Snip-SNPs in the worm genome

SNPs (single nucleotide polymorphisms) are valuable markers for mapping mutations and human disease-related genes. In the June issue of Nature Genetics, Wicks et al. describe a SNP-based strategy for rapid mapping in the C. elegans genome (Nature Genetics 2001, 28:160-164). They sequenced the entire genome of the CB4856 Hawaiian worm isolate and compared it with the standard laboratory wild type strain (Bristol N2). This alignment identified 6,222 potential polymorphisms, more than half of which modify restriction enzyme sites (referred to as 'snip-SNPs'). Such a high-density map of snip-SNPs (about one every 200 kb) allows for rapid mapping of gene mutations using RFLP analysis. To demonstrate the efficiency of such a mapping approach, Wicks et al. used their snip-SNP map and bulked segregant analysis to localize the dyf-5gene. They claim that the successful mapping could be achieved with 36 PCR reactions within 12 hours of isolating F2 animals from a single cross between CB4856 and N2 strains.