Animal QTL database: Development and Release Notes

This work has been published

X-P. Li et al. Development of an in silico coding gene SNP map in pigs Animal Genetics, Volume39, Issue4, August 2008, Pages 446-450. DOI: https://doi.org/10.1111/j.1365-2052.2008.01727.x

Development and characterization of an in silico Coding Gene SNP map in pigs

Xiao-Ping Li¹, Zhi-Liang Hu², Kyungtag Do¹, Sunjin Moon³, Youkyoung Ha¹, Heebal Kim³, Max F. Rothschild², James M Reecy² and Kwan Suk Kim¹

1. Department of Animal Science, Chungbuk National University, Cheongju, South Korea

2. Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011-3150, USA

3. Department of Food and Animal Biotechnology, Seoul National University, Seoul, Korea

(Paper in press)

ABSTRACT:

A total of 5,450 sequences obtained from NCBI pig SNP database were consolidated into 465 unique sequences (185 single sequences and 280 contigs). These 465 sequences containing 1,553 public SNPs showed high homology to 433 human genes from BLAST analysis, and were assigned to the pig QTL maps (http://www.animalgenome.org/QTLdb/pig.html) via the human and pig comparative map established by a pig RH map. The SNP information characterized from this study provides a useful functional gene variation resource to facilitate QTL data mining in the pig genome.

Acknowledgement:

This work was supported by a research program of National Livestock Research Institute, a grant from BioGreen 21 program of Korea Rural Administration (Grant no. 20050401034804), and partly by the U.S. NRSP-8 Bioinformatics Coordination Program.