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A radiation hybrid map of the zebrafish genome

Abstract

Recent large-scale mutagenesis screens have made the zebrafish the first vertebrate organism to allow a forward genetic approach to the discovery of developmental control genes1,2,3. Mutations can be cloned positionally, or placed on a simple sequence length polymorphism (SSLP) map4,5,6 to match them with mapped candidate genes and expressed sequence tags7,8 (ESTs). To facilitate the mapping of candidate genes and to increase the density of markers available for positional cloning, we have created a radiation hybrid (RH) map of the zebrafish genome. This technique is based on somatic cell hybrid lines produced by fusion of lethally irradiated cells of the species of interest with a rodent cell line. Random fragments of the donor chromosomes are integrated into recipient chromosomes or retained as separate minichromosomes9,10. The radiation-induced breakpoints can be used for mapping in a manner analogous to genetic mapping, but at higher resolution and without a need for polymorphism. Genome-wide maps exist for the human, based on three RH panels of different resolutions11,12,13, as well as for the dog14, rat15 and mouse16,17. For our map of the zebrafish genome, we used an existing RH panel18,19 and 1,451 sequence tagged site (STS) markers, including SSLPs, cloned candidate genes and ESTs. Of these, 1,275 (87.9%) have significant linkage to at least one other marker. The fraction of ESTs with significant linkage, which can be used as an estimate of map coverage, is 81.9%. We found the average marker retention frequency to be 18.4%. One cR3000 is equivalent to 61 kb, resulting in a potential resolution of approximately 350 kb.

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References

  1. 1

    Driever, W. et al. A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123, 37– 46 (1996).

  2. 2

    Haffter, P. et al. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development 123, 1–36 (1996).

  3. 3

    Haffter, P. & Nüsslein-Volhard, C. Large scale genetics in a small vertebrate, the zebrafish. Int. J. Dev. Biol. 40, 221–227 (1996).

  4. 4

    Knapik, E.W. et al. A reference cross DNA panel for zebrafish (Danio rerio) anchored with simple sequence length polymorphisms. Development 123, 451–460 (1996).

  5. 5

    Knapik, E.W. et al. A microsatellite genetic linkage map for zebrafish (Danio rerio). Nature Genet. 18, 338– 343 (1998).

  6. 6

    Shimoda, N. et al. Zebrafish genetic map with 2000 microsatellite markers. Genomics 58, 219–232 ( 1999).

  7. 7

    Postlethwait, J.H. et al. Vertebrate genome evolution and the zebrafish gene map. Nature Genet. 18, 345– 349 (1998).

  8. 8

    Gates, M.A. et al. A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome Res. 9, 334–347 ( 1999).

  9. 9

    Goss, S.J. & Harris, H. New method for mapping genes in human chromosomes. Nature 255, 680– 684 (1975).

  10. 10

    Walter, M.A., Spillett, D.J., Thomas, P., Weissenbach, J. & Goodfellow, P.N. A method for constructing radiation hybrid maps of whole genomes. Nature Genet. 7, 22–28 (1994).

  11. 11

    Hudson, T.J. et al. An STS-based map of the human genome. Science 270, 1945–1954 ( 1995).

  12. 12

    Gyapay, G. et al. A radiation hybrid map of the human genome. Hum. Mol. Genet. 5, 339–346 ( 1996).

  13. 13

    Stewart, E.A. et al. An STS-based radiation hybrid map of the human genome. Genome Res. 7, 422–433 ( 1997).

  14. 14

    Priat, C. et al. A whole-genome radiation hybrid map of the dog genome. Genomics 54, 361–378 ( 1998).

  15. 15

    Watanabe, T.K. et al. A radiation hybrid map of the rat genome containing 5,255 markers. Nature Genet. 22, 27– 36 (1999).

  16. 16

    McCarthy, L.C. et al. A first-generation whole genome-radiation hybrid map spanning the mouse genome. Genome Res. 7, 1153–1161 (1997).

  17. 17

    Van Etten, W.J. et al. Radiation hybrid map of the mouse genome. Nature Genet. 22, 384–387 (1999).

  18. 18

    Kwok, C. et al. Characterization of whole genome radiation hybrid mapping resources for non-mammalian vertebrates. Nucleic Acids Res. 26 , 3562–3566 (1998).

  19. 19

    Kwok, C., Critcher, R. & Schmitt, K. Construction and characterization of zebrafish whole genome radiation hybrids. Methods Cell Biol. 60, 287–302 (1999).

  20. 20

    Cox, D.R., Burmeister, M., Price, E.R., Kim, S. & Myers, R.M. Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science 250, 245–250 (1990).

  21. 21

    Boehnke, M., Lange, K. & Cox, D.R. Statistical methods for multipoint radiation hybrid mapping. Am. J. Hum. Genet. 49, 1174– 1188 (1991).

  22. 22

    Hinegardner, R. & Rosen, D.E. Cellular DNA content and the evolution of teleostean fishes. Am. Natur. 166, 621–644 (1972).

  23. 23

    Bennet, M.D. & Smith, J.B. Nuclear DNA amounts in angiosperms. Philos. Trans. R. Soc. Lond. B 274, 227 –273 (1976).

  24. 24

    Hukriede, N. et al. Radiation hybrid mapping of the zebrafish genome. Proc. Natl Acad. Sci. USA (in press).

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Acknowledgements

We thank F. Bonhoeffer for support of our project; N. Shimoda, D. Jackson and M. Fishman for genetic map data and primer sequences; and N. Hukriede for helpful discussions. W.S.T. is supported by NIH grant R01RR12349. P.H. is supported by a grant from the German Human Genome Project.

Author information

Correspondence to Robert Geisler.

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Table 2 (PDF 34 kb)

Figure 1 (PDF 118 kb)

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Figure 1: Radiation hybrid map of zebrafish chromosome LG1 anchored to the published genetic map5,6.
Figure 2: Marker retention of the zebrafish radiation hybrid panel.