Rapid single nucleotide polymorphism mapping in C. elegans

BMC Genomics. 2005 Sep 12;6:118. doi: 10.1186/1471-2164-6-118.


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.

MeSH terms

  • Animals
  • Caenorhabditis elegans / genetics*
  • Chromosome Mapping / methods*
  • DNA Primers / chemistry
  • Female
  • Genetic Linkage
  • Genetic Markers
  • Genome
  • Male
  • Models, Genetic
  • Mutation
  • Nucleotide Mapping
  • Phenotype
  • Physical Chromosome Mapping
  • Polymerase Chain Reaction
  • Polymorphism, Single Nucleotide*
  • Recombination, Genetic


  • DNA Primers
  • Genetic Markers