The fine‐scale genetic structure and selection signals of Chinese indigenous pigs

Abstract

Evolutionary Applications. 2020;13:458-475. wileyonlinelibrary.com/journal/eva | INTRODUC TI ONThe domestication of farm animals is a groundbreaking event that has deeply influenced human history. The pig (Sus scrofa) was domesticated largely in China and the Near East approximately 10,000 years ago (Frantz et al., 2015;Larson et al., 2005). Since then, human-mediated artificial selection and natural selection have resulted in diverse pig breeds in the world. Chinese domestic pigs represent a rich genetic resource. More than one-third (~100) of global pig breeds are found in China (Wang et al., 2011). These diverse breeds are 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. K E Y W O R D S Chinese pig, coat color, genetic diversity, high-altitude adaptation, phylogenetic relationship, population structure | 459 HUANG et Al. renowned for desirable traits related to reproduction, disease resistance, docility, and meat quality, providing valuable germplasm that supports the sustainable development of the pig industry not only in China but also in Western countries (Wang et al., 2011). For instance, S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Huang M, Yang B, Chen H, et al. The fine-scale genetic structure and selection signals of Chinese indigenous pigs. Evol Appl. 2020;13:458-475. https ://doi.

Whole‐genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs

“…The possibility was supported by our recent study based on whole-genome SNP markers. We showed that approximately one-fourth of genetic components in the genome of Laiwu pig are of European origin (Huang et al, 2019).…”

“…The possibility was supported by our recent study based on whole‐genome SNP markers. We showed that approximately one‐fourth of genetic components in the genome of Laiwu pig are of European origin (Huang et al., 2019). However, the genomic distribution and phenotypic effect of the introgressed European haplotypes in Laiwu pigs remain elusive.…”

Longitudinal Expression of Testicular TAS1R3 from Prepuberty to Sexual Maturity in Congjiang Xiang Pigs

“…The minipig is considered a convenient animal model for preclinical studies because they rapidly achieve sexual maturity (before the age of six months) and the duration of the spermatogenic cycle is short (i.e., 35 day) [36]. Although there are structural variations at the genome level between relatively large litter sizes (average litter size: 13 piglets) and small litter sizes (average litter size: 8 piglets) in Congjiang Xiang pigs for long-term grazing and inbreeding [37,38], the breed is clearly characterized by early sexual maturity [39,40]. According to our study, Congjiang Xiang pigs exhibit the onset of puberty at approximately 2 months [40], similar to Gottingen pigs, and earlier than Yucatan minipigs (3.6-4 months) and Yorkshire (around 6 months) [41].…”

Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed

“…Since the extent of LD ( r 2 ) depends on MAF, it is expected that there would be a little difference in the r 2 value obtained from both studies, partly due to SNP ascertainment bias on SNP chip data ( Lachance and Tishkoff, 2013 ; Geibel et al, 2019 ). This kind of bias was reduced in a recent study by Huang et al (2020) which had more Chinese breeds represented in the design of the SNP array used. The study reported an LD ( r 2 > 0.3) at SNPs-distance of 36.10 kb for the JQ breed.…”