Copy number variations in Hanwoo and Yanbian cattle genomes using the massively parallel sequencing data

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Title
Copy number variations in Hanwoo and Yanbian cattle genomes using the massively parallel sequencing data
Author(s)
J W Choi; W H Chung; K S Lim; Won-Jun Lim; B H Choi; S H Lee; H C Kim; S S Lee; E S Cho; K T Lee; Namshin Kim; J D Kim; J B Kim; H N Chai; Y M Cho; T H Kim; D Lim
Bibliographic Citation
Gene, vol. 589, pp. 36-42
Publication Year
2016
Abstract
Hanwoo is an indigenous Korean beef cattle breed, and it shared an ancestor with Yanbian cattle that are found in the Northeast provinces in China until the last century. During recent decades, those cattle breeds experienced different selection pressures. Here, we present genome-wide copy number variations (CNVs) by comparing Hanwoo and Yanbian cattle sequencing data. We used ~3.12 and ~3.07 billion sequence reads from Hanwoo and Yanbian cattle, respectively. A total of 901 putative CNV regions (CNVRs) were identified throughout the genome, representing 5,513,340bp. This is a smaller number than has been reported in previous studies, indicating that Hanwoo are genetically close to Yanbian cattle. Of the CNVRs, 53.2% and 46.8% were found to be gains and losses in Hanwoo. Potential functional roles of each CNVR were assessed by annotating all CNVRs and gene ontology (GO) enrichment analysis. We found that 278 CNVRs overlapped with cattle gene-sets (genic-CNVRs) that could be promising candidates to account for economically important traits in cattle. The enrichment analysis indicated that genes were significantly over-represented in GO terms, including developmental process, multicellular organismal process, reproduction, and response to stimulus. These results provide a valuable genomic resource for determining how CNVs are associated with cattle traits.
Keyword
Yanbian cattleCopy number variationWhole-genome sequencingHanwoo
ISSN
0378-1119
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.gene.2016.05.017
Type
Article
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1. Journal Articles > Journal Articles
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