Genetic Diversity, Linkage Disequilibrium and Selection Signatures in Chinese and Western Pigs Revealed by Genome-Wide SNP Markers

To investigate population structure, linkage disequilibrium (LD) pattern and selection signature at the genome level in Chinese and Western pigs, we genotyped 304 unrelated animals from 18 diverse populations using porcine 60 K SNP chips. We confirmed the divergent evolution between Chinese and Western pigs and showed distinct topological structures of the tested populations. We acquired the evidence for the introgression of Western pigs into two Chinese pig breeds. Analysis of runs of homozygosity revealed that historical inbreeding reduced genetic variability in several Chinese breeds. We found that intrapopulation LD extents are roughly comparable between Chinese and Western pigs. However, interpopulation LD is much longer in Western pigs compared with Chinese pigs with average r20.3 values of 125 kb for Western pigs and only 10.5 kb for Chinese pigs. The finding indicates that higher-density markers are required to capture LD with causal variants in genome-wide association studies and genomic selection on Chinese pigs. Further, we looked across the genome to identify candidate loci under selection using FST outlier tests on two contrast samples: Tibetan pigs versus lowland pigs and belted pigs against non-belted pigs. Interestingly, we highlighted several genes including ADAMTS12, SIM1 and NOS1 that show signatures of natural selection in Tibetan pigs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports indicates that the underlying genetic basis for high-altitude adaptation in Tibetan pigs, Tibetan peoples and yaks is likely distinct from one another. Moreover, we identified the strongest signal of directional selection at the EDNRB loci in Chinese belted pigs, supporting EDNRB as a promising candidate gene for the white belt coat color in Chinese pigs. Altogether, our findings advance the understanding of the genome biology of Chinese and Western pigs.

为探究中外家猪的群体结构、连锁不平衡（linkage disequilibrium, LD）模式及基因组水平的选择印记，本研究利用猪60K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片，对来自18个不同群体的304头无亲缘关系个体进行基因分型。本研究证实了中外家猪的演化分化，并揭示了受试群体间显著的拓扑结构差异，同时获得了西方家猪向两个中国地方猪品种渗入的遗传学证据。通过对纯合子片段（Runs of Homozygosity, ROH）的分析，本研究发现历史近交事件降低了多个中国地方猪品种的遗传多样性。本研究发现，中外家猪的群体内LD延伸范围大致相当；但群体间LD的延伸长度差异显著：西方家猪在r²=0.3阈值下的平均LD延伸长度为125 kb，而中国家猪仅为10.5 kb。该结果表明，在中国家猪的全基因组关联分析及基因组选择研究中，需使用更高密度的分子标记才能精准捕获与因果变异相关的LD信息。进一步，本研究针对两组对比样本（藏猪与低地猪、带纹猪与非带纹猪）采用固定指数（Fixation Index, FST）离群值检测法开展全基因组扫描，以鉴定受选择的候选位点。值得注意的是，本研究筛选出ADAMTS12、SIM1及NOS1等多个基因，这些基因在藏猪中呈现自然选择印记，推测其对藏猪的高海拔遗传适应具有重要作用。将本研究结果与既往报道对比后发现，藏猪、藏族人群与牦牛的高海拔适应遗传基础可能各不相同。此外，本研究还在中国带纹猪中鉴定到位于EDNRB位点的最强定向选择信号，证实EDNRB是调控中国家猪白色带纹毛色的潜在候选基因。综上，本研究结果深化了我们对中外家猪基因组生物学的认知。