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

Chenxi Liu,Yanzhen Yin,Moran Zhao,Pinghua Li,Yan Xu,Tianwei Zhou,Nengjing Jiang,Jun Ren,Xiaopeng Wang,Wuduo Zhou,Xiang Ma,Ruihua Huang

doi:10.3389/fgene.2020.00591

Abstract

Chinese indigenous pig breeds in the Taihu Lake (TL) region of Eastern China are well documented by their exceptional prolificacy. There are seven breeds in this region including Meishan (MS), Erhualian (EHL), Jiaxing Black (JXB), Fengjing (FJ), Shawutou (SWT), Mi (MI), and Hongdenglong (HDL). At present, these breeds are facing a great threat of population decline, inbreeding depression and lineage admixture since Western commercial pigs have dominated in Chinese pig industry. To provide better conservation strategies and identify candidate genes under selection for these breeds, we explored genome-wide single nucleotide polymorphism (SNP) markers to uncover genetic variability and relatedness, population structure, historical admixture and genomic signature of selection of 440 pigs representing the most comprehensive lineages of these breeds in TL region in a context of 1228 pigs from 45 Eurasian breeds. We showed that these breeds were more closely related to each other as compared to other Eurasian breeds, defining one of the main ancestral lineages of Chinese indigenous pigs. These breeds can be divided into two subgroups, one including JXB and FJ, and the other comprising of EHL, MI, HDL, MS, and SWT. In addition, HDL was highly inbred whereas EHL and MS had more abundant genetic diversity owing to their multiple conservation populations. Moreover, we identified a list of candidate genes under selection for body size and prolificacy. Our results would benefit the conservation of these valuable breeds and improve our understanding of the genetic mechanisms of body size and fecundity in pigs.

Highlights

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)
All Hongdenglong pig (HDL) pigs clustered together and displayed a close relationship with the other six breeds in Taihu Lake (TL) region but not with Huai pigs, which were assumed to share a common ancestor with HDL pigs (China National Commission of Animal Genetic Resources, 2011)
When we focused on the seven breeds in TL region only, the neighbor-joining (Figure 2A), principal component analysis (PCA) (Figures 2B,C) and ADMIXTURE (Figure 2D) analyses indicated that HDL, MI, and EHL were more closely related while FJ and Jiaxing Black (JXB) appeared as another subgroup

Summary

Introduction

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). Hongdenglong pig (HDL) is an indigenous breed in TL region (Figure 1A) It remains a subject of debate whether HDL is a sub-population of Chinese Huai pig indigenous in Anhui and Henan provinces or is an ancestral genetic lineage having close genetic relationship with MI and EHL (Chen et al, 2016). Since some conservation farms have collected new boars without pedigree records from the origin or distribution areas of these indigenous pig genetic resources to avoid inbreeding depression and these new boars might create new consanguinities For this reason, this study aimed to unravel genetic variability and relatedness, population structure, historical admixture and genomic selection signature of 440 pigs representing the most comprehensive consanguinities of the seven indigenous breeds in TL region in a context of 45 Eurasian breeds. This work will benefit the efficient conservation and utilization of these breeds in TL region, and our findings will advance our understanding of the genetic mechanisms underlying the germplasm characteristics of these breeds, such as fecundity and body size

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Conclusion