Abstract
Genome‐wide SNP profiling has yielded insights into the genetic structure of China indigenous pigs, but has focused on a limited number of populations. Here, we present an analysis of population structure and signals of positive selection in 42 Chinese pig populations that represent the most extensive pig phenotypic diversity in China, using genotype data of 1.1 million SNPs on customized Beadchips. This unravels the fine‐scale genetic diversity, phylogenic relationships, and population structure of these populations, which shows remarkably concordance between genetic clusters and geography with few exceptions. We also reveal the genetic contribution to North Chinese pigs from European modern pigs. Furthermore, we identify possible targets of selection in the Tibetan pig, including the well‐characterized hypoxia gene (EPAS1) and several previously unrecognized candidates. Intriguingly, the selected haplotype in the EPAS1 gene is associated with higher hemoglobin contents in Tibetan pigs, which is different from the protective role of EPAS1 in the high‐altitude adaptation in Tibetan dogs and their owners. Additionally, we present evidence for the causality between EDNRB variants and the two‐end‐black (TEB) coat color phenotype in all Chinese pig populations except the Jinhua pig. We hypothesize that distinct targets have been independently selected for the formation of the TEB phenotype in Chinese pigs of different geographic origins. This highlights the importance of characterizing population‐specific genetic determinants for heritable phenotype in diverse pig populations.
Highlights
The domestication of farm animals is a groundbreaking event that has deeply influenced human history
Human‐me‐ diated artificial selection and natural selection have resulted in di‐ verse pig breeds in the world
By using a customized DNA chip containing 1.1 million SNPs, we provide the most comprehensive genomic analysis of Chinese local pigs from 42 diverse breeds, covering the majority (n = 36) of the 42 breeds listed in the Chinese national conservation program for livestock genetic resources
Summary
The domestication of farm animals is a groundbreaking event that has deeply influenced human history. | 459 renowned for desirable traits related to reproduction, disease resis‐ tance, docility, and meat quality, providing valuable germplasm that supports the sustainable development of the pig industry in China and in Western countries (Wang et al, 2011) Both historical documents and genomic analyses have shown that Chinese aboriginal pigs have significantly contributed to the forma‐ tion of European modern breeds such as Large White via a human‐ mediated introgression during the onset of Industrial Revolution (Bosse et al, 2014; Chen et al, 2019). Due to the preferential use of European modern breeds and the indiscrimi‐ nate hybridization between European and Chinese breeds, the pop‐ ulation sizes of the majority of Chinese local breeds have reduced dramatically over the past decades, of which at least 20 breeds are extinct (Wang et al, 2011) To solve this alarming problem, Chinese government launched a national conservation program for 42 indigenous pig breeds, a representative of Chinese pig germ‐ plasm. The chip SNP data enabled us to obtain the compelling evidence that EDNRB is the gene responsible for the TEB phenotype and to identify a candidate caus‐ ative mutation at the EDNRB locus for this phenotype in Chinese pigs
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