Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Yifei Fang; Xinyu Hao; Zhong Xu; Hao Sun; Qingbo Zhao; Rui Cao; Zhe Zhang; Peipei Ma; Yanxiao Sun; Zengmin Qi; Qingkui Wei; Qishan Wang; Yuchun Pan

doi:10.3389/fgene.2021.629966

Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Front Genet. 2021 Apr 29:12:629966. doi: 10.3389/fgene.2021.629966. eCollection 2021.

Authors

Yifei Fang¹, Xinyu Hao¹, Zhong Xu¹, Hao Sun¹, Qingbo Zhao¹, Rui Cao¹, Zhe Zhang², Peipei Ma¹, Yanxiao Sun³, Zengmin Qi³, Qingkui Wei³, Qishan Wang², Yuchun Pan²

Affiliations

¹ Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
² Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
³ Breeding Company of Pigs, Laiwu, China.

Abstract

Laiwu pigs, distinguished by their high intramuscular fat of 7-9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1-5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.

Keywords: Laiwu pig; candidate genes; inbreeding coefficient; runs of homozygosity; selection.