| Title | SNP and haplotype mapping for genetic analysis in the rat. |
| Publication Type | Journal Article |
| Year of Publication | 2008 |
| Authors | 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, 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 Authors | STAR Consortium |
| Journal | Nat Genet |
| Volume | 40 |
| Issue | 5 |
| Pagination | 560-6 |
| Date Published | 2008 May |
| ISSN | 1546-1718 |
| Keywords | Animals; 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. |
| DOI | 10.1038/ng.124 |
| Alternate Journal | Nat Genet |
| PubMed ID | 18443594 |
| PubMed Central ID | PMC5915293 |
| Grant List | / WT / Wellcome Trust / United Kingdom 062023 / WT / Wellcome Trust / United Kingdom 057733/Z/99/A / WT / Wellcome Trust / United Kingdom 066780/Z/01/Z / WT / Wellcome Trust / United Kingdom |
