A radiation hybrid map of the zebrafish genome

Robert Geisler; Gerd Jörg Rauch; Herwig Baier; Frauke Van Bebber; Linda Broß; Marcus P.S. Dekens; Karin Finger; Cornelia Fricke; Michael A. Gates; Horst Geiger; Silke Geiger-Rudolph; Darren Gilmour; Stefanie Glaser; Lara Gnügge; Hinrich Habeck; Katy Hingst; Scott Holley; Jeremy Keenan; Anette Kirn; Holger Knaut; Deval Lashkari; Florian Maderspacher; Ulrike Martyn; Stephan Neuhauss; Carl Neumann; Teresa Nicolson; Francisco Pelegri; Russell Ray; Jens M. Rick; Henry Roehl; Tobias Roeser; Heike E. Schauerte; Alexander F. Schier; Ulrike Schönberger; Helia Berrit Schönthaler; Stefan Schulte-Merker; Catrin Seydler; William S. Talbot; Christian Weiler; Christiane Nüsslein-Volhard; Pascal Haffter

doi:10.1038/12692

A radiation hybrid map of the zebrafish genome

Robert Geisler, Gerd Jörg Rauch, Herwig Baier, Frauke Van Bebber, Linda Broß, Marcus P.S. Dekens, Karin Finger, Cornelia Fricke, Michael A. Gates, Horst Geiger, Silke Geiger-Rudolph, Darren Gilmour, Stefanie Glaser, Lara Gnügge, Hinrich Habeck, Katy Hingst, Scott Holley, Jeremy Keenan, Anette Kirn, Holger KnautDeval Lashkari, Florian Maderspacher, Ulrike Martyn, Stephan Neuhauss, Carl Neumann, Teresa Nicolson, Francisco Pelegri, Russell Ray, Jens M. Rick, Henry Roehl, Tobias Roeser, Heike E. Schauerte, Alexander F. Schier, Ulrike Schönberger, Helia Berrit Schönthaler, Stefan Schulte-Merker, Catrin Seydler, William S. Talbot, Christian Weiler, Christiane Nüsslein-Volhard, Pascal Haffter

Research output: Contribution to journal › Article › peer-review

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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 genes. Mutations can be cloned positionally, or placed on a simple sequence length polymorphism (SSLP) map to match them with mapped candidate genes and expressed sequence tags (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 minichromosomes. 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 resolutions, as well as for the dog, rat and mouse. For our map of the zebrafish genome, we used an existing RH panel 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.

Original language	English (US)
Pages (from-to)	86-89
Number of pages	4
Journal	Nature genetics
Volume	23
Issue number	1
DOIs	https://doi.org/10.1038/12692
State	Published - Sep 1999
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1038/12692

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Geisler, R., Rauch, G. J., Baier, H., Van Bebber, F., Broß, L., Dekens, M. P. S., Finger, K., Fricke, C., Gates, M. A., Geiger, H., Geiger-Rudolph, S., Gilmour, D., Glaser, S., Gnügge, L., Habeck, H., Hingst, K., Holley, S., Keenan, J., Kirn, A., ... Haffter, P. (1999). A radiation hybrid map of the zebrafish genome. Nature genetics, 23(1), 86-89. https://doi.org/10.1038/12692

Geisler, R, Rauch, GJ, Baier, H, Van Bebber, F, Broß, L, Dekens, MPS, Finger, K, Fricke, C, Gates, MA, Geiger, H, Geiger-Rudolph, S, Gilmour, D, Glaser, S, Gnügge, L, Habeck, H, Hingst, K, Holley, S, Keenan, J, Kirn, A, Knaut, H, Lashkari, D, Maderspacher, F, Martyn, U, Neuhauss, S, Neumann, C, Nicolson, T, Pelegri, F, Ray, R, Rick, JM, Roehl, H, Roeser, T, Schauerte, HE, Schier, AF, Schönberger, U, Schönthaler, HB, Schulte-Merker, S, Seydler, C, Talbot, WS, Weiler, C, Nüsslein-Volhard, C & Haffter, P 1999, 'A radiation hybrid map of the zebrafish genome', Nature genetics, vol. 23, no. 1, pp. 86-89. https://doi.org/10.1038/12692

