Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data

Abstract

Background Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight into the genetic architecture of complex traits. Here, we systematically investigated the population genetic structure of five Anhui indigenous pig breeds (AHIPs), and compared them to those of five Western commercial pig breeds (WECPs). Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (FROH) and homozygosity (FHOM). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein. Results The WECPs and AHIPs were clearly differentiated into two separate clades consistent with their geographical origins, as revealed by the population structure and principal component analysis. We identified 13,530 ROHs across all individuals, of which 4,555 and 8,975 ROHs were unique to AHIPs and WECPs, respectively. Most ROHs identified in our study were short (< 10 Mb) or medium (10–20 Mb) in length. WECPs had significantly higher numbers of short ROHs, and AHIPs generally had longer ROHs. FROH values were significantly lower in AHIPs than in WECPs, indicating that breed improvement and conservation programmes were successful in AHIPs. On average, FROH and FHOM values were highly correlated (0.952–0.991) in AHIPs and WECPs. A total of 27 regions had a high frequency of ROHs and contained 17 key candidate genes associated with economically important traits in pigs. Among these, nine candidate genes (CCNT2, EGR2, MYL3, CDH13, PROX1, FLVCR1, SETD2, FGF18, and FGF20) found in WECPs were related to muscular and skeletal development, whereas eight candidate genes (CSN1S1, SULT1E1, TJP1, ZNF366, LIPC, MCEE, STAP1, and DUSP) found in AHIPs were associated with health, reproduction, and fatness traits. Conclusion Our findings provide a useful reference for the selection and assortative mating of pig breeds, laying the groundwork for future research on the population genetic structures of AHIPs, ultimately helping protect these local varieties.

A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond

“…In contrast, our estimates were based on a large sample size (N = 2077). On average, there were 32.2 ROH per animal in Ningxiang pigs, whereas Jiang et al [25] reported between 15.0 and 44.0 ROH in Aihui indigenous pigs. Fang et al [26] classified ROH into three length bins: 1-5 Mb, 5-10 Mb, and >10 Mb.…”

“…Jiang et al [25] used the same five ROH categories as ours, and they reported similar ROH frequencies in Aihui indigenous pigs: 44.7-55.1% (1-5 Mb), 28.2-37.1% (5-10 Mb), 12.1-16.6% (10-20 Mb), 2.9-5.6% (20-40 Mb), and 0.1-0.7% (>40 Mb). Nevertheless, our results demonstrated a slightly higher frequency for the first category (1-5 Mb) and a lower frequency in the last category (>40 Mb).…”

“…For example, Tong et al [27] reported different ROH structures among three pig breeds (Erhualian pigs, Mi pigs, and Meishan pigs) in the region of Taihu Lake, China. By comparing five Aihui Indigenous pig breeds with five Western pig breeds, Jiang et al [25] demonstrated that chromosome 18 had the highest chromosomal coverage by ROH (31.3%) in Piétrain pigs, and chromosome 17 had the highest chromosomal coverage by ROH in Wannanhua pigs. Varying ROH coverages on different chromosomes also suggest varying selection and genetic drift operating on these chromosomes.…”

Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip

“…A total of 320 blood samples were collected from 10 breeds of pigs, including 5 foreign breeds (WECP): Yorkshire (n = 50), Landrace (n = 30), Duroc (n = 30), Pietrain (n = 30), Berkshire (n = 30), and 5 indigenous Anhui pig populations (AHIP): Anqing six-end-white pig (ASP, n = 30), Wei pig (WP, n = 30), Wannan Spotted pig (WSP, n = 30), Wannan Black pig (WBP, n = 30), and Huai pig (HP, n = 30). We considered two different groups based on the results obtained in the previous study [ 20 ]. We extracted genomic DNA from ear tissues using the traditional phenol/chloroform method.…”

Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: A case study with litter traits in pigs

“…China has the most genetic resources of domestic pigs [22] , [23] . Jinhua ( JH ), Chun’an ( CA ), Longyou Black ( LY ), and Shengxian Spotted ( SX ) pigs originated in eastern China and have similar characteristics to other indigenous breeds, e.g., improved meat quality, disease resistance, and high fertility in comparison with intensively-reared commercial pig breeds (e.g., Large white, Landrace, and Duroc pig breeds) [24] , [25] , [26] . These excellent characteristics mark them as the best material to uncover the genetic mechanism of economic traits and support the sustainable development of the pig industry [27] .…”