College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Chongqing Academy of Animal Sciences, Chongqing 402460, China.
Int J Mol Sci. 2023 Dec 5;24(24):17154. doi: 10.3390/ijms242417154.
Indigenous pig populations, including Bamei pigs (BM), Hezuo pigs (HZ), Huixian Qingni Black pigs (HX), and Minxian Black pigs (MX) in Gansu Province, live in a particular climate and a relatively closed geographical environment. These local pig breeds are characterized by excellent characteristics (e.g., cold tolerance, robust disease resistance, and superior meat quality). In the past few years, pig populations in Gansu Province have decreased significantly because of their poor lean meat percentage, high fat content, and slow growth rate. Maintaining the diversity of these four breeds can act as a source of new alleles to be incorporated into commercial breeds which are more susceptible to disease and less adaptable to changing conditions because of inbreeding. Genomic data analysis is adequate for determining the genetic diversity and livestock breeding population structure, even in local pig populations. However, the genetic diversity and population structure of the four native pig populations in Gansu Province are still unknown. Thus, we used "Zhongxin-I" porcine chip for the SNP detection of 102 individuals living on four pig conservation farms. A total of 57,466 SNPs were identified among the four pig breeds. The linkage disequilibrium (LD) plot showed that MX had the highest level of LD, followed by BM, HZ, and HX. The observed heterozygosity (Ho) in all four populations was higher than the expected heterozygosity (He). A principal component analysis (PCA) demonstrated that the four local pig populations were isolated. The identity displayed by the state matrix and G matrix heat map results indicated that small numbers of individuals among the four pig breeds had a high genetic distance and weak genetic relationships. The results of the population genetic structure of BM, HZ, HX, and MX pigs showed a slight genetic diversity loss. Our findings enabled us to better understand the genome characteristics of these four indigenous pig populations, which will provide novel insights for the future germplasm conservation and utilization of these indigenous pig populations.
甘肃省的本土猪种群包括八眉猪（BM）、合作猪（HZ）、会宁青宁黑猪（HX）和岷县黑猪（MX），它们生活在特殊的气候和相对封闭的地理环境中。这些地方猪种具有优良的特性（如耐寒、强壮的抗病能力和卓越的肉质）。近年来，由于瘦肉率低、脂肪含量高、生长速度慢，甘肃省的猪种群数量显著减少。维持这四个品种的多样性可以作为新等位基因的来源，这些新等位基因可以被整合到商业品种中，商业品种由于近亲繁殖更容易患病，对环境变化的适应能力也较低。基因组数据分析足以确定遗传多样性和家畜养殖群体结构，即使是在当地猪种群中也是如此。然而，甘肃省四个本土猪种群的遗传多样性和群体结构仍然未知。因此，我们使用“中兴一号”猪芯片对四个保种场的 102 个个体进行 SNP 检测。在四个猪品种中共鉴定出 57466 个 SNP。连锁不平衡（LD）图谱显示，MX 的 LD 水平最高，其次是 BM、HZ 和 HX。四个种群的观测杂合度（Ho）均高于预期杂合度（He）。主成分分析（PCA）表明，四个本地猪种群是孤立的。状态矩阵和 G 矩阵热图结果显示的个体身份表明，四个猪品种中的少数个体具有较高的遗传距离和较弱的遗传关系。BM、HZ、HX 和 MX 猪的种群遗传结构结果表明，遗传多样性略有丧失。我们的研究结果使我们能够更好地了解这四个本土猪种群的基因组特征，这将为未来这些本土猪种群的种质保护和利用提供新的见解。
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