Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels = NGS를 이용한 칙소의 SNP와 INDEL 발굴

Cited 25 time in scopus
Metadata Downloads
Title
Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels = NGS를 이용한 칙소의 SNP와 INDEL 발굴
Author(s)
J W Choi; X Liao; S Park; H J Jeon; Won Hyung Chung; P Stothard; Y S Park; J K Lee; K T Lee; S H Kim; J D Oh; Namshin Kim; T H Kim; H K Lee; S J Lee
Bibliographic Citation
Molecules and Cells, vol. 36, no. 3, pp. 203-211
Publication Year
2013
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.
Keyword
ChiksoInDelmassively parallel sequencingSNP
ISSN
1016-8478
Publisher
South Korea
DOI
http://dx.doi.org/10.1007/s10059-013-2347-0
Type
Article
Appears in Collections:
Division of Biomedical Research > Genome Editing Research Center > 1. Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.