不同地方猪重要经济性状关联位点SNP芯片分型及群体遗传结构研究

旨在分析四川省7个地方猪种类群和山东省徒河黑猪重要经济性状关联SNP位点基因型分布及群体间遗传结构。本研究采用中芯一号芯片对23头成华猪、26头雅南猪、60头青峪猪、57头内江猪、151头丫杈猪、57头乌金猪（凉山类群）、51头平原藏猪、109头高原藏猪和28头徒河黑猪共562头健康种猪进行了单核苷酸多态性（single nucleotide polymorphism，SNP）分析，利用Plink软件对获得的基因型数据进行质控，结合R等软件，统计分析猪7个重要经济性状的基因型；采用Mega X软件进行聚类分析，使用Plink软件进行主成分（PCA）分析，通过VCFtools软件计算猪群间的群体遗传分化指数（Fst），分析群体间遗传关系远近。结果显示，四川省地方猪群体中，采食量、酸肉和应激性状的非优势基因型比例均在2.20%以下；抗仔猪腹泻、料重比（FCR）、公猪精液品质和多肋性状的非优势基因型比例分别为8.99%、11.80%、73.97%和95.32%；徒河黑猪群体中，应激性状已无q等位基因，采食量和酸肉性状的非优势基因型比例较低，均为3.57%；公猪精液品质、抗仔猪腹泻、料重比和多肋性状的非优势基因型比例较高，分别为39.29%、50.00%、82.14%和92.86%；聚类和主成分分析显示，徒河黑猪与四川地方猪种间遗传距离远，丫杈猪、乌金猪、内江猪和藏猪（平原和高原）各自聚为一类，品种间群体分层结构明显，雅南猪、成华猪、青峪猪聚为一类；Fst指数计算结果表明，同属于湖川山地猪的丫杈猪和青峪猪间存在高度遗传分化。结果提示，四川省地方猪群体的采食量、酸肉、应激、抗仔猪腹泻和料重比性状的非优势基因型比例较低，公猪精液品质和多肋性状的非优势基因型比例较高；徒河黑猪群体的应激性状已无q等位基因，采食量和酸肉性状的非优势基因型比例较低，公猪精液品质、抗仔猪腹泻、料重比和多肋性状的非优势基因型比例较高；群体遗传结构研究结果表明，丫杈猪与青峪猪都归类于湖川山地猪有待商榷。

SNP Genotyping of Important Economic Traits,and Population Genetic Structure in Different Local Pig Breeds

This experiment was conducted to study genotype distribution of SNPs associated with important economic traits, and inter-population genetic structure in 7 local pig breeds in Sichuan province and Tuhe black pig in Shandong province. The single nucleotide polymorphism (SNP) of 8 pig breeds was measured using the porcine 50K SNP bead chip, which include 23 Chenghua pigs, 26 Ya'nan pigs, 60 Qingyu pigs, 57 Neijiang black pigs, 151 Yacha pigs, 57 Wujin pigs, 51 plain Tibetan pigs, 109 plateau Tibetan pigs and 28 Tuhe black pigs (562 healthy pigs in all). Next, data quality controls and genotypes related to 7 economic traits were performed by employing Plink and R software. Cluster analysis and principal component analysis (PCA) were conducted by Mega X and Plink softwares, respectively. The population genetic differentiation index (Fst) was calculated by VCFtools software and to analyze the genetic relationship between populations. The results showed that the proportion of non-advantage genotypes of feed intake, sour meat and stress traits were all lower than 2.20% in local pig breeds in Sichuan province, while the proportion of non-advantage genotypes of resistance to piglet diarrhea, FCR, boar semen quality and multi-rib were 8.99%, 11.80%, 73.97% and 95.32%, respectively. In Tuhe black pigs, q allele of stress trait wasn't existed, the proportion of non-advantage genotypes of feed intake and sour meat traits both were 3.57%, while the proportion of non-advantage genotypes of boar semen quality, resistance to piglet diarrhea, FCR and multi-rib were 39.29%, 50.00%, 82.14% and 92.86%, respectively. Clustering and PCA showed that a relatively distant genetic distance appeared between Tuhe black pigs and Sichuan local pig breeds, and Yacha, Wujin, Neijiang and Tibetan pigs (plain and plateau) were clustered into one group respectively, indicating that the population hierarchy among breeds was obvious. In addition, Ya'nan, Chenghua and Qingyu pigs were clustered together. The Fst index showed that there was a high genetic differentiation between Yacha and Qingyu pigs, both of which belong to Huchuan mountain pigs. The proportion of non-advantage genotypes of feed intake, sour meat, stress, resistance to piglet diarrhea and FCR traits were low, while that of boar semen quality and multi-rib traits were high. In Tuhe black pigs, the q allele of stress trait wasn't existed, and the proportion of non-advantage genotypes of feed intake and sour meat traits were low, while that of boar semen quality, resistance to piglet diarrhea, FCR and multi-rib traits were high. Population genetic structure results showed that the Yacha pigs and Qingyu pigs were classified as Huchuan mountain pigs is still debatable.