SNP and haplotype mapping for genetic analysis in the rat.

TitleSNP and haplotype mapping for genetic analysis in the rat.
Publication TypeJournal Article
Year of Publication2008
AuthorsSaar, 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, IG, Gauguier, D, Guigó, 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, G Lathrop, 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, Hubner, N
Corporate AuthorsSTAR Consortium
JournalNat Genet
Volume40
Issue5
Pagination560-6
Date Published2008 May
ISSN1546-1718
KeywordsAnimals; Chromosome Mapping; Databases, Genetic; Genome; Haplotypes; Linkage Disequilibrium; Phylogeny; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Rats; Rats, Inbred Strains; Recombination, Genetic
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.

DOI10.1038/ng.124
Alternate JournalNat. Genet.
PubMed ID18443594
PubMed Central IDPMC5915293
Grant List / / Wellcome Trust / United Kingdom
062023 / / Wellcome Trust / United Kingdom
057733/Z/99/A / / Wellcome Trust / United Kingdom
066780/Z/01/Z / / Wellcome Trust / United Kingdom