Qiu Yibin, Liu Langqing, Huang Min, Ruan Donglin, Ding Rongrong, Zhang Zebin, Zheng Enqin, Wang Shiyuan, Deng Shaoxiong, Meng Xianglun, Cheng Xinyan, Shi Jiaxin, Yang Yingshan, Zhou Fuchen, Huang Sixiu, Yang Huaqiang, Li Zicong, Cai Gengyuan, Wu Zhenfang, Yang Jie
State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
Adv Sci (Weinh). 2025 Jun;12(22):e2416573. doi: 10.1002/advs.202416573. Epub 2025 Apr 1.
Human mediated intra-continental exchange of genetic material among domesticated organisms has never been restricted to a single direction. The introduction of pig breeds between China and Europe aims to enhance economically important traits in local populations. However, the reciprocal introgression pattern, specifically the role of introgressed genes and structural variations (SVs), remains underexplored. A global collection of whole-genome resequencing data is utilized from 418 pigs to generate comprehensive dataset, including single-nucleotide polymorphisms (SNPs) as well as SVs. The analysis reveals incomplete linkage disequilibrium between SVs and adjacent SNPs, highlighting the limitations of conventional SNP-based analyses in capturing the genetic effects of SVs. By examining both population-level SNPs and SVs, bidirectional introgression between Chinese and European pig populations is characterized. It is identified 3558 bidirectional introgressed genomic segments and 30 SVs, with haplotypes at BMP2, which are associated with improved body size. The origin and allele frequency trajectory of the BMP2 segment are further validated using ancient genomes, suggesting that the body size-enhancing haplotype likely originated from ancient European populations and has since maintained a relatively high allele frequency. Overall, the results highlight the significant role of bidirectional introgression in shaping the genetic composition and phenotypic traits in modern pig breeds.
人类介导的家养生物间洲际遗传物质交换从未局限于单一方向。中国与欧洲之间猪品种的引入旨在增强当地种群中具有经济重要性的性状。然而，相互渗入模式，特别是渗入基因和结构变异（SVs）的作用，仍未得到充分探索。利用来自418头猪的全球全基因组重测序数据来生成综合数据集，包括单核苷酸多态性（SNPs）以及SVs。分析揭示了SVs与相邻SNPs之间不完全的连锁不平衡，凸显了传统基于SNP的分析在捕捉SVs遗传效应方面的局限性。通过研究群体水平的SNPs和SVs，对中国和欧洲猪种群之间的双向渗入进行了表征。确定了3558个双向渗入的基因组片段和30个SVs，其中BMP2的单倍型与体型改善相关。使用古代基因组进一步验证了BMP2片段的起源和等位基因频率轨迹，表明体型增强单倍型可能起源于古代欧洲种群，此后一直保持相对较高的等位基因频率。总体而言，结果突出了双向渗入在塑造现代猪品种遗传组成和表型性状中的重要作用。
