this experiment for genome sequencing with genotype chips.The data sets of the the genotype chips were used to conduct a variety of population genetic analyses,in order to determine the internal genetic structure of the indigenous pig breeds in the Taihu Lake region,and to identify candidate SNP loci and genes accounting for the differentiation in the body weight and body size traits between the Meishan pig subgroups,and Erhualian versus Mi pig populations.The results showed that,within the indigenous pig breeds in the Taihu Lake region,the genetic relationship between Erhualian and Mi pigs was the closest,and this genetic distance was shorter than that between the two subgroups of Meishan pigs,and the relationship demonstrated a most consistent evolutionary route.In addition,both the indigenous pig breeds in the Taihu Lake region and the two subgroups of Meishan pigs had a high level of differentiation with each other,with all the Fst values greater than 0.25.The ADMIXTURE analysis showed that the population structure of the eight populations,including the two subgroups of Meishan pigs,was not completely the same at K=8,where each of the eight populations exhibited a completely different ancestral lineage composition.Finally,we conducted Fst analyses between the Meishan pig subgroups,and Erhualian versus Mi pig populations,respectively.Consequently,a total of 24 loci were identified on 1,3 and 6 and so on,which showed a state of being selected in both analyses,and 20 genes were annotated in the 50 kb range upstream and downstream of these loci.Of the 20 genes,8 were reported to be related to their body weight and body size traits.In addition,the selection intervals formed by the loci were overlapped with multiple QTLs related to the body weight and body size traits of the pigs.In this experiment,the internal genetic structure of the indigenous pig breeds in the Taihu Lake region was deterined and the genetic basis of the differentiation in the body weight and body size traits of these pig breeds were analyzed,which laid a theoretical foundation for further protection and utilization of these pig breeds.