Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map

Single nucleotide polymorphisms (SNPs) are valuable genetic markers of huma n disease(1-3). They also comprise the highest potential density marker set available for mapping experimentally derived mutations in model organisms such as Caenorhabditis elegans. To facilitate the positional cloning of mut ations we have identified polymorphisms in CB4856, an isolate from a Hawaii an island that shows a uniformly high density of polymorphisms compared wit h the reference Bristol N2 strain. Based on 5.4 Mbp of aligned sequences, w e predicted 6.222 polymorphisms. Furthermore, 3,457 of these markers modify restriction enzyme recognition sites ('snip-SNPs') and are therefore easil y detected as RFLPs. Of these, 493 were experimentally confirmed by restric tion digest to produce a snip-SNP map of the worm genome. A mapping strateg y using snip-SNPs and bulked segregant analysis(4) (BSA) is outlined. CB485 6 is crossed into a mutant strain, and exclusion of CB4856 alleles of a sub set of snip-SNPs in mutant progeny is assesed with BSA. The proximity of a linked marker to the mutation is estimated by the relative proportion of ea ch form of the biallelic marker in populations of wildtype and mutant genom es. The usefulness of this approach is illustrated by the rapid mapping of the dyf-5 gene.