Journal of Animal Breeding and Genomics (J Anim Breed Genom)
Khaliunaa Tseveen1, Gwang Hyeon Lee1, Chan Mi Bang2, Dae Yong Yang3, Chang Wan Sun3, Yoon Seok Lee4,5,7 and Hong Sik Kong1,4,5,6,7*
1Department of Applied Biotechnology, The Graduate School of Hankyong National University, Anseong 17579, Korea
2Department of Genomic Informatics, Graduate School of Future Convergence Technology, Hankyong National University, Anseong 17579, Korea
3Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
4Department of Applied Biotechnology, Hankyong National University, Anseong 17579, Korea
5Genomic Informatics Center, Hankyong National University, Anseong 17579, Korea
6Hankyong and Genetics, Hankyong National University, Anseong 17579, Korea
7Gyeonggi Regional Research Center, Hankyong National University, Anseong 17579, Korea
Correspondence to Hong Sik Kong, E-mail: kebinkhs@hknu.ac.kr
Volume 7, Number 3, Pages 113-122, September 2023.
Journal of Animal Breeding and Genomics 2023, 7(3), 113-122. https://doi.org/10.12972/jabng.20230013
Received on 11 August, 2023, Revised on 22 September, 2023, Accepted on 27 September, 2023, Published on 30 September, 2023.
Copyright © 2023 Korean Society of Animal Breeding and Genetics.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0).
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.
Copy number variation (CNV), CNV Region, Hanwoo
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