SNP and haplotype mapping for genetic analysis in the rat

Saar, K; Beck, Alfred; Bihoreau, MT; Birney, E; Brocklebank D, D; Chen, Y; Cuppen, E; Demonchy, S; Dopazo, J; Flicek, P; Foglio, M; Fujiyama, A; Gut, IG; Gauguier, D; Guigo, R; Guryev, V; Heinig, M; Hummel, O; Jahn, N; Klages, S; Kren, V; Kube, Michael; Kuhl, Heiner; Kuramoto, T; Kuroki, Y; Lechner, D; Lee, YA; Lopez-Bigas, N; Lathrop, GM; Mashimo, T; Medina, I; Mott, R; Patone, G; Perrier-Cornet, JA; Platzer, M; Pravenec, M; Reinhardt, Richard; Sakaki, Y; Schilhabel, M; Schulz, H; Serikawa, T; Shikhagaie, M; Tatsumoto, S; Taudien, S; Toyoda, A; Voigt, B.; Zelenika, D; Zimdahl, H; Hubner, N.; The STAR Consortium

doi:10.1038/ng.124

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SNP and haplotype mapping for genetic analysis in the rat

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Beck, Alfred
Computing (Head: Donald Buczek/Peter Marquardt), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Kube, Michael
High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society;

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Kuhl, Heiner
Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Manuela B. Urban), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Reinhardt, Richard
High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Saar, K., Beck, A., Bihoreau, M., Birney, E., Brocklebank D, D., Chen, Y., et al. (2008). SNP and haplotype mapping for genetic analysis in the rat. Nature Genetics, 40(5), 560-566. doi:10.1038/ng.124.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-8007-E

Abstract

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.