Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed.

Zhong Xu,Jiawei Zhou,Favour Oluwapelumi Oyelami,Binke Dong,Junjing Wu,Xianwen Peng,Shuqi Mei,Hua Sun,Mu Qiao,Lianghua Li,Zipeng Li,Yu Zhang

doi:10.3389/fgene.2021.720081

Abstract

The primary purpose of the current study was to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection. First, we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine SNP50 BeadChip and compared the estimates of inbreeding coefficients, which were calculated based on ROHs (FROH) and homozygosity (FHOM). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, Sus scrofa chromosome (SSC) 8 and SSC10, respectively, has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on total ROH may be a useful method, especially for crossbreed or composite populations. We also calculated an inbreeding coefficient of 0.077 from the total ROH. Eight ROH islands were found in this study. These ROH islands harbored genes associated with fat deposition, muscular development, reproduction, ear shape, and adaptation, such as TRAF7, IGFBP7, XPO1, SLC26A8, PPARD, and OR1F1. These findings may help to understand the effects of environmental and artificial selection on the genome structure of composite pigs. Our results provide a basis for subsequent genomic selection (GS), and provides a reference for the hybrid utilization of other pig breeds.

Highlights

Crossbreeding is a common strategy to improve livestock production because it can explore complementarities of additive genetic effects as well as heterosis caused by non-additive genetic effects (Howard et al, 2016)
Genotype quality control was carried out using PLINK v1.90 (Chang et al, 2015) software based on the following filtering criteria: (1) the call rate of Single nucleotide polymorphism (SNPs) and individuals were higher than 0.9; (2) the minor allele frequency (MAF) was greater than 0.01; and (3) only SNPs mapped to autosomes were included
In this study, we investigated the patterns of runs of homozygosity (ROH), inbreeding coefficients and linkage disequilibrium (LD) in the Xidu black pigs

Summary

Introduction

Crossbreeding is a common strategy to improve livestock production because it can explore complementarities of additive genetic effects as well as heterosis caused by non-additive genetic effects (Howard et al, 2016). The Enshi black pig, a typical native black breed in China, mainly lives in mountainous areas of southwest China at an average altitude of more than 800 m It is well-known for its adaptability to a mountainous environment, excellent meat quality, fat storage ability, and cold-wet tolerance Since the 1990s, under the impact of exotic germplasm with high growth rate and lean meat rate, the Enshi black pig has been facing extinction due to its low growth rate. To overcome these deficiencies and conserve the Enshi black pig, crossbreeding programs have been implemented to increase productivity, and the Xidu black pig is a new composite breed that has been developed for this situation. It is worth noting that the Xidu black pig is well established and can be used as a purebred without the need for any ongoing crossbreeding programs

Objectives

Methods

Results

Conclusion