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

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• 作者：Kwondo Kim (1)
  Woori Kwak (2) (3)
  Sam-Sun Sung (2)
  Seoae Cho (2)
  Heebal Kim (1) (2) (3)
  Duhak Yoon (4)
  Hyun-Jeong Lee (5)
  
• 关键词：Database ; Hanwoo ; Genetic variants ; SNP ; Cattle
• 刊名：Genes & Genomics
• 出版年：2015
• 出版时间：January 2015
• 年：2015
• 卷：37
• 期：1
• 页码：15-22
• 全文大小：1,334 KB
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• 作者单位：Kwondo Kim (1)
  Woori Kwak (2) (3)
  Sam-Sun Sung (2)
  Seoae Cho (2)
  Heebal Kim (1) (2) (3)
  Duhak Yoon (4)
  Hyun-Jeong Lee (5)
  
  1. Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea
  2. C&K Genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea
  3. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea
  4. Department of Animal Science, Kyungpook National University, Sangju, 742-711, Republic of Korea
  5. Division of Animal Genomics and Bioinformatics, National Institute of Animal science, Rural Development Administration, #564 Omockchun-dong, Suwon, 441-706, Republic of Korea
  
• ISSN：2092-9293

文摘

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.