Huang Min, Yang Bin, Chen Hao, Zhang Hui, Wu Zhongping, Ai Huashui, Ren Jun, Huang Lusheng
State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang China.
Present address: College of Animal Science South China Agricultural University Guangzhou China.
Evol Appl. 2019 Nov 22;13(2):458-475. doi: 10.1111/eva.12887. eCollection 2020 Feb.
Genome-wide SNP profiling has yielded insights into the genetic structure of China indigenous pigs, but has focused on a limited number of populations. Here, we present an analysis of population structure and signals of positive selection in 42 Chinese pig populations that represent the most extensive pig phenotypic diversity in China, using genotype data of 1.1 million SNPs on customized Beadchips. This unravels the fine-scale genetic diversity, phylogenic relationships, and population structure of these populations, which shows remarkably concordance between genetic clusters and geography with few exceptions. We also reveal the genetic contribution to North Chinese pigs from European modern pigs. Furthermore, we identify possible targets of selection in the Tibetan pig, including the well-characterized hypoxia gene () and several previously unrecognized candidates. Intriguingly, the selected haplotype in the gene is associated with higher hemoglobin contents in Tibetan pigs, which is different from the protective role of in the high-altitude adaptation in Tibetan dogs and their owners. Additionally, we present evidence for the causality between variants and the two-end-black (TEB) coat color phenotype in all Chinese pig populations except the Jinhua pig. We hypothesize that distinct targets have been independently selected for the formation of the TEB phenotype in Chinese pigs of different geographic origins. This highlights the importance of characterizing population-specific genetic determinants for heritable phenotype in diverse pig populations.
全基因组单核苷酸多态性（SNP）分析已为中国地方猪种的遗传结构提供了见解，但研究重点集中在少数群体上。在此，我们利用定制基因芯片上110万个SNP的基因型数据，对代表中国最广泛猪种表型多样性的42个中国猪种群体的种群结构和正选择信号进行了分析。这揭示了这些群体的精细遗传多样性、系统发育关系和种群结构，结果表明，除少数例外，遗传聚类与地理分布之间具有显著的一致性。我们还揭示了欧洲现代猪对中国北方猪种的遗传贡献。此外，我们确定了藏猪可能的选择靶点，包括特征明确的低氧基因（）和几个以前未被识别的候选基因。有趣的是，该基因中选择的单倍型与藏猪较高的血红蛋白含量相关，这与该基因在藏獒及其主人高海拔适应中的保护作用不同。此外，我们提供了除金华猪外所有中国猪种群体中变异与两端黑色（TEB）毛色表型之间因果关系的证据。我们假设，在不同地理起源的中国猪中，不同的靶点被独立选择用于形成TEB表型。这突出了在不同猪种群体中表征可遗传表型的群体特异性遗传决定因素的重要性。
