The Rat: A Model Used in Biomedical Research.

The laboratory rat, Rattus norvegicus, has been used in biomedical research for more than 150 years, and in many cases remains the model of choice for studies of physiology, behavior, and complex human disease. This book provides detailed information on a number of methodologies that can be used in rat. This chapter gives an introduction to rat as a species and as a biomedical model, providing historical information, a brief introduction to the current state of rat research, and a perspective on the future of rat as a model for human disease.

Rat Genome Assemblies, Annotation, and Variant Repository.

The first and only published version of the rat reference genome sequence was RGSC3.1, accomplished by the Rat Genome Sequencing Project Consortium. Here we present the history of the community effort in the correction of sequence errors and filling missing gaps in the process of refining and providing researchers with a high-quality rat reference sequence. The genome assembly improvements, addition of different evidence resources over time, such as RNA-Seq data, and software development methodologies had a positive impact on the gene model annotations. Over the years we observed a great increase in the numbers of genes, protein coding sequences, predicted transcripts and transcript features. Before the sequencing of the rat genome was possible, first biochemical and next genomic markers like RAPD, AFLP, RFLP, and SSLP were fundamental in research studies involving cross-breeding between different rat strains, in finding the level of polymorphism, linkage mapping, and phylogeny. Linkage maps provide information on recombination rates, give insight into intra- and interspecies gene rearrangements, and help to identify Mendelian loci and