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

Kejun Wang,Xuelei Han,Xinjian Li,Lige Zhang,Dongdong Duan,Ruimin Qiao,Xiuling Li

doi:10.3389/fgene.2021.705803

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.

Highlights

Livestock animals were domesticated from wild ancestors for human use, subsequently undergoing contiguous breeding and improvement through the generation of breeds with distinct phenotypes
We found that a cluster of three Henan indigenous pig (CDh) breeds showed a closer relatedness to European pigs (Figure 1A)
We found that the loci GPD2 and CSRNP3 were introgressed from Duroc pigs into three Henan indigenous pig breeds (Figure 3)

Summary

Introduction

Livestock animals were domesticated from wild ancestors for human use, subsequently undergoing contiguous breeding and improvement through the generation of breeds with distinct phenotypes. According to Genetic Structure of Indigenous Pigs historical records, the Chinese pig was imported into Europe in the mid-to-late 18th century (Chen et al, 2020) This introgression was likely to have played an important role in improving the reproductive traits of the Large White (LW) pig (Chen et al, 2020). The Nanyang Black pig (NY), the Huainan pig (HN), and the Queshan black pig (QS), have been named based on the classification scheme from the National Commission of Animal Genetics resource book (2011). These three pig breeds exhibited strong disease-resistance, high meat yield and early maturation (Qiao et al, 2019). The genomic differences and potential role of introgression in Henan indigenous pigs is still unclear

Methods

Results

Conclusion