@article{6447553b291b45ea94cf3a8c5591fc1d,

title = "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 genes. Mutations can be cloned positionally, or placed on a simple sequence length polymorphism (SSLP) map to match them with mapped candidate genes and expressed sequence tags (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 minichromosomes. 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 resolutions, as well as for the dog, rat and mouse. For our map of the zebrafish genome, we used an existing RH panel 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.",

author = "Robert Geisler and Rauch, {Gerd J{\"o}rg} and Herwig Baier and {Van Bebber}, Frauke and Linda Bro{\ss} and Dekens, {Marcus P.S.} and Karin Finger and Cornelia Fricke and Gates, {Michael A.} and Horst Geiger and Silke Geiger-Rudolph and Darren Gilmour and Stefanie Glaser and Lara Gn{\"u}gge and Hinrich Habeck and Katy Hingst and Scott Holley and Jeremy Keenan and Anette Kirn and Holger Knaut and Deval Lashkari and Florian Maderspacher and Ulrike Martyn and Stephan Neuhauss and Carl Neumann and Teresa Nicolson and Francisco Pelegri and Russell Ray and Rick, {Jens M.} and Henry Roehl and Tobias Roeser and Schauerte, {Heike E.} and Schier, {Alexander F.} and Ulrike Sch{\"o}nberger and Sch{\"o}nthaler, {Helia Berrit} and Stefan Schulte-Merker and Catrin Seydler and Talbot, {William S.} and Christian Weiler and Christiane N{\"u}sslein-Volhard and Pascal Haffter",

note = "Funding Information: 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.",

year = "1999",

month = sep,

doi = "10.1038/12692",

language = "English (US)",

volume = "23",

pages = "86--89",

journal = "Nature genetics",

issn = "1061-4036",

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number = "1",

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T1 - A radiation hybrid map of the zebrafish genome

AU - Geisler, Robert

AU - Rauch, Gerd Jörg

AU - Baier, Herwig

AU - Van Bebber, Frauke

AU - Broß, Linda

AU - Dekens, Marcus P.S.

AU - Finger, Karin

AU - Fricke, Cornelia

AU - Gates, Michael A.

AU - Geiger, Horst

AU - Geiger-Rudolph, Silke

AU - Gilmour, Darren

AU - Glaser, Stefanie

AU - Gnügge, Lara

AU - Habeck, Hinrich

AU - Hingst, Katy

AU - Holley, Scott

AU - Keenan, Jeremy

AU - Kirn, Anette

AU - Knaut, Holger

AU - Lashkari, Deval

AU - Maderspacher, Florian

AU - Martyn, Ulrike

AU - Neuhauss, Stephan

AU - Neumann, Carl

AU - Nicolson, Teresa

AU - Pelegri, Francisco

AU - Ray, Russell

AU - Rick, Jens M.

AU - Roehl, Henry

AU - Roeser, Tobias

AU - Schauerte, Heike E.

AU - Schier, Alexander F.

AU - Schönberger, Ulrike

AU - Schönthaler, Helia Berrit

AU - Schulte-Merker, Stefan

AU - Seydler, Catrin

AU - Talbot, William S.

AU - Weiler, Christian

AU - Nüsslein-Volhard, Christiane

AU - Haffter, Pascal

N1 - Funding Information: 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.

PY - 1999/9

Y1 - 1999/9

N2 - 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 genes. Mutations can be cloned positionally, or placed on a simple sequence length polymorphism (SSLP) map to match them with mapped candidate genes and expressed sequence tags (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 minichromosomes. 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 resolutions, as well as for the dog, rat and mouse. For our map of the zebrafish genome, we used an existing RH panel 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.

AB - 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 genes. Mutations can be cloned positionally, or placed on a simple sequence length polymorphism (SSLP) map to match them with mapped candidate genes and expressed sequence tags (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 minichromosomes. 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 resolutions, as well as for the dog, rat and mouse. For our map of the zebrafish genome, we used an existing RH panel 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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A radiation hybrid map of the zebrafish genome

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