Research paper Copy number variations in Hanwoo and Yanbian cattle genomes using the massively parallel sequencing data Jung-Woo Choi a,g,1 , Won-Hyong Chung a,1 , Kyu-Sang Lim a , Won-Jun Lim b,c , Bong-Hwan Choi a , Seung-Hwan Lee d , Hyeong-Cheol Kim e , Seung-Soo Lee f , Eun-Seok Cho a , Kyung-Tai Lee a , Namshin Kim b,c , Jeong-Dae Kim g , Jong-Bok Kim g , Han-Ha Chai a , Yong-Min Cho a , Tae-Hun Kim a , Dajeong Lim a, ⁎ a Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea b Personalized Genomic Medicine Research Center, Division of Strategic Research Groups, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea c Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34141, Republic of Korea d Division of Animal and Dairy Science, Chung Nam National University, Daejeon 305-764, Republic of Korea e Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang 232-950, Korea f Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An 331-808, Korea g College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea abstract article info Article history: Received 4 August 2015 Received in revised form 28 April 2016 Accepted 12 May 2016 Available online 14 May 2016 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 ge- nome, representing 5,513,340 bp. 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 on- tology (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 geno- mic resource for determining how CNVs are associated with cattle traits. © 2016 Published by Elsevier B.V. Keywords: Hanwoo Yanbian cattle Copy number variation Whole-genome sequencing 1. Introduction Copy number variation (CNV) is an important genomic variation that pertains to an abnormal number of copies of large genomic regions. Landmark studies revealed that the CNVs are extensively distributed across the human genome (Iafrate et al., 2004; Sebat et al., 2004). The definition of CNV continues to change as there are improvements in ex- perimental approaches that are used in the CNV detection, including array comparative genomic hybridization, single nucleotide polymor- phism arrays, and next-generation sequencing (NGS). In particular, such technological advances have significantly improved the resolution of identified CNVs, leading to CNV size classification changes during the most recent decade. In cattle, genome-wide CNVs have mainly been assessed since the completion of the bovine sequencing project (Bovine Genome et al., 2009; Liu et al., 2009; Zimin et al., 2009) as well as commercial and cus- tom array developments (Matukumalli et al., 2009; Fadista et al., 2010). In particular, the array-based approaches granted the opportunity to detect genome-wide CNVs at a population scale using multiple cattle breeds (Fadista et al., 2010; Hou et al., 2011, 2012; Jiang et al., 2013). Furthermore, recent advances in NGS technologies have successfully been used to detect CNVs with higher resolution and accuracy in cattle genomes (Stothard et al., 2011; Bickhart et al., 2012; Choi et al., 2013, 2014); however, sequencing is still too expensive to perform genome- wide population-scale CNV analyses. Hanwoo (HAN) is a native Korean cattle breed that is renowned as the representative beef cattle on the Korean peninsula, and it is nor- mally referred to as the brown-colored cattle. HAN were mainly used as draft animals until a selective breeding program was initiated in the late 1970s. The breeding program has contributed to substantial genetic improvement in economically important traits for HAN, and it is cur- rently the most preferred beef cattle breed among Korean consumers Gene 589 (2016) 36–42 ⁎ Corresponding author at: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea. E-mail address: lim.dj@korea.kr (D. Lim). 1 These authors contributed equally to this work. http://dx.doi.org/10.1016/j.gene.2016.05.017 0378-1119/© 2016 Published by Elsevier B.V. Contents lists available at ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene