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Mammalian Genome

, Volume 24, Issue 3–4, pp 151–163 | Cite as

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

  • Jung-Woo Choi
  • Kyung-Tai Lee
  • Xiaoping Liao
  • Paul Stothard
  • Hyeon-Seung An
  • Sungmin Ahn
  • Seunghwan Lee
  • Sung-Yeoun Lee
  • Stephen S. Moore
  • Tae-Hun KimEmail author
Article

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.

Keywords

Gene Ontology Copy Number Variation Draft Animal Potential Functional Role Cellular Component Organization 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

This work was supported by a grant (No. PJ007197) from the BioGreen21 program, Rural Development Administration (RDA), Korea, and through University of Alberta program funds provided to Professor Moore. Xiaoping Liao is funded by the Genome Canada project entitled “Whole Genome Selection Through Genome Wide Imputation in Beef Cattle.”

Supplementary material

335_2013_9449_MOESM1_ESM.xlsx (180 kb)
Supplementary material 1 (XLSX 179 kb)
335_2013_9449_MOESM2_ESM.xlsx (93 kb)
Supplementary material 2 (XLSX 92 kb)

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Jung-Woo Choi
    • 1
  • Kyung-Tai Lee
    • 2
  • Xiaoping Liao
    • 1
  • Paul Stothard
    • 1
  • Hyeon-Seung An
    • 2
  • Sungmin Ahn
    • 3
  • Seunghwan Lee
    • 2
  • Sung-Yeoun Lee
    • 3
  • Stephen S. Moore
    • 1
    • 4
  • Tae-Hun Kim
    • 2
    Email author
  1. 1.Department of Agricultural, Food and Nutritional ScienceUniversity of AlbertaEdmontonCanada
  2. 2.Division of Animal Genomics and BioinformaticsNational Institute of Animal Science, Rural Development AdministrationSuwonRepublic of Korea
  3. 3.Laboratory of Genomics and Genomic Medicine, Lee Gil Ya Cancer and Diabetes InstituteGachon University of Medicine and ScienceIncheonRepublic of Korea
  4. 4.Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandQLDAustralia

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