Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array.

Shuqi Diao,Zanmou Chen,Zhe Zhang,Hao Zhang,Shaopan Ye,Jiaqi Li,Zhiting Xu,Shuwen Huang,Xiaolong Yuan

doi:10.3390/ani9060361

Abstract

Simple SummaryThe pig is one of the most important livestock animals, providing the majority of protein for humans. The population genetics analysis of pigs not only helps humans understand the domestication of the pig but also helps breeders in the genetic improvement of pigs. In this study, the population genetics of 11 pig breeds of South China were analyzed with the help of single nucleotide polymorphism (SNP) chips. The results showed that the genetic diversity of South China indigenous pigs is declining rapidly, and gene introgression from commercial pigs to indigenous pigs was detected. Selection signature analysis showed differences among South China indigenous pig breeds, commercial pig breeds, and wild pig breeds were present for meat quality and growth. Our study deepened understanding of the conservation status and selection mechanisms of Chinese indigenous pigs.To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

Highlights

The pig is one of the most important livestock animals, providing the majority of protein for humans [1]
12,808 single nucleotide polymorphism (SNP) with minor allele frequency (MAF) ≥ 0.200 were found in both Western pigs and Chinese pigs; these SNPs were used in genetic diversity analysis
MAF ≥ 0.200 were found in Western pigs, but only 18,306 SNPs were found in Chinese pigs

Summary

Introduction

The pig is one of the most important livestock animals, providing the majority of protein for humans [1]. In China, the slaughtering capacity of pigs reaches 0.650 billion every year and pork. Animals 2019, 9, 361 accounts for about 52% of the meat consumption of Chinese citizens. Chinese indigenous pigs have many desirable characteristics such as high reproduction, high intramuscular fat content, disease-resistance ability, and strong resistance to extreme climates [3]. Chinese indigenous pig breeds have been used for meat production for thousands of years in China. With the introduction and popularization of Western commercial pig breeds, the populations of indigenous pigs have rapidly decreased. Many Chinese indigenous pig breeds are only preserved in a few reservation farms with small populations, and some pig breeds are even reported to be extinct [4]

Methods

Results

Discussion

Conclusion