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A novel genetic variant database for Korean native cattle (Hanwoo): HanwooGDB

Author:
Kim, Kwondo, Kwak, Woori, Sung, Sam-Sun, Cho, Seoae, Kim, Heebal, Yoon, Duhak, Lee, Hyun-Jeong
Source:
Genes & genomics 2015 v.37 no.1 pp. 15-22
ISSN:
1976-9571
Subject:
breeding, cattle, databases, draft animals, genome, high-throughput nucleotide sequencing, single nucleotide polymorphism, Korean Peninsula
Abstract:
Korean native cattle, known as Hanwoo, have been raised in the Korean Peninsula since 2000 B.C. for use as a draft animal. However, Hanwoo now have an important position in the Korean livestock industry as a meat source. Therefore, the breeding and selection of Hanwoo are crucial for the industry. Although many researchers have studied the genetic architecture of Hanwoo, no well-established Hanwoo-related databases exist. In order to better understand the genetic contents of Hanwoo, an integrated database is necessary. We constructed a genetic variants database including annotation information. HanwooGDB (http://hanwoogdb.snu.ac.kr) provides genetic variants (SNPs, INDELs, CNVs) in the Hanwoo genome produced by Next Generation Sequencing data collected from 23 cattle. The identified SNPs were integrated with SNP chip data and annotation information for checking the concordance of position of each SNP and inferring functional aspects. This database provides browsers to understand and visualize the comprehensive information of these variants and allows users to download data according to their preference from this database without limitation. This database will contribute to genetic research and development of Hanwoo breeding strategies.
Agid:
1196621