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A new framework marker-based linkage map and SDPs for the Rat HXB/BXH strain set

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Abstract

A new contiguous genetic linkage map of the HXB/BXH set of rat recombinant inbred (RI) strains was constructed to enhance QTL mapping power and precision, and thereby make the RI strain set a better genomics resource. The HXB/BXH rat RI strains were developed from a cross between the hypertensive SHR/OlaIpcv and normotensive BN-Lx/Cub rat strains and have been shown useful for identifying quantitative trait loci (QTL) for a variety of cardiovascular, metabolic, and behavioral phenotypes. In the current analysis, the DNAs from 31 existing strains, 1 substrain, and 4 extinct strains were genotyped for a selection of polymorphic microsatellite marker loci, predominantly polymorphic framework markers from high-density integrated rat genome maps. The resulting linkage map consists of 245 microsatellite markers spanning a total length of 1789 cM with an average inter-marker distance of ~8.0 cM. This map covers the rat genome contiguously and completely with the exception of two locations on Chromosomes (Chrs) 11 and 16. The new genotypic information obtained also permitted further genetic characterization of the RI strain set including strain independence, genetic similarity among the individual strains, and non-syntenic associations between loci.

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Acknowledgements

We acknowledge the advice and guidance of Drs. M. Anne Spence and Pam Flodman in the early stages of this effort, and the valuable contributions of the Rat Genome Database and of Dr. Fredrik Stahl and the RatMap staff for accommodating our data in the RatMap web site. This research was supported by the following grants: NIH PO1 HL-35018 (to M.P. Printz); U01 HL69758-02 and U01 HL64777-04 (to N.J. Schork); UCSD Academic Senate Grant (to M. Jirout and M.P. Printz); and GA CR 204/98/K015 (to V. Křen and M. Pravenec); M. Pravenec is an International Research Scholar of the Howard Hughes Medical Institute.

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Authors and Affiliations

  1. Dept of Pharmacology 0636, University of California San Diego, La Jolla, California 92093-0636, USA

    Martin Jirout, Laura Breen & Morton P. Printz

  2. Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague,

    Martin Jirout, Drahomíra Křenová, Vladimír Křen & Michal Pravenec

  3. The Academy of Sciences of the Czech Republic and Centre for Integrated Genomics, Videnska, Prague, Czech Republic

    Vladimír Křen & Michal Pravenec

  4. Dept of Psychiatry, University of California San Diego, La Jolla, California, USA

    Nicholas J. Schork

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  1. Martin Jirout
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  2. Drahomíra Křenová
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  3. Vladimír Křen
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  4. Laura Breen
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  5. Michal Pravenec
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  6. Nicholas J. Schork
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  7. Morton P. Printz
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Correspondence to Martin Jirout.

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Jirout, M., Křenová, D., Křen, V. et al. A new framework marker-based linkage map and SDPs for the Rat HXB/BXH strain set . Mamm Genome 14, 537–546 (2003). https://doi.org/10.1007/s00335-003-2266-z

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  • DOI: https://doi.org/10.1007/s00335-003-2266-z

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