Introgression of Eastern Chinese and Southern Chinese haplotypes contributes to the improvement of fertility and immunity in European modern pigs.

Bin Yang,Hao Chen,Jun Ren,Lusheng Huang,Min Huang,Yong Hou,Zheng Deng,Zhongping Wu

doi:10.1093/gigascience/giaa014

Abstract

BackgroundPigs were domesticated independently from European and Asian wild boars nearly 10,000 years ago. Chinese indigenous pigs have been historically introduced to improve Europe local pigs. However, the geographic origin and biological functions of introgressed Chinese genes in modern European pig breeds remain largely unknown.ResultsHere we explored whole-genome sequencing data from 266 Eurasian wild boars and domestic pigs to produce a fine-scale map of introgression between French Large White (FLW) and Chinese pigs. We show that FLW pigs had historical admixture with both Southern Chinese (SCN) and Eastern Chinese (ECN) pigs ∼200–300 years ago. Moreover, a set of SCN haplotypes was shown to be beneficial for improving disease resistance and ECN haplotypes are favorable for improved reproductive performance in FLW pigs. In addition, we confirm human-mediated introgression events at the AHR locus, at which the haplotype of most likely ECN origin contributes to increased fertility of FLW pigs.ConclusionsThis study advances our understanding of the breeding history of global domestic pigs and highlights the importance of artificial introgression in the formation of phenotypic characteristics in domestic animals.

Highlights

Integrated genomic and archaeological evidence has illuminated the fact that the wild boar (Sus scrofa) originated in the islands of southeast Asia ∼5 million years ago and dispersed throughout Eurasia
We demonstrated that 14 individuals belonged to the American Large White (ALW) lineage, and the other 14 individuals belonged to the Dutch Large White (NLW) line (Supplementary Fig. S2)
Given the geographic distance between Tibet and Europe and the lack of any historical records describing the importation of Tibetan pigs into Europe, we argue that Chinese-derived AHR haplotypes in French Large White (FLW) pigs were most likely introgressed from Eastern Chinese (ECN) pigs such as EHL pigs through human-mediated transportation ∼200–300 years ago

Summary

Introduction

Integrated genomic and archaeological evidence has illuminated the fact that the wild boar (Sus scrofa) originated in the islands of southeast Asia ∼5 million years ago and dispersed throughout Eurasia. 1 million years ago, geographic isolation caused by glacial events hampered the continuous gene flow among Eurasian wild boars, causing European and Asian wild boars to differentiate from each other [1,2,3,4]. 10,000 years ago, European and Asian wild boars were domesticated independently in the Near East and China, respectively [3, 5, 6]. Pigs were domesticated independently from European and Asian wild boars nearly 10,000 years ago. The geographic origin and biological functions of introgressed Chinese genes in modern European pig breeds remain largely unknown. Results: Here we explored whole-genome sequencing data from 266 Eurasian wild boars and domestic pigs to produce a fine-scale map of introgression between French Large White (FLW) and Chinese pigs. Conclusions: This study advances our understanding of the breeding history of global domestic pigs and highlights the importance of artificial introgression in the formation of phenotypic characteristics in domestic animals

Methods

Results

Conclusion