title: Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels.
abstract: Since the completion of the bovine sequencing projects, a substantial number of genetic variations such as single nucleotide polymorphisms have become available across the cattle genome. Recently, cataloguing such genetic variations has been accelerated using massively parallel sequencing technology. However, most of the recent studies have been concentrated on European Bos taurus cattle breeds, resulting in a severe lack of knowledge for valuable native cattle genetic resources worldwide. Here, we present the first whole-genome sequencing results for an endangered Korean native cattle breed, Chikso, using the Illumina HiSeq 2,000 sequencing platform. The genome of a Chikso bull was sequenced to approximately 25.3-fold coverage with 98.8% of the bovine reference genome sequence (UMD 3.1) covered. In total, 5,874,026 single nucleotide polymorphisms and 551,363 insertion/deletions were identified across all 29 autosomes and the X-chromosome, of which 45% and 75% were previously unknown, respectively. Most of the variations (92.7% of single nucleotide polymorphisms and 92.9% of insertion/deletions) were located in intergenic and intron regions. A total of 16,273 single nucleotide polymorphisms causing missense mutations were detected in 7,111 genes throughout the genome, which could potentially contribute to variation in economically important traits in Chikso. This study provides a valuable resource for further investigations of the genetic mechanisms underlying traits of interest in cattle, and for the development of improved genomics-based breeding tools.
authors.affiliation: Centre for Genetic Improvement of Livestock, Animal & Poultry Science, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
authors.forename: Jung-Woo
authors.initials: JW
authors.lastname: Choi
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Liao
authors.forename: Sairom
authors.initials: S
authors.lastname: Park
authors.forename: Heoyn-Jeong
authors.initials: HJ
authors.lastname: Jeon
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
authors.forename: Yeon-Soo
authors.initials: YS
authors.lastname: Park
authors.forename: Jeong-Koo
authors.initials: JK
authors.lastname: Lee
authors.forename: Kyung-Tai
authors.initials: KT
authors.lastname: Lee
authors.forename: Sang-Hwan
authors.initials: SH
authors.lastname: Kim
authors.forename: Jae-Don
authors.initials: JD
authors.lastname: Oh
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.forename: Tae-Hun
authors.initials: TH
authors.lastname: Kim
authors.forename: Hak-Kyo
authors.initials: HK
authors.lastname: Lee
authors.forename: Sung-Jin
authors.initials: SJ
authors.lastname: Lee
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D021901:DNA, Intergenic; D056727:Endangered Species; D014644:Genetic Variation; D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054643:INDEL Mutation; D008297:Male; D058977:Molecular Sequence Annotation; D020125:Mutation, Missense; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D021901:DNA, Intergenic
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