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High-resolution, high-throughput SNP mapping in Drosophila melanogaster

Nature Methods volume 5, pages 323–329 (2008)Cite this article

Abstract

Single nucleotide polymorphisms (SNPs) are useful markers for genetic mapping experiments in model organisms. Here we report the establishment of a high-density SNP map and high-throughput genotyping assays for Drosophila melanogaster. Our map comprises 27,367 SNPs in common laboratory Drosophila stocks. These SNPs were clustered within 2,238 amplifiable markers at an average density of 1 marker every 50.3 kb, or 6.3 genes. We have also constructed a set of 62 Drosophila stocks, each of which facilitates the generation of recombinants within a defined genetic interval of 1–2 Mb. For flexible, high-throughput SNP genotyping, we used fluorescent tag-array mini-sequencing (TAMS) assays. We designed and validated TAMS assays for 293 SNPs at an average resolution of 391.3 kb, and demonstrated the utility of these tools by rapidly mapping 14 mutations that disrupt embryonic muscle patterning. These resources enable high-resolution high-throughput genetic mapping in Drosophila.

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Figure 1: Overall mapping strategy.
Figure 2: TAMS assays.
Figure 3: SNPmapper output for quality control and genetic mapping.
Figure 4: Mapping muscle morphogenesis mutants.

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References

  1. Davis, M.W. et al. Rapid single nucleotide polymorphism mapping in C. elegans. BMC Genomics 6, 118 (2005).

    Article  Google Scholar 

  2. Davis, M.W. & Hammarlund, M. Single-nucleotide polymorphism mapping. Methods Mol. Biol. 351, 75–92 (2006).

    CAS  PubMed  Google Scholar 

  3. Zipperlen, P. et al. A universal method for automated gene mapping. Genome Biol. 6, R19 (2005).

    Article  Google Scholar 

  4. Wicks, S.R., Yeh, R.T., Gish, W.R., Waterston, R.H. & Plasterk, R.H. Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat. Genet. 28, 160–164 (2001).

    Article  CAS  Google Scholar 

  5. Teeter, K. et al. Haplotype dimorphism in a SNP collection from Drosophila melanogaster. J. Exp. Zool. 288, 63–75 (2000).

    Article  CAS  Google Scholar 

  6. Berger, J. et al. Genetic mapping with SNP markers in Drosophila. Nat. Genet. 29, 475–481 (2001).

    Article  CAS  Google Scholar 

  7. Hoskins, R.A. et al. Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster. Genome Res. 11, 1100–1113 (2001).

    Article  CAS  Google Scholar 

  8. Martin, S.G., Dobi, K.C. & St. Johnston, D. A rapid method to map mutations in Drosophila. Genome Biol. 2, Research0036 (2001).

    Article  CAS  Google Scholar 

  9. Stickney, H.L. et al. Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res. 12, 1929–1934 (2002).

    Article  CAS  Google Scholar 

  10. Cho, R.J. et al. Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat. Genet. 23, 203–207 (1999).

    Article  CAS  Google Scholar 

  11. Torjek, O. et al. Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis. Plant J. 36, 122–140 (2003).

    Article  CAS  Google Scholar 

  12. Nairz, K., Stocker, H., Schindelholz, B. & Hafen, E. High-resolution SNP mapping by denaturing HPLC. Proc. Natl. Acad. Sci. USA 99, 10575–10580 (2002).

    Article  CAS  Google Scholar 

  13. Underhill, P.A. et al. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 7, 996–1005 (1997).

    Article  CAS  Google Scholar 

  14. Orita, M., Iwahana, H., Kanazawa, H., Hayashi, K. & Sekiya, T. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86, 2766–2770 (1989).

    Article  CAS  Google Scholar 

  15. Macdonald, S.J., Pastinen, T., Genissel, A., Cornforth, T.W. & Long, A.D. A low-cost open-source SNP genotyping platform for association mapping applications. Genome Biol. 6, R105 (2005).

    Article  Google Scholar 

  16. Xu, T. & Rubin, G.M. Analysis of genetic mosaics in developing and adult Drosophila tissues. Development 117, 1223–1237 (1993).

    CAS  Google Scholar 

  17. Rorth, P. et al. Systematic gain-of-function genetics in Drosophila. Development 125, 1049–1057 (1998).

    CAS  PubMed  Google Scholar 

  18. Lindroos, K., Sigurdsson, S., Johansson, K., Ronnblom, L. & Syvänen, A.C. Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Res. 30, e70 (2002).

    Article  Google Scholar 

  19. Lovmar, L., Fredriksson, M., Liljedahl, U., Sigurdsson, S. & Syvänen, A.C. Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA. Nucleic Acids Res. 31, e129 (2003).

