title: Copy number variations in Hanwoo and Yanbian cattle genomes using the massively parallel sequencing data.
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.
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea; College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
authors.forename: Jung-Woo
authors.initials: JW
authors.lastname: Choi
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Kyu-Sang
authors.initials: KS
authors.lastname: Lim
authors.affiliation: Personalized Genomic Medicine Research Center, Division of Strategic Research Groups, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34141, Republic of Korea.
authors.forename: Won-Jun
authors.initials: WJ
authors.lastname: Lim
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Bong-Hwan
authors.initials: BH
authors.lastname: Choi
authors.affiliation: Division of Animal and Dairy Science, Chung Nam National University, Daejeon 305-764, Republic of Korea.
authors.forename: Seung-Hwan
authors.initials: SH
authors.lastname: Lee
authors.affiliation: Hanwoo Experiment Station, National Institute of Animal Science, RDA, Pyeongchang 232-950, Korea.
authors.forename: Hyeong-Cheol
authors.initials: HC
authors.lastname: Kim
authors.affiliation: Animal Genetic and Breeding Division, National Institute of Animal Science, Cheon-An 331-808, Korea.
authors.forename: Seung-Soo
authors.initials: SS
authors.lastname: Lee
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Eun-Seok
authors.initials: ES
authors.lastname: Cho
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Kyung-Tai
authors.initials: KT
authors.lastname: Lee
authors.affiliation: Personalized Genomic Medicine Research Center, Division of Strategic Research Groups, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34141, Republic of Korea.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.affiliation: College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
authors.forename: Jeong-Dae
authors.initials: JD
authors.lastname: Kim
authors.affiliation: College of Animal Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
authors.forename: Jong-Bok
authors.initials: JB
authors.lastname: Kim
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Han-Ha
authors.initials: HH
authors.lastname: Chai
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Yong-Min
authors.initials: YM
authors.lastname: Cho
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea.
authors.forename: Tae-Hun
authors.initials: TH
authors.lastname: Kim
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea. Electronic address: lim.dj@korea.kr.
authors.forename: Dajeong
authors.initials: D
authors.lastname: Lim
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle; D002681:China; D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D063990:Gene Ontology; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D056910:Republic of Korea; D012641:Selection, Genetic
keywords: Copy number variation; Hanwoo; Whole-genome sequencing; Yanbian cattle