Nature Genetics
28, 160 - 164 (2001)
doi:10.1038/88878
Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism mapStephen R. Wicks1, Raymond T. Yeh2, Warren R. Gish2, Robert H. Waterston2
& Ronald H.A. Plasterk11
The Hubrecht Laboratory and Center for Biomedical Genetics. Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands. 2
Washington University, Department of Genetics and Genome Sequencing Center. 4444 Forest Park Parkway, St. Louis, Missouri 63108, USA.
Correspondence should be addressed to Ronald H.A. Plasterk plasterk@niob.knaw.nlSingle nucleotide polymorphisms (SNPs) are valuable genetic markers of human disease1,
2,
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 mutations we have identified polymorphisms in CB4856, an isolate from a Hawaiian island that shows a uniformly high density of polymorphisms compared with the reference Bristol N2 strain. Based on 5.4 Mbp of aligned sequences, we predicted 6,222 polymorphisms. Furthermore, 3,457 of these markers modify restriction enzyme recognition sites ('snip-SNPs') and are therefore easily detected as RFLPs. Of these, 493 were experimentally confirmed by restriction digest to produce a snip-SNP map of the worm genome. A mapping strategy using snip-SNPs and bulked segregant analysis4 (BSA) is outlined. CB4856 is crossed into a mutant strain, and exclusion of CB4856 alleles of a subset 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 each form of the biallelic marker in populations of wildtype and mutant genomes. The usefulness of this approach is illustrated by the rapid mapping of the dyf-5 gene.
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