    Article  Google Scholar 

  20. Bradley, P.S., Mangasarian, O.L. & Street, W.N. Clustering via concave minimization. in Advances in Neural Information Processing Systems (eds., Mozer, M.C., Jordan, M.I. & Petsche, T.) 368–374 (MIT Press, Cambridge, Massachusetts, 1997).

    Google Scholar 

  21. Jain, A.K. & Dubes, R.C. Algorithms for Clustering Data. (Prentice-Hall, Englewood Cliffs, New Jersey, 1988).

    Google Scholar 

  22. Schnorrer, F., Kalchhauser, I. & Dickson, B.J. The transmembrane protein kon-tiki couples to Dgrip to mediate myotube targeting in Drosophila. Dev. Cell 12, 751–766 (2007).

    Article  CAS  Google Scholar 

  23. Ryder, E. et al. The DROSDEL collection: A set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster. Genetics 167, 797–813 (2004).

    Article  CAS  Google Scholar 

  24. Parks, A.L. et al. Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome. Nat. Genet. 36, 288–292 (2004).

    Article  CAS  Google Scholar 

  25. Steemers, F.J. et al. Whole-genome genotyping with the single-base extension assay. Nat. Methods 3, 31–33 (2006).

    Article  CAS  Google Scholar 

  26. Kurg, A. et al. Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology. Genet. Test. 4, 1–7 (2000).

    Article  CAS  Google Scholar 

  27. Banér, J. et al. Parallel gene analysis with allele-specific padlock probes and tag microarrays. Nucleic Acids Res. 31, e103 (2003).

    Article  Google Scholar 

  28. Fan, J.B. et al. Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68, 69–78 (2003).

    Article  CAS  Google Scholar 

  29. Hardenbol, P. et al. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21, 673–678 (2003).

    Article  CAS  Google Scholar 

  30. Chen, E.H. & Olson, E.N. Antisocial, an intracellular adaptor protein, is required for myoblast fusion in Drosophila. Dev. Cell 1, 705–715 (2001).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank J. Berger and T. Suzuki for initial help in the creation of the SNP map, R. Figueroa for printing the tag arrays, S. Krüttner for help mapping the muscle mutants, J. Saharinen for the SNPSnapper v4.0 software (National Public Health Institute, Finland), and J. Braisted and N. Bhagabati for support in using the source code of the Multiple Experiment Viewer. This work was supported by funds from the EU Fifth Framework Programme, the Austrian Science Fund, and the Swedish Research Council for Science and Technology. Work at the IMP is supported by Boehringer Ingelheim GmbH. F.S. was supported by a long term fellowship from the Human Frontier Science Program.

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Author notes

  1. Doris Chen, Annika Ahlford and Frank Schnorrer: These authors contributed equally to this work.

Authors and Affiliations

  1. Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, Vienna, A-1030, Austria

    Doris Chen, Frank Schnorrer, Irene Kalchhauser, Michaela Fellner & Barry J Dickson

  2. Department of Medical Sciences, Uppsala University, Molecular Medicine, Ing70 3tr foavd2, Uppsala, S-75185, Sweden

    Annika Ahlford & Ann-Christine Syvänen

  3. Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr-Gasse 3-5, Vienna, A-1030, Austria

    Michaela Fellner

  4. Biological Research Centre, Hungarian Academy of Sciences, Temesvari kft. 62, P.P. Box 521, Szeged, H-6701, Hungary

    Erika Viràgh & Istvàn Kiss

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  1. Doris Chen
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Contributions

D.C. and M.F. generated the SNP map; D.C. developed SNPmapper; A.A., D.C. and F.S. established the TAMS assays; E.V. and Is.K. generated and M.F., E.V. and D.C. verified the 2EP stocks; F.S. generated the muscle mutants; F.S., Ir.K., A.A. and D.C. mapped the muscle mutants; B.J.D. and A.-C.S. coordinated the project; D.C., A.A., F.S., A.-C.S. and B.J.D. wrote the manuscript.

Corresponding authors

Correspondence to Ann-Christine Syvänen or Barry J Dickson.

Supplementary information

Supplementary Text and Figures

Supplementary Figure 1, Supplementary Tables 1–4, Supplementary Methods (PDF 812 kb)

Supplementary Table 5

Pre-computed 2EP TAMS assays. (XLS 562 kb)

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Chen, D., Ahlford, A., Schnorrer, F. et al. High-resolution, high-throughput SNP mapping in Drosophila melanogaster. Nat Methods 5, 323–329 (2008). https://doi.org/10.1038/nmeth.1191

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