数字农科院2.0

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

文献类型： 外文期刊

作者： Jiang Y.; Li X.; Liu J.; Zhang W.; Zhou M.; Wang J.; Liu L.; Su S.; Zhao F.; Chen H.; Wang C.

作者机构：

关键词： Anhui indigenous pig breed; animal health; Article; assortative mating; bone development; CCNT2 gene; CDH13 gene; cladistics; controlled study; CSN1S1 gene; DUSP gene; EGR2 gene; FGF18 gene; FGF20 gene; FLVCR1 gene; gene; gene frequency; genome; geographic origin; homozygosity; LIPC gene; MCEE gene; muscle development; MYL3 gene; nonhuman; pig breed; population genetic structure; principal component analysis; PROX1 gene; reproduction; runs of homozygosity; SETD2 gene; single nucleotide polymorphism; STAP1 gene; SULT1E1 gene; TJP1 gene; Western commercial pig breed; ZNF366 gene; animal; genetics; genotype; homozygote; inbreeding; pig; Animals; Genome; Genotype; Homozygote; Inbreeding; Polymorphism; Single Nucleotide; Swine

期刊名称： BMC Genomics

ISSN： 1471-2164

年卷期： 2022 年 23 卷 1 期

页码：

收录情况： SCIE（2022版）

摘要： 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. © 2022, The Author(s).

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