TitleSNP and haplotype mapping for genetic analysis in the rat.
Publication TypeJournal Article
Year of Publication2008
AuthorsConsortium STAR, Saar K, Beck A, Bihoreau M-TT, Birney E, Brocklebank 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 M, Kuhl H, Kuramoto T, Kuroki Y, Lechner D, Lee Y-AA, Lopez-Bigas N, Lathrop MG, Mashimo T, Medina I, Mott R, Patone G, Perrier-Cornet J-AA, 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
JournalNat Genet
Volume40
Pagination560-6
Date Published5
ISSN1546-1718
KeywordsAnimals, Chromosome Mapping, Databases, Genetic, Genome, Haplotypes, Inbred Strains, Linkage Disequilibrium, non-u.s. gov't, Phylogeny, Polymorphism, Quantitative Trait Loci, Rats, Recombination, research support, Single Nucleotide, technical report
AbstractThe 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