Liu Yuqiang, Li Guangzhen, Ayalew Wondossen, Zhong Zhanming, Liu Xiaohong, Sun Jiajie, Li Jiaqi
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.
Animals (Basel). 2025 Mar 29;15(7):988. doi: 10.3390/ani15070988.
Runs of homozygosity (ROH) are contiguous homozygous genomic segments that provide valuable insights into population history, selection pressures, and inbreeding levels. However, the global distribution of ROH and their implications for pig domestication and breeding are not yet fully understood. In this study, we analyzed whole-genome resequencing data from 1203 pigs across 49 breeds to characterize ROH patterns worldwide. European commercial pigs exhibited longer and more numerous ROH segments than Asian indigenous breeds, indicative of stronger artificial selection and higher inbreeding. Crossbreeding led to a reduction in ROH burden, with greater reductions observed when parental genetic divergence was larger. Notably, Asian and European pigs displayed distinct ROH islands, reflecting divergent selection pressures. Functional analysis revealed that these ROH islands were associated with growth, immunity, and reproduction. These findings enhance our understanding of the genetic diversity and selection history of global pig populations, providing valuable insights for future breeding strategies.
纯合性片段（ROH）是连续的纯合基因组片段，能为种群历史、选择压力和近亲繁殖水平提供有价值的见解。然而，ROH的全球分布及其对猪驯化和育种的影响尚未完全明晰。在本研究中，我们分析了来自49个品种的1203头猪的全基因组重测序数据，以描绘全球范围内的ROH模式。欧洲商业猪比亚洲本土品种表现出更长且更多的ROH片段，这表明人工选择更强且近亲繁殖程度更高。杂交导致ROH负担减轻，当亲本遗传差异更大时，观察到的减轻幅度更大。值得注意的是，亚洲和欧洲猪呈现出不同的ROH岛，反映了不同的选择压力。功能分析表明，这些ROH岛与生长、免疫和繁殖相关。这些发现增进了我们对全球猪种群遗传多样性和选择历史的理解，为未来的育种策略提供了有价值的见解。
