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Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level
Cited 32 time in
Web of Science
Cited 33 time in Scopus
- Authors
- Issue Date
- 2014-03-27
- Publisher
- BioMed Central
- Citation
- BMC Genomics, 15(1):240
- Keywords
- Cattle ; Hanwoo ; Holstein ; Copy Number Variation ; NGS ; Domestication ; Selection signal
- Description
- This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
- Abstract
- 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 = 2732.2bp) 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.
- Language
- English
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