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Updated: Jul 11, 2026

A Rapid and Facile Pipeline for Generating Genomic Point Mutants in C. elegans Using CRISPR/Cas9 Ribonucleoproteins
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Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map.

S R Wicks1, R T Yeh, W R Gish

  • 1The Hubrecht Laboratory and Center for Biomedical Genetics. Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.

Nature Genetics
|May 31, 2001
PubMed
Summary

We identified thousands of single nucleotide polymorphisms (SNPs) in the CB4856 Caenorhabditis elegans strain, including many

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Single nucleotide polymorphisms (SNPs) are crucial genetic markers for human disease research.
  • SNPs offer high-density marker sets for mapping mutations in model organisms like Caenorhabditis elegans.
  • The CB4856 isolate from Hawaii exhibits a high density of polymorphisms compared to the standard Bristol N2 strain.

Purpose of the Study:

  • To identify and characterize polymorphisms in the CB4856 C. elegans strain for enhanced genetic mapping.
  • To develop a high-density genetic map using novel SNP markers.
  • To establish a strategy for positional cloning of mutations using these markers.

Main Methods:

  • Sequencing and alignment of 5.4 Mbp of CB4856 and N2 strains.

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  • Prediction and identification of single nucleotide polymorphisms (SNPs), focusing on those altering restriction enzyme sites ('snip-SNPs').
  • Experimental confirmation of snip-SNPs using restriction digests and development of a snip-SNP map.
  • Outlining a mapping strategy employing snip-SNPs and bulked segregant analysis (BSA).

    • Main Results:

    • Prediction of 6,222 polymorphisms between CB4856 and N2 strains.
    • Identification of 3,457 'snip-SNPs' easily detectable as restriction fragment length polymorphisms (RFLPs).
    • Experimental confirmation of 493 snip-SNPs, forming a genetic map of the C. elegans genome.
    • Successful rapid mapping of the dyf-5 gene using the developed snip-SNP and BSA strategy.

    Conclusions:

    • The CB4856 isolate provides a rich source of high-density genetic markers for C. elegans.
    • Snip-SNPs are effective markers for constructing high-resolution genetic maps.
    • The outlined strategy using snip-SNPs and BSA facilitates efficient positional cloning of mutations in C. elegans.