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Open Access Research article

A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

Daniel C Koboldt1, Julia Staisch1, Bavithra Thillainathan2, Karen Haines2, Scott E Baird3, Helen M Chamberlin4, Eric S Haag5, Raymond D Miller1 and Bhagwati P Gupta2*

Author Affiliations

1 Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA

2 Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada

3 Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA

4 Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA

5 Department of Biology, University of Maryland, College Park, MD 20742, USA

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BMC Genomics 2010, 11:236  doi:10.1186/1471-2164-11-236

Published: 13 April 2010

Abstract

Background

The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers.

Results

We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 bp and 2 kb. We established bulk segregant and single animal-based PCR assay conditions and used these to test 107 polymorphisms. A total of 75 polymorphisms, consisting of 14 snip-SNPs and 61 indels, were experimentally confirmed with an overall success rate of 83%. The utility of polymorphisms in genetic studies was demonstrated by successful mapping of 12 mutations, including 5 that were localized to sub-chromosomal regions. Our mapping experiments have also revealed one case of a misassembled contig on chromosome 3.

Conclusions

We report a comprehensive set of polymorphisms in C. briggsae wild-type strains and demonstrate their use in mapping mutations. We also show that molecular markers can be useful tools to improve the C. briggsae genome sequence assembly. Our polymorphism resource promises to accelerate genetic and functional studies of C. briggsae genes.