NDLI: Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle

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Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle

Mammalian Genome : Volume 24, Issue 1-2, February 2013

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Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle

Content Provider	Springer Nature Link
Author	Choi, Jung Woo Lee, Kyung Tai Liao, Xiaoping Stothard, Paul An, Hyeon Seung Ahn, Sungmin Lee, Seunghwan Lee, Sung Yeoun Moore, Stephen S. Kim, Tae Hun
Copyright Year	2013
Abstract	Hanwoo, Korean native cattle, is indigenous to the Korean peninsula. They have been used mainly as draft animals for about 5,000 years; however, in the last 30 years, their main role has been changed to meat production by selective breeding which has led to substantial increases in their productivity. Massively parallel sequencing technology has recently made possible the systematic identification of structural variations in cattle genomes. In particular, copy number variation (CNV) has been recognized as an important genetic variation complementary to single-nucleotide polymorphisms that can be used to account for variations of economically important traits in cattle. Here we report genome-wide copy number variation regions (CNVRs) in Hanwoo cattle obtained by comparing the whole genome sequence of Hanwoo with Black Angus and Holstein sequence datasets. We identified 1,173 and 963 putative CNVRs representing 16.7 and 7.8 Mbp from comparisons between Black Angus and Hanwoo and between Holstein and Hanwoo, respectively. The potential functional roles of the CNVRs were assessed by Gene Ontology enrichment analysis. The results showed that response to stimulus, immune system process, and cellular component organization were highly enriched in the genic-CNVRs that overlapped with annotated cattle genes. Of the 11 CNVRs that were selected for validation by quantitative real-time PCR, 9 exhibited the expected copy number differences. The results reported in this study show that genome-wide CNVs were detected successfully using massively parallel sequencing technology. The CNVs may be a valuable resource for further studies to correlate CNVs and economically important traits in cattle.
Starting Page	151
Ending Page	163
Page Count	13
File Format	PDF
ISSN	09388990
Journal	Mammalian Genome
Volume Number	24
Issue Number	3-4
e-ISSN	14321777
Language	English
Publisher	Springer-Verlag
Publisher Date	2013-03-30
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Cell Biology Anatomy Zoology
Content Type	Text
Resource Type	Article
Subject	Genetics

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