title: Discovery of Gene Sources for Economic Traits in Hanwoo by Whole-genome Resequencing.
abstract: Hanwoo, a Korean native cattle (Bos taurus coreana), has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generation sequencing technologies and the availability of an appropriate reference genome were applied to discover a large amount of single nucleotide polymorphisms (SNPs) in ten Hanwoo bulls. Analysis of whole-genome resequencing generated a total of 26.5 Gb data, of which 594,716,859 and 592,990,750 reads covered 98.73% and 93.79% of the bovine reference genomes of UMD 3.1 and Btau 4.6.1, respectively. In total, 2,473,884 and 2,402,997 putative SNPs were discovered, of which 1,095,922 (44.3%) and 982,674 (40.9%) novel SNPs were discovered against UMD3.1 and Btau 4.6.1, respectively. Among the SNPs, the 46,301 (UMD 3.1) and 28,613 SNPs (Btau 4.6.1) that were identified as Hanwoo-specific SNPs were included in the functional genes that may be involved in the mechanisms of milk production, tenderness, juiciness, marbling of Hanwoo beef and yellow hair. Most of the Hanwoo-specific SNPs were identified in the promoter region, suggesting that the SNPs influence differential expression of the regulated genes relative to the relevant traits. In particular, the non-synonymous (ns) SNPs found in CORIN, which is a negative regulator of Agouti, might be a causal variant to determine yellow hair of Hanwoo. Our results will provide abundant genetic sources of variation to characterize Hanwoo genetics and for subsequent breeding.
authors.affiliation: Codes Division, Insilicogen Inc., Yongin 446-908, Korea.
authors.forename: Younhee
authors.initials: Y
authors.lastname: Shin
authors.affiliation: Codes Division, Insilicogen Inc., Yongin 446-908, Korea.
authors.forename: Ho-Jin
authors.initials: HJ
authors.lastname: Jung
authors.affiliation: Codes Division, Insilicogen Inc., Yongin 446-908, Korea.
authors.forename: Myunghee
authors.initials: M
authors.lastname: Jung
authors.affiliation: Codes Division, Insilicogen Inc., Yongin 446-908, Korea.
authors.forename: Seungil
authors.initials: S
authors.lastname: Yoo
authors.affiliation: Codes Division, Insilicogen Inc., Yongin 446-908, Korea.
authors.forename: Sathiyamoorthy
authors.initials: S
authors.lastname: Subramaniyam
authors.affiliation: Codes Division, Insilicogen Inc., Yongin 446-908, Korea.
authors.forename: Kesavan
authors.initials: K
authors.lastname: Markkandan
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea.
authors.forename: Jun-Mo
authors.initials: JM
authors.lastname: Kang
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea.
authors.forename: Rajani
authors.initials: R
authors.lastname: Rai
authors.affiliation: Codes Division, Insilicogen Inc., Yongin 446-908, Korea.
authors.forename: Junhyung
authors.initials: J
authors.lastname: Park
authors.affiliation: School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea.
authors.forename: Jong-Joo
authors.initials: JJ
authors.lastname: Kim
keywords: Btau 4.6.1; Hanwoo; Next Generation Sequencing; Quantitative Trait Locus; Single Nucleotide Polymorphism [SNP]; UMD 3.1