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Snipping away at wild worms
SNP collection in Hawaiian C. elegans strains
  
By Bijal P. Trivedi

A freezer at the University of Wisconsin in Madison houses an international consort of worms that lie suspended in time in small tubes, ready to be sent out to researchers all over the world. The worm, Caenorhabditis elegans (C. elegans) was the first animal to have its genome sequenced. Now Dutch researchers are probing random genetic sequences of specimens from Australia, California, Germany, Wisconsin, France, Canada and Hawaii, and comparing them with the UK's Bristol strain, whose entire genetic sequence is known. The goal is to find SNPs among the different stains.

The Dutch researchers report that C. elegans from Hawaii contains the greatest number of SNPs or single nucleotide polymorphisms. This is probably because the strains have been geographically isolated for so long, says Ronald Plasterk, of the Netherlands Institute for Developmental Biology, in Utrecht.

Plasterk and his colleagues also observed that the majority of SNPs are located on the arms of the chromosomes, whereas genes that are more conserved are closer to the center of the chromosome and contain fewer variations. The more variable genes are located further out on the arms of the chromosomes. The incidence of SNPs is 4.5 times more frequent in these regions, which suggests that these areas are evolving at a faster rate, says Plasterk. "The arms are the Wild West of the genome," he adds.

Classical genetics of any kind—whether its focus is the fly, human, or worm—is done by looking for an interesting mutant and then searching for the mutated gene responsible for the defect. Gene hunting can be done at a quicker pace if geneticist have unique signposts scattered throughout the genome that they could use to narrow down the region where a gene lies; the SNPs are these signposts.

Plasterk is collaborating with a team from Washington University to publish a collection of 17,000 SNPs from the Hawaii C. elegans.

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Koch, R. et al. Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans. Genome Res 10, 1690-1696 (December 2000).
 

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