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

TL;DR

This study identifies copy number variations in crossbred pigs, linking them to traits like growth and meat quality.

Contribution

The study reveals how crossbreeding influences genomic variations in WRH pigs, particularly traits inherited from DUC and KNP.

Findings

WRH CNV regions overlapped with QTLs for average daily gain, suggesting inheritance of growth traits from DUC.

CNVRs in WRH also overlapped with meat quality-related QTLs, indicating contributions from KNP.

DUC had the highest number of CNVRs, while F1 and F2 generations had significantly fewer.

Abstract

Copy number variations (CNVs) are segments of DNA that vary in number between individuals or populations. CNVs can potentially influence various traits of interest in livestock species, such as growth, reproduction, and meat quality. Woori–Heukdon (WRH) was developed through a crossbreeding process, mainly using Korean Duroc (DUC) and Korean native pig (KNP). This involved crossing DUC and KNP to produce the F1, generation backcrossing DUC with F1 to generate F2, and subsequently breeding F2 with F1 to produce WRH. Here, we utilized PennCNV v1.0.5 and QuantiSNP v2.3 software to identify CNVs across the genomes of WRH, its parental breeds (DUC and KNP), and intermediate generations (F1 and F2). The results revealed distinct CNV patterns across those populations, with WRH CNV regions (CNVRs) showing the highest overlap with quantitative trait loci (QTLs) related to average daily gain (ADG). This suggests that DUC’s rapid-growth traits have been incorporated into WRH through crossbreeding. Additionally, QTLs overlapping with CNVRs in WRH also included some related to meat quality traits, indicating contributions from KNP. These findings highlight the genomic variations associated with the development of WRH and provide valuable insights for breeding programs aimed at enhancing economically important traits in pigs.

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.

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