Gao Yahui, Feng Xueyan, Diao Shuqi, Liu Yuqiang, Zhong Zhanming, Cai Xiaotian, Li Guangzhen, Teng Jinyan, Liu Xiaohong, Li Jiaqi, Zhang Zhe
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
BMC Genomics. 2024 Dec 18;25(1):1191. doi: 10.1186/s12864-024-11119-y.
Indigenous pig breeds in China have accumulated significant genetic diversity due to regional selection pressures. Investigating the selection signatures of these populations helps to understand their adaptive evolution and contributes to genetic improvement programs.
We collected whole-genome sequencing data from 133 individuals, including South China and North China indigenous pigs and Asian wild boars. After data filtering, we retained 31,521,978 high-quality SNPs. Population structure analysis using PCA revealed distinct genetic clustering among these populations. Selection signature detection identified 5,227 loci under selection in South China indigenous pigs and 5,800 in North China indigenous pigs compared to Asian wild boars. Candidate genes were enriched in immune response pathways, reproductive traits, and pigmentation pathways. South China indigenous pigs exhibited selection signals for fat deposition and immune responses, while North China indigenous pigs showed stronger signals related to growth, blood physiology, and reproductive performance. Additionally, key genes such as MC1R and KIT were associated with coat color variation, and IGF1R and IGF2R were linked to growth regulation.
Our results demonstrate that indigenous pigs in China have undergone selection for distinct traits aligned with their regional environments and farming systems. South China indigenous pigs have been selected for traits related to fat deposition and immunity, while North China indigenous pigs have been selected for growth and reproductive traits. The findings offer crucial insights into the genetic architecture of indigenous pig breeds, providing a valuable foundation for future genetic breeding programs.
由于区域选择压力，中国的本土猪品种积累了显著的遗传多样性。研究这些群体的选择印记有助于了解它们的适应性进化，并为遗传改良计划做出贡献。
我们收集了133个个体的全基因组测序数据，包括中国南方和北方的本土猪以及亚洲野猪。经过数据过滤，我们保留了31,521,978个高质量单核苷酸多态性（SNP）。使用主成分分析（PCA）进行的群体结构分析揭示了这些群体之间明显的遗传聚类。与亚洲野猪相比，选择印记检测在中国南方本土猪中鉴定出5227个受选择的位点，在中国北方本土猪中鉴定出5800个。候选基因在免疫反应途径、繁殖性状和色素沉着途径中富集。中国南方本土猪在脂肪沉积和免疫反应方面表现出选择信号，而中国北方本土猪则表现出与生长、血液生理学和繁殖性能相关的更强信号。此外，关键基因如MC1R和KIT与毛色变异有关，IGF1R和IGF2R与生长调节有关。
我们的结果表明，中国本土猪针对与其区域环境和养殖系统相适应的不同性状进行了选择。中国南方本土猪在与脂肪沉积和免疫相关的性状上受到选择，而中国北方本土猪在生长和繁殖性状上受到选择。这些发现为本土猪品种的遗传结构提供了关键见解，为未来的遗传育种计划提供了宝贵的基础。
