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A major zebrafish polymorphism resource for genetic mapping

Kevin M Bradley1, J Bradford Elmore1, Joan P Breyer1, Brian L Yaspan23, Jason R Jessen1, Ela W Knapik1 and Jeffrey R Smith1234*

Author Affiliations

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

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

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

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

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Genome Biology 2007, 8:R55  doi:10.1186/gb-2007-8-4-r55

Published: 11 April 2007

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.