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

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Authors
Shin, Dong-Hyun; Lee, Hyun-Jeong; Cho, Seoae; Kim, Hyeon Jeong; Hwang, Jae Yeon; Lee, Chang-Kyu; Jeong, JinYoung; Yoon, Duhak; Kim, Heebal
Issue Date
2014-03-27
Publisher
BioMed Central
Citation
BMC Genomics, 15(1):240
Keywords
CattleHanwooHolsteinCopy Number VariationNGSDomesticationSelection 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 = 2732.2 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.
Language
English
URI
http://hdl.handle.net/10371/100469
DOI
https://doi.org/10.1186/1471-2164-15-240
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College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Food and Animal Biotechnology (식품·동물생명공학부)Journal Papers (저널논문_식품·동물생명공학부)
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