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

Abstract

Background Pigs 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. 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. 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. 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.

Pig genome functional annotation enhances biological interpretations of complex traits and comparative epigenomics

“…Consequently, tissuespecific gene regulation may have played an essential role in the adaptive selection processes that resulted in Asian and European pig domestication. This result was also in agreement with the observation that Asian domesticated pigs being more disease resistant 41 , whereas European domesticated pigs are more active and aggressive 42,43 .…”

“…Specifically, genetic variants in the spleen-specific promoters were enriched during Asian pig domestication, whereas variants within cortex-specific promoters were enriched during European pig domestication. This novel insight may reflect the observed distinct phenotypic difference between Asian (more disease resistance 41 ) and European domesticated pigs (more active and aggressive 42,43 ). Further investigation is warranted to deepen our understanding of genetic selection and domestication in the pig.…”

Genome Data Uncover Conservation Status, Historical Relatedness and Candidate Genes Under Selection in Chinese Indigenous Pigs in the Taihu Lake Region

“…China has a variety of indigenous pig breeds that represent extensive phenotypic diversity and account for approximately one-third of global breeds (Chen et al, 2020). At present, six wellrecognized pig breeds are distributed in the Taihu Lake (TL) region in East China (Figure 1A), including Meishan (MS), Erhualian (EHL), Jiaxing Black (JXB), Fengjing (FJ), Shawutou (SWT), and Mi (MI) pigs (China National Commission of Animal Genetic Resources, 2011).…”

Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing Black and Large White Pigs

“…Excessive SC fat deposition greatly decreases the growth performance and meat production efficiency, which results in profit reduction [7,8]. However, Chinese indigenous pig breeds often exhibit better fertility, disease resistance and IM fat content than foreign pig breeds [9][10][11]. Understanding the porcine adipocyte regulation network to decrease SC fat deposition is a key issue in genetic improvement of Chinese indigenous pig breeds.…”