Copy Number Variation Frequency Analysis by Regions of Hanwoo (Korean Native Cattle) Using Hanwoo SNP 50K Chip

Abstract

Recently another type of genetic polymorphism, called copy number variation (CNV), has been discovered in the whole genome variation. SNP chips have also been used for CNVs analysis, making them a useful analytical tool. In this study, we evaluated CNVs and identified the relationship between CNV regions (CNVRs) in Hanwoo (n=1500) using the Illumina Hanwoo SNP 50K BeadChip in four South Korean regions. PennCNV software was used to identify CNVs, followed by CNV Ruler software to locate diverse CNVRs. We identified 8686 CNVs (6666 gains; 2020 loss), with lengths varying from 2,182 to 2,957,803 bp. Additionally, 689 CNVRs (480 gains; 153 losses; 56 both) were identified, with lengths varying from 2,820 to 2,957,803 bp, with an average of 124,881 bp, encompassing 86,042,896 bp (3.48%). Bioinformatic analysis was conducted using Biomart tools, gene ontology analysis, and the DAVID program. We identified 27 genes that were associated with IGF2, INS, SOCS3, and TH and found that they were related to insulin (GO:0046626, GO:1900076, bta04917). In conclusion, CNVs were identified using the HanwooSNP50k chip, CNVR with characteristics for each region was identified, and a part overlapping with the gene was verified. It is essential to verify that insulin-related genes differ by region and to understand the relationship between regional economic traits and CNV.