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

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.

Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations

“…In addition, genomic data was utilized to explore selection signatures and reveal potential genetic mechanisms underlying the domestication and evolution of Duroc pigs ( Kim et al, 2015 ; Zhang et al, 2020 ). For instance, runs of homozygosity (ROH) were widely applied to identify candidate regions and genes in the pig genome that were subject to selection and associated with important traits (carcass and reproduction traits) ( Hong et al, 2021 ), because positive selection reduces genetic diversity and increases homozygosity ( Fang et al, 2021 ). These methods have contributed to elucidating the genetic architecture of Duroc pigs, primarily focusing on haplotypes and homozygosity.…”

Sequencing Reveals Population Structure and Selection Signatures for Reproductive Traits in Yunnan Semi-Fine Wool Sheep (Ovis aries)

“…Using ROHs to calculate the inbreeding coefficient ( F ROH ) is more accurate than estimating the inbreeding coefficient from pedigree data ( Kim et al, 2015 ). In this study, the average inbreeding coefficient (0.0099: 0.0004–0.0239) was lower than that of other sheep breeds, e.g., Chaka sheep ( F ROH = 0.032) ( Cheng et al, 2020 ), Italian Alpagota sheep ( F ROH = 0.053) ( Mastrangelo et al, 2018 )) and other species, e.g., white leghorn ( F ROH = 0.28) ( Zhang et al, 2020 ) and Laiwu pigs ( F ROH = 0.133) ( Fang et al, 2021 ), indicating that the population structure of Yunnan semi-fine wool sheep is ideal. Combining the average inbreeding coefficient and heterozygosity rate, we could preliminarily infer that although these two parameters varied greatly within the Yunnan semi-fine wool sheep population, sufficient genetic diversity was maintained overall during cultivation and artificial selection.…”

Genome-Wide Association Studies, Runs of Homozygosity Analysis, and Copy Number Variation Detection to Identify Reproduction-Related Genes in Bama Xiang Pigs

“…In this study, we successfully identified 9,322 ROHs. Similar to Laiwu pig ( 45 ), Diannan xiaoer pig ( 46 ) and Large White ( 47 ), the majority ROHs in Bama Xiang pigs were short segments. The significant Spearman correlation coefficient of F ROH and litter size ranged from −0.14 to −0.28.…”