Detection of Copy Number Variations in Woori-Heukdon Populations with the Illumina PorcineSNP60 Bead-Chip Array

Abstract

This study investigated copy number variations (CNVs) in 2112 pigs from five populations: Korean Duroc (DUC), Korean Native Pig (KNP), and their crossbred offspring (F1, F2, and WRH). CNVs were detected using PennCNV and QuantiSNP, with CNVRuler identifying 698 CNV regions (CNVRs), covering 109 Mb (4.83%) of the porcine genome. Comparison with previous CNV studies on swine revealed CNVR overlap rates ranging from 31.12% (French Yorkshire) to 81.27% (Xiang), and 9.06% newly identified CNVRs. DUC showed the most CNVRs (n = 384), followed by WRH (n = 225). Meanwhile, F1 and F2 exhibited far fewer CNVRs (five and seven, respectively). Functional enrichment analysis highlighted various genes overlapping with the CNVRs, including 1236 genes in DUC and 572 genes in WRH, linked to biological processes. The quantitative trait loci (QTLs), overlapping with CNVRs, exhibited particular overlapping with traits such as average daily gain (4.24% of QTLs in DUC, 4.51% of QTLs in WRH). In contrast, KNP, F1, and F2 populations exhibited a higher frequency of CNVRs containing QTLs overlapped with drip loss. These findings indicate that WRH may inherit growth traits from DUC. This study provides a better understanding of CNVs in the pigs, which can potentially be used in improving genetic merits of pig populations.