Technical Report abstract
Nature Genetics 40, 560 - 566 (2008)
Published online: 28 April 2008 | doi:10.1038/ng.124
SNP and haplotype mapping for genetic analysis in the rat
The STAR Consortium
The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.
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Max-Delbrück Center for Molecular Medicine, Robert-Rossle-Stra
e 10, 13125 Berlin, Germany. -
Max Planck Institute for Molecular Genetics, Ihnestrae 63-73, 14195 Berlin, Germany.
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK.
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
- Commissariat à l'Énergie Atomique, Institut de Génomique, Centre National de Génotypage, 2 rue Gaston Crémieux CP 5721, 91 057 Evry Cedex, France.
- Department of Bioinformatics, and Functional Genomics Node, Centro de Investigación Príncipe Felipe, Avenida Autopista del Saler 16, 46012 Valencia, Spain.
- RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo, 101-8430, Japan.
- Center for Genomic Regulation, C/Dr. Aiguader 88, Barcelona Biomedical Research Park Building, 08003 Barcelona, Catalonia, Spain.
- Experimental and Health Science Department, Universitat Pompeu Fabra, C/Dr. Aiguader 88, Barcelona Biomedical Research Park Building, 08003 Barcelona, Catalonia, Spain.
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Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstrae 11, 07745 Jena, Germany.
- Institute of Physiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic.
- Institute of Biology and Medical Genetics, First Medical Faculty, Charles University, Albertov 4, 12800 Prague 2, Czech Republic.
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
- Pediatric Pneumology and Immunology, Charite, Campus Virchow Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany.
Correspondence to: e-mail: nhuebner@mdc-berlin.de
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