National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China.
Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
Genome Biol Evol. 2020 Oct 1;12(10):1751-1764. doi: 10.1093/gbe/evaa142.
Introgression events and population admixture occurred among Sus species across the Eurasian mainland in the Middle Pleistocene, which reflects the local adaption of different populations and contributes to evolutionary novelty. Previous findings on these population introgressions were largely based on extensive genome-wide single-nucleotide polymorphism information, ignoring structural variants (SVs) as an important alternative resource of genetic variations. Here, we profiled the genome-wide SVs and explored the formation of pattern-related SVs, indicating that PRE1-SS is a recently active subfamily that was strongly associated with introgression events in multiple Asian and European pig populations. As reflected by the three different combination haplotypes from two specific patterns and known phylogenetic relationships in Eurasian boars, we identified the Asian Northern wild pigs as having experienced introgression from European wild boars around 0.5-0.2 Ma and having received latitude-related selection. During further exploration of the influence of pattern-related SVs on gene functions, we found substantial sequence changes in 199 intron regions of 54 genes and 3 exon regions of 3 genes (HDX, TRO, and SMIM1), implying that the pattern-related SVs were highly related to positive selection and adaption of pigs. Our findings revealed novel introgression events in Eurasian wild boars, providing a timeline of population admixture and divergence across the Eurasian mainland in the Middle Pleistocene.
中更新世期间，欧亚大陆的各类野猪之间发生了基因渗入事件和种群混合，这反映了不同种群的局部适应，并有助于进化的新颖性。先前关于这些种群基因渗入的发现主要基于广泛的全基因组单核苷酸多态性信息，而忽略了结构变异（SVs）作为遗传变异的重要替代资源。在这里，我们对全基因组 SVs 进行了分析，并探讨了模式相关 SVs 的形成，结果表明 PRE1-SS 是一个最近活跃的亚家族，与多个亚洲和欧洲猪种群的基因渗入事件密切相关。从两个特定模式的三种不同组合单倍型和欧亚野猪已知的系统发育关系来看，我们确定亚洲北方野猪经历了大约 0.5-0.2 百万年前欧洲野猪的基因渗入，并受到了纬度相关的选择。在进一步探索模式相关 SVs 对基因功能的影响时，我们在 54 个基因的 199 个内含子区域和 3 个基因（HDX、TRO 和 SMIM1）的 3 个外显子区域发现了大量的序列变化，这表明模式相关 SVs 与猪的正选择和适应密切相关。我们的研究结果揭示了欧亚野猪中新的基因渗入事件，为中更新世期间欧亚大陆野猪种群混合和分化提供了时间线。
