A major zebrafish polymorphism resource for genetic mapping

Kevin M Bradley¹ , J Bradford Elmore¹ , Joan P Breyer¹ , Brian L Yaspan²^,3 , Jason R Jessen¹ , Ela W Knapik¹ and Jeffrey R Smith¹^,2^,3^,4

¹Department of Medicine, Vanderbilt University School of Medicine, Garland Avenue, Nashville, TN 37232-0275, USA

²Department of Cancer Biology, Vanderbilt University School of Medicine, Garland Avenue, Nashville, TN 37232-0275, USA

³Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Garland Avenue, Nashville, TN 37232-0275, USA

⁴Medical Research Service, VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA

author email corresponding author email

Genome Biology 2007, 8:R55doi:10.1186/gb-2007-8-4-r55


Published:	11 April 2007

Subject areas: Genome studies, Model organisms, Methods

Abstract

We have identified 645,088 candidate polymorphisms in zebrafish and observe a single nucleotide polymorphism (SNP) validation rate of 71% to 86%, improving with polymorphism confidence score. Variant sites are non-random, with an excess of specific novel T- and A-rich motifs. We positioned half of the polymorphisms on zebrafish genetic and physical maps as a resource for positional cloning. We further demonstrate bulked segregant analysis using the anchored SNPs as a method for high-throughput genetic mapping in zebrafish.