title: A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae.
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.
authors.affiliation: Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Koboldt
authors.forename: Julia
authors.initials: J
authors.lastname: Staisch
authors.forename: Bavithra
authors.initials: B
authors.lastname: Thillainathan
authors.forename: Karen
authors.initials: K
authors.lastname: Haines
authors.forename: Scott E
authors.initials: SE
authors.lastname: Baird
authors.forename: Helen M
authors.initials: HM
authors.lastname: Chamberlin
authors.forename: Eric S
authors.initials: ES
authors.lastname: Haag
authors.forename: Raymond D
authors.initials: RD
authors.lastname: Miller
authors.forename: Bhagwati P
authors.initials: BP
authors.lastname: Gupta
mesh_terms: D000818:Animals; D002107:Caenorhabditis / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D054643:INDEL Mutation; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide
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