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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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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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.
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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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DOI: https://doi.org/10.1038/nmeth.1191
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