DataSheet1_Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds.docx

Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68–98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.

探究不同畜禽品种间的基因流（gene flow），将有助于发掘与生产性状（production traits）相关的基因，并为人类历史育种研究提供新视角。中国猪（Chinese pigs）在西方商品猪的育种进程中发挥了不可或缺的作用。然而，不同中国地域猪群对西方商品猪的遗传贡献，在贡献时机与贡献规模上的差异仍未明确。本研究整合了来自多项研究的592头猪的全基因组测序（whole-genome sequencing）数据，阐明了中国猪向西方商品猪的基因流模式。我们解析了4个不同中国地方猪群向5个西方商品猪群的基因渐渗（introgression）模式。不同贡献型中国猪群向西方商品猪品种提供的推定渐渗片段，其数量与长度存在显著差异。地理来源不同的中国猪群对单一西方商品猪品种的遗传贡献差异，大于某一特定中国猪群对不同西方商品猪品种的贡献差异，这表明基因渐渗后欧洲猪群内部发生了遗传混合。同一品种下的不同西方商业品系中，来自特定中国猪群的基因渐渗模式高度保守，这表明中国猪向西方商品猪品种的基因渐渗主要发生在品种形成的早期阶段。最后，通过对渐渗信号、等位基因频率（allele frequencies）及选择印迹（selection footprints）的分析，我们在杜洛克猪（Duroc pigs）中鉴定到一段受选择的、源自中国猪的~2.65 Mb单倍型（haplotype），其位于14号染色体（CHR14）：95.68–98.33 Mb区域。功能与表型研究表明，该PRKG1单倍型与杜洛克猪的背膘厚及眼肌深度相关。综上，本研究表明家猪的基因渐渗历史极为复杂，西方商品猪携带清晰的混合血统痕迹，其血统大概率源自多个中国猪品种。