Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

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

Abstract

Single 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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Characteristics of 6222 predicted polymorphisms from CB4856.
Figure 2: A snip-SNP map of the nematode genome.
Figure 3: Linkage of dyf-5 to chromosome I using bulked segregant analysis.
Figure 4: The dyf-5 mutant was further localised to a small region to the right of centre on chromosome I by testing a higher density of markers on the same bulked lysates used in Fig. 3.

Similar content being viewed by others

References

  1. Kruglyak, L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet. 22, 139–144 (1999).

    Article  CAS  Google Scholar 

  2. Collins, F.S., Guyer, M.S. & Chakravarti, A. Variations on a theme: cataloguing human DNA sequence variation. Science 278, 1580–1581 (1997).

    Article  CAS  Google Scholar 

  3. Wang, D.G. et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082 (1997).

    Article  Google Scholar 

  4. Michelmore, R.W., Paran, I. & Kesseli, R.V. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. USA 88, 9828–983–. (1991).

    Article  CAS  Google Scholar 

  5. Koch, R., van Luenen, H.G.A.M., van der Horst, M., Thijssen, K.L. & Plasterk, R.H.A.P. Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans. Genome Res. 10, 1690–1696 (2000).

    Article  CAS  Google Scholar 

  6. Hodgkin, J. & Doniach, T. Natural variation and copulatory plug formation in Caenorhabditis elegans. Genetics 146, 149–164 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Starich, T.A. et al. Mutations affecting the chemosensory neurons of Caenorhabditis elegans. Genetics 139, 171–188 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. De Tomaso, A.W., Saito, Y., Ishizuka, K.J., Palemri, K.J. & Weisman, I.L. Mapping the genome of a model protochordate. I. A low resolution genetic map encompassing the fusion/histocompatibility (Fu/HC) locus of Botryllus schlosseri. Genetics 149, 277–287 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Kolchinsky, A., Landau-Ellis, D. & Gresshoff, P.M. Map order and linkage distances of molecular markers close to the supernodulation (nts-1) locus of soybean. Mol. Gen. Genet. 254, 29–36 (1997).

    Article  CAS  Google Scholar 

  10. Villar, M., Lefevre, F., Bradshaw, H.D.J. & Teissier du Cros, E. Molecular genetics of rust resistance in poplars by bulked segregant analysis in a 2x2 factorial mating design. Genetics 143, 531–536 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Severson, D.W., Zaitlin, D. & Kassner, V.A. Targeted identification of markers linked to malaria and filarioid nematode parasite resistance genes in the mosquito Aedes aegypti. Genet. Res. 73, 217–224 (1999).

    Article  CAS  Google Scholar 

  12. Mello, C.C., Kramer, J.M., Stinchcomb, D. & Ambros, V. Efficient gene transfer in C. elegans: extrachromosomal maintenance and integration of transforming sequences. EMBO J. 10, 3959–3970 (1991).

    Article  CAS  Google Scholar 

  13. Jakubowski, J. & Kornfeld, K. A local high-density, single-nucleotide polymorphism map used to clone Caenorhabditis elegans cdf-1. Genetics 153, 743–752 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Gilles, P.N., Wu, D.J., Foster, C.B., Dillon, P.J. & Chanock, S.J. Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nature Biotechnol. 17, 365–370 (1999).

    Article  CAS  Google Scholar 

  15. Kurian, K.M., Watson, C.J. & Wyllie, A.H. DNA chip technology. J. Pathol. 187, 267–271 (1999).

    Article  CAS  Google Scholar 

  16. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995).

    Article  CAS  Google Scholar 

  17. Reed, P.W. et al. Chromosome-specific microsatellite sets for fluorescence-based, semi- automated genome mapping. Nature Genet. 7, 390–395 (1994).

    Article  CAS  Google Scholar 

  18. de Bono, M. & Bargmann, C.I. Natural variation in a neuropeptide Y receptor homolog modifies social behavior and food response in C. elegans. Cell 94, 679–689 (1998).

    Article  CAS  Google Scholar 

  19. Ewing, B. & Green, P. Base-calling of automated traces using Phred. II. Error probabilities. Genome Res. 8, 186–194 (1998).

    Article  CAS  Google Scholar 

  20. Ewing, B., Hillier, L., Wendl, M.C. & Green, P. Base-calling of automated traces using Phred. I. Accuracy assessment. Genome Res. 8, 175–185 (1998).

    Article  CAS  Google Scholar 

  21. Bedell, J.A., Korf, I. & Gish, W. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics 16, 1040–1041 (2001).

    Article  Google Scholar 

  22. Marth, G.T. et al. A general approach to single-nucleotide polymorphism discovery. Nature Genet. 23, 452–456 (1999).

    Article  CAS  Google Scholar 

  23. Perkins, L.A., Hedgecock, E.M., Thomson, J.N. & Culotti, J.G. Mutant sensory cilia in the nematode C. elegans. Dev. Biol. 117, 456–487 (1986).

    Article  CAS  Google Scholar 

  24. Hedgecock, E.M., Culotti, J.G., Thomson, J.N. & Perkins, L.A. Axonal guidance mutants of Caenorhabditis elegans identified by filling sensory neurons with fluorescein dyes. Dev. Biol. 111, 158–170 (1985).

    Article  CAS  Google Scholar 

  25. Arratia, R., Lander, E.S., Tavare, S. & Waterman, M.S. Genomic mapping by anchoring random clones: a mathematical analysis. Genomics 11, 806–827 (1991).

    Article  CAS  Google Scholar 

  26. Petrov, D.A. & Hartl, D.L. Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc. Natl. Acad. Sci. USA 96, 1475–1479 (1999).

    Article  CAS  Google Scholar 

  27. Hacia, J.G. et al. Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nature Genet. 22, 164–167 (1999).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Nematode stocks were obtained from the Caenorhabditis Genetics Center. We thank S. Fischer, D. Weinkove and R. Korswagen for comments on the manuscript and numerous members of the C. elegans community who have contributed markers for this study.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ronald H.A. Plasterk.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wicks, S., Yeh, R., Gish, W. et al. Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat Genet 28, 160–164 (2001). https://doi.org/10.1038/88878

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/88878

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing