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

Overview

Journal Front Genet

Date 2021 Sep 20

PMID 34539748

Citations 13

Authors

Zhong Xu

Shuqi Mei

Jiawei Zhou

Yu Zhang

Mu Qiao

Hua Sun

Zipeng Li

Lianghua Li

Binke Dong

Favour Oluwapelumi Oyelami

Junjing Wu

Xianwen Peng

Affiliations

Soon will be listed here.

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 (F) and homozygosity (F). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, 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 , , , , , and . 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.

Citing Articles

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