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Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB

  • Lee, Joon-Ho (Genomic Informatics Center, Hankyong National University) ;
  • Lee, Taeheon (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Lee, Hak-Kyo (Genomic Informatics Center, Hankyong National University) ;
  • Cho, Byung-Wook (Department of Animal Science, College of Life Sciences, Pusan National University) ;
  • Shin, Dong-Hyun (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Do, Kyoung-Tag (Department of Equine Sciences, Sorabol College) ;
  • Sung, Samsun (C&K Genomics, Seoul National University Research) ;
  • Kwak, Woori (C&K Genomics, Seoul National University Research) ;
  • Kim, Hyeon Jeong (C&K Genomics, Seoul National University Research) ;
  • Kim, Heebal (Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Cho, Seoae (C&K Genomics, Seoul National University Research) ;
  • Park, Kyung-Do (Genomic Informatics Center, Hankyong National University)
  • Received : 2013.11.04
  • Accepted : 2014.06.21
  • Published : 2014.09.01

Abstract

Genetics is important for breeding and selection of horses but there is a lack of well-established horse-related browsers or databases. In order to better understand horses, more variants and other integrated information are needed. Thus, we construct a horse genomic variants database including expression and other information. Horse Single Nucleotide Polymorphism and Expression Database (HSDB) (http://snugenome2.snu.ac.kr/HSDB) provides the number of unexplored genomic variants still remaining to be identified in the horse genome including rare variants by using population genome sequences of eighteen horses and RNA-seq of four horses. The identified single nucleotide polymorphisms (SNPs) were confirmed by comparing them with SNP chip data and variants of RNA-seq, which showed a concordance level of 99.02% and 96.6%, respectively. Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants. The database will contribute to genetic improvement and breeding strategies of Thoroughbreds.

Keywords

Database;Thoroughbred;Variants;Expression;Horse

Acknowledgement

Supported by : Rural Development Administration

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