title: Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing.
abstract: A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea--Hanwoo, Jeju Heugu, and Korean Holstein--using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions-deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.
authors.affiliation: Centre for Genetic Improvement of Livestock, Animal & Poultry Science, University of Guelph, Guelph, Ontario, Canada; Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon, Republic of Korea.
authors.forename: Jung-Woo
authors.initials: JW
authors.lastname: Choi
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Liao
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.affiliation: Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon, Republic of Korea.
authors.forename: Heoyn-Jeong
authors.initials: HJ
authors.lastname: Jeon
authors.affiliation: Centre for Genetic Improvement of Livestock, Animal & Poultry Science, University of Guelph, Guelph, Ontario, Canada.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Miller
authors.affiliation: College of Animal Life Sciences, Kangwon National University, Chuncheon, Republic of Korea.
authors.forename: So-Young
authors.initials: SY
authors.lastname: Choi
authors.affiliation: College of Animal Life Sciences, Kangwon National University, Chuncheon, Republic of Korea.
authors.forename: Jeong-Koo
authors.initials: JK
authors.lastname: Lee
authors.affiliation: Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea.
authors.forename: Bokyoung
authors.initials: B
authors.lastname: Yang
authors.affiliation: Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon, Republic of Korea.
authors.forename: Kyung-Tai
authors.initials: KT
authors.lastname: Lee
authors.affiliation: Dairy Cattle Improvement Center, National Agricultural Cooperative Federation, Goyang-Si, Republic of Korea.
authors.forename: Kwang-Jin
authors.initials: KJ
authors.lastname: Han
authors.affiliation: Hanwoo Experiment Station, National Institute of Animal Science, Rural Development Administration, Gangwon-do, Republic of Korea.
authors.forename: Hyeong-Cheol
authors.initials: HC
authors.lastname: Kim
authors.affiliation: Department of Biotechnology, Jeju National University, Jeju, Republic of Korea.
authors.forename: Dongkee
authors.initials: D
authors.lastname: Jeong
authors.affiliation: Department of Biotechnology, Hankyong National University, Anseong, Republic of Korea.
authors.forename: Jae-Don
authors.initials: JD
authors.lastname: Oh
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.affiliation: Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon, Republic of Korea.
authors.forename: Tae-Hun
authors.initials: TH
authors.lastname: Kim
authors.affiliation: Department of Biotechnology, Hankyong National University, Anseong, Republic of Korea.
authors.forename: Hak-Kyo
authors.initials: HK
authors.lastname: Lee
authors.affiliation: College of Animal Life Sciences, Kangwon National University, Chuncheon, Republic of Korea.
authors.forename: Sung-Jin
authors.initials: SJ
authors.lastname: Lee
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D056915:DNA Copy Number Variations; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006720:Homozygote; D054643:INDEL Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D056910:Republic of Korea