Impacts of Chinese-introgressed sequence on the landscape of European commercial breeds genome

Introgression, the transfer of alleles from one (sub)species into another (sub)species, is widely believed to be common in nature. Such introgression of alleles can affect the phenotype and fitness of the recipient species/population. During evolution, it has been shown to provide novel genetic materials, affect speciation and shape the development of specific traits. Human-mediated introgressions have had a significant impact on the breeding history of global domestic animals and plants. The pig is the primary source of meat production worldwide. The widely distributed commercial pig breeds in the world are bred from Europe and America, including Duroc, Large White, Landrace, Hampshire, Pietrain, and Berkshire. In Asia, particular in China, there is a large variety of indigenous pigs that are famous for various traits, such as Meishan pigs a breed renowned for its prolificacy. It is well known that in the 18th and 19th centuries, Chinese breeds were imported to Europe to improve the commercial traits of European breeds. Many Introgressed regions from Chinese breeds have been identified in the genomes of European domestic pigs. However, the biological functions and regulatory impacts of these introgressed Chinese sequences in modern European pig breeds remain largely unknown. In this project, we will uniformly analyze ~ 1163 whole genome sequences (WGS) and thousands of RNA-seq data in pigs from public databases. Based on this large-scale WGS data, we will generate a high-resolution map of the introgressed region between six European domestic breeds and Chinese breeds. We will use a combinational of omics data (e.g., epigenome, transcriptome, and chromatin conformation) to explore the functional and regulatory impacts of the introgression regions across various tissues and cell types. By combining these introgressed regions with GWAS results, we will quantify the contribution of introgressed regions to the heritability of complex traits of economic value. This project will further our insight into the process of domestication and breeding of commercial pigs and enable the identification of critical genes involved in economically important traits. This research will provide a valuable resource for the genetic improvement program in pigs and serve as a prototype for studying introgression in other livestock species.