SNP and haplotype mapping for genetic analysis in the rat

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Item Type:	Article
Title:	SNP and haplotype mapping for genetic analysis in the rat
Creators Name:	Saar, K., Beck, A., Bihoreau, M.T., Birney, E., Brocklebank, D., Chen, Y., Cuppen, E., Demonchy, S., Dopazo, J., Flicek, P., Foglio, M., Fujiyama, A., Gut, I.G., Gauguier, D., Guigo, R., Guryev, V., Heinig, M., Hummel, O., Jahn, N., Klages, S., Kren, V., Kube, M., Kuhl, H., Kuramoto, T., Kuroki, Y., Lechner, D., Lee, Y.A., Lopez-Bigas, N., Lathrop, G.M., Mashimo, T., Medina, I., Mott, R., Patone, G., Perrier-Cornet, J.A., Platzer, M., Pravenec, M., Reinhardt, R., Sakaki, Y., Schilhabel, M., Schulz, H., Serikawa, T., Shikhagaie, M., Tatsumoto, S., Taudien, S., Toyoda, A., Voigt, B., Zelenika, D., Zimdahl, H. and Huebner, N.
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 F(2) 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.
Keywords:	Chromosome Mapping, Genetic Databases, Genome, Haplotypes, Linkage Disequilibrium, Phylogeny, Single Nucleotide Polymorphism, Quantitative Trait Loci, Inbred Strains Rats, Genetic Recombination, Animals, Rats
Source:	Nature Genetics
ISSN:	1061-4036
Publisher:	Nature Publishing Group
Volume:	40
Number:	5
Page Range:	560-566
Date:	May 2008
Official Publication:	https://doi.org/10.1038/ng.124
PubMed:	View item in PubMed

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