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More than 500 inbred rat strains have been developed during the past 100 years for a wide range of biomedical applications. In addition to these traditionally bred strains, many induced mutants and several thousand mutagenized sperm samples have recently been generated. At present this huge number of strains is mainly managed by two rat resource centers, the National Bio Resource Project for the Rat in Japan (NBRP-Rat) and the US based Rat Resource and Research Center (RRRC). These resource centers not only collect, maintain and distribute rat strains as animals or cryopreserved embryos and spermatozoa, but also perform additional tasks such as phenotypic and genetic characterization as well as microbiological cleaning. Furthermore, they support researchers through informative databases in the selection of rat strains for specific research purposes. These global rat resource centers are essential for successful and sustainable research using the rat as a model species.

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.