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Open Access Highly Accessed Methodology article

Rapid single nucleotide polymorphism mapping in C. elegans

M Wayne Davis, Marc Hammarlund, Tracey Harrach, Patrick Hullett, Shawn Olsen and Erik M Jorgensen*

Author Affiliations

Department of Biology, University of Utah, Salt Lake City, Utah 84112-0840, USA

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BMC Genomics 2005, 6:118  doi:10.1186/1471-2164-6-118

Published: 12 September 2005

Abstract

Background

In C. elegans, single nucleotide polymorphisms (SNPs) can function as silent genetic markers, with applications ranging from classical two- and three-factor mapping to measuring recombination across whole chromosomes.

Results

Here, we describe a set of 48 primer pairs that flank SNPs evenly spaced across the C. elegans genome and that work under identical PCR conditions. Each SNP in this set alters a DraI site, enabling rapid and parallel scoring. We describe a procedure using these reagents to quickly and reliably map mutations. We show that these techniques correctly map a known gene, dpy-5. We then use these techniques to map mutations in an uncharacterized strain, and show that its behavioral phenotype can be simultaneously mapped to three loci.

Conclusion

Together, the reagents and methods described represent a significant advance in the accurate, rapid and inexpensive mapping of genes in C. elegans.