Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

Abstract

Introgression of genetic features from European pigs into Chinese pigs was reported possibly contributing to improvements in productivity traits, such as feed conversion efficiency and body size. However, the genomic differences from European pigs and the potential role of introgression in Henan indigenous pigs remains unclear. In this study, we found significant introgression from European pigs into the genome of Chinese indigenous pigs, especially in Henan indigenous pigs. The introgression in Henan indigenous pigs, particularly in the Nanyang black pig, was mainly derived from Duroc pigs. Most importantly, we found that the NR6A1, GPD2, and CSRNP3 genes were introgressed and reshaped by artificial selection, and these may have contributed to increases in pig body size and feed conversion efficiency. Our results suggest that human-mediated introgression and selection have reshaped the genome of Henan pigs and improved several of their desired traits. These findings contribute to our understanding of the history of Henan indigenous pigs and provide insights into the genetic mechanisms affecting economically important traits in pig populations.

Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes

“…This has led to an update in the genetic resources of Chinese domestic pigs. Previous studies have found genetic components from EP in Chinese breeds, [ 11 , 14 – 16 , 40 , 41 ], but EP introgression into LJP (a specific Chinese pig populations) has not been studied. Our study confirms the presence of EP introgression into multiple Chinese pig populations, including NCDP, SWCDP, TIBP-E, and LJP.…”

“…Previous research has documented three distinct waves of introgression from Europe to Asia over the past 200 years [ 13 ]. In addition, EP introgression may have induced phenotypic changes in indigenous Chinese pigs, such as introgression of the European NR6A1 haplotype, which can increase the number of vertebrae, body size, and feed-conversion efficiency [ 14 , 15 ] and of the KIT alleles from the Large White (LW) breed into the Pudong white pig, which has resulted in expression of the white coat colour phenotype [ 16 ]. Furthermore, transmission of EP-introgressed segments among Chinese pig populations may also have occurred in China in recent decades [ 12 ].…”

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

“…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.…”

Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds

“…In our previous study, using genomic SNP array data of core population of native Henan pig breeds, we found that native Henan pig breeds have a common lineage with some representative northern and eastern Chinese pig breeds (Bamei, Min, Laiwu, and Erhualian). We also detected the introgression of foreign genes on native Henan pig breeds (under review; Qiao et al, 2019; Wang et al, 2021) using DNA deep sequencing data and reduced‐representation genome sequencing data of random selected individuals of native Henan pig breeds.…”