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

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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.

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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.”

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Authors and Affiliations

  1. Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada

    Jung-Woo Choi, Xiaoping Liao, Paul Stothard & Stephen S. Moore

  2. Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon, Republic of Korea

    Kyung-Tai Lee, Hyeon-Seung An, Seunghwan Lee & Tae-Hun Kim

  3. Laboratory of Genomics and Genomic Medicine, Lee Gil Ya Cancer and Diabetes Institute, Gachon University of Medicine and Science, Incheon, Republic of Korea

    Sungmin Ahn & Sung-Yeoun Lee

  4. Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia

    Stephen S. Moore

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  1. Jung-Woo Choi
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  2. Kyung-Tai Lee
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  3. Xiaoping Liao
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Correspondence to Tae-Hun Kim.

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Jung-Woo Choi and Kyung-Tai Lee contributed equally to this work.

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Choi, JW., Lee, KT., Liao, X. et al. Genome-wide copy number variation in Hanwoo, Black Angus, and Holstein cattle. Mamm Genome 24, 151–163 (2013). https://doi.org/10.1007/s00335-013-9449-z

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