Multiple Domestication Centers Revealed by the Geographical Distribution of Chinese Native Pigs.

Yuan Cai,Wangshan Zheng,Yongbo Guo,Qianyun Ge,Shengguo Zhao,Caixia Gao,Jinqiang Quan,Ting Jiao

doi:10.3390/ani9100709

Abstract

Simple SummaryPhylogenetic analysis of Chinese native pigs was performed by screening for haplotypes inferred from a phylogenetic tree of pig mitochondrial DNA (mtDNA) sequences based on sequence-specific mutations. Our results suggest there are at least four domestication or expansion centers of Chinese native pigs, of which at least two domestication or expansion centers of Tibetan pigs are located in the Qinghai-Tibet Plateau and the intersection of the Hengduan Mountains (YSGH) of Yunnan, Sichuan, and Gansu provinces. The other two domestication or expansion centers are the Mekong River Basin in Yunnan Province and the middle and downstream regions of the Yangtze River.Previous studies have shown that Southeast Asian pigs were independently domesticated from local wild boars. However, the domestication of Chinese native pigs remains a subject of debate. In the present study, phylogenetic analysis of Chinese native pigs was performed by screening for haplotypes inferred from a phylogenetic tree of pig mitochondrial DNA (mtDNA) sequences based on sequence-specific mutations. A total of 2466 domestic pigs formed 124 haplotypes and were assigned to four clades. Clade A comprised pigs distributed mainly in the Qinghai-Tibet Plateau and its surrounding areas; these pigs clustered into three groups. The pigs of clade B were mainly from the Mekong River Basin in Yunnan Province and had been exposed to genetic infiltration from European populations. Clade C comprised pigs mainly from the middle and lower reaches of the Yangtze River. The pigs of clade D were distributed mainly at the intersection of Yunnan, Sichuan, and Gansu provinces east of the Hengduan Mountains (YSGH). Compared with wild boar, at least three domestication centers and one expansion center of pigs in China were detected. Among the four centers detected, two were for Tibetan pigs and were in the Qinghai-Tibet Plateau and at the YSGH intersection, and the other two were in the Mekong River Basin in Yunnan Province and the middle and downstream regions of the Yangtze River.

Highlights

Pigs (Sus scrofa) are one of the oldest domesticated and most important socioeconomic livestock species in the world [1]
With the construction of a maternal phylogenetic map with mitochondrial DNA, a large amount of research has focused on analyzing the domestication process of global domestic pigs by mtDNA sequence data
We analyzed the genetic diversity of 2466 domestic pigs of 87 breeds from six geographic regions in China

Summary

Introduction

Pigs (Sus scrofa) are one of the oldest domesticated and most important socioeconomic livestock species in the world [1]. Human activities have changed the genetic structure of domestic pigs; as a Animals 2019, 9, 709; doi:10.3390/ani9100709 www.mdpi.com/journal/animals. The history of pig breeding in China can be traced to more than 9000 years ago [6]. By the Neolithic Age, a large number of wild boars had been domesticated, which indicates that pig breeding had become an important part of the social economy by that time [7,8,9]. Genetic and archeological evidence indicates that domestic and Asian pigs were independently domesticated from local wild boars and that there are significant differences in mtDNA between European and Asian domestic pigs [3,10,11,12]. Larson et al [4] confirmed that the globally distributed wild boar originated on the island of Southeast Asia (ISEA), and subsequently distributed in Eurasia and multiple domestication centers in Europe and

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