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Open Access Research article

Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

Dong-Hyun Shin1, Hyun-Jeong Lee2, Seoae Cho4, Hyeon Jeong Kim4, Jae Yeon Hwang1, Chang-Kyu Lee1, JinYoung Jeong2, Duhak Yoon3* and Heebal Kim14*

Author Affiliations

1 Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea

2 Division of Animal Genomics and Bioinformatics, National Institute of Animal science, Rural Development Administration, #564 Omockchun-dong, Suwon 441-706, Korea

3 Department of Animal Science, Kyungpook National University, Sangju 742-711, Korea

4 C&K genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, Gwanakgu, Seoul 151-919, Republic of Korea

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BMC Genomics 2014, 15:240  doi:10.1186/1471-2164-15-240

Published: 27 March 2014

Abstract

Background

Copy number variation (CNV), a source of genetic diversity in mammals, has been shown to underlie biological functions related to production traits. Notwithstanding, there have been few studies conducted on CNVs using next generation sequencing at the population level.

Results

Illumina NGS data was obtained for ten Holsteins, a dairy cattle, and 22 Hanwoo, a beef cattle. The sequence data for each of the 32 animals varied from 13.58-fold to almost 20-fold coverage. We detected a total of 6,811 deleted CNVs across the analyzed individuals (average length =‚ÄČ2732.2 bp) corresponding to 0.74% of the cattle genome (18.6 Mbp of variable sequence). By examining the overlap between CNV deletion regions and genes, we selected 30 genes with the highest deletion scores. These genes were found to be related to the nervous system, more specifically with nervous transmission, neuron motion, and neurogenesis. We regarded these genes as having been effected by the domestication process. Further analysis of the CNV genotyping information revealed 94 putative selected CNVs and 954 breed-specific CNVs.

Conclusions

This study provides useful information for assessing the impact of CNVs on cattle traits using NGS at the population level.

Keywords:
Cattle; Hanwoo; Holstein; Copy Number Variation; NGS; Domestication; Selection signal