Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

Abstract

Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We re-sequenced 80 Eurasian pigs from 9 different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene-flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y-chromosomes.

Genomic analyses of Asiatic Mouflon in Iran provide insights into the domestication and evolution of sheep

“…Genetic variants of uniparental inheritance offer insights into the domestication and evolutionary history of farm animals, such as pigs 63 , sheep 5,14 and goats 64,65 . In domestic sheep, here we identified five maternal haplogroups (A, B, C, D, and E) in two monophyletic groups (A+B+D and C+E), and two paternal clades (HY1 and HY2) (Figure 2B, C).…”

Evolutionary insights into porcine genomic structural variations based on a novel‐constructed dataset from 24 worldwide diverse populations

“…Next, we clustered the samples based on the 112,890 SVs and compared the neighbor‐joining tree constructed from these SVs with that constructed using genome‐wide SNPs (58,733,085) (Ai et al, 2021). By comparing SV‐ and SNP‐based neighbor‐joining (NJ) tree, we further excluded three Tibetan pigs that were misclassified by SV data.…”

Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations

“…Indeed, both the selection and genetic admixture from exotic breeds have significant roles in the breeding process of domestic pigs, contributing to their genetic architecture and improvements in important economic traits. Several lines of evidence support this: During the Industrial Revolution, the presence of shared haplotypes between Meishan and Duroc pig breeds further supported the notion of Asian-derived introgression and the specific contribution of Meishan pigs to increasing sow fertility in European pigs [ 7 , 13 , 14 , 15 ]; the detection of more than a quarter of the genetic components of European commercial pigs in current Laiwu pig populations indicates large-scale interspecific crosses and gene introgression; these processes have been instrumental in incorporating genetic material from European breeds and improving important economic traits in Laiwu pigs [ 16 ]. These findings collectively emphasize the role of selection and genetic admixture in pig breeding, showcasing how intentional hybridization and introgression can lead to the enhancement of desired traits and improvements in economic performance in pig populations [ 7 , 9 , 13 , 14 , 15 , 16 ].…”

“…It serves as the raw material upon which the genetic variation within a species is built [ 1 , 2 , 3 , 4 ]. Both naturally occurring and artificially mediated genetic introgressions among pig breeds/populations have the potential to significantly impact and reshape a wide range of phenotypes [ 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. The Large White pig breed is renowned for its prolificacy, meat quality, and adaptability to various environments.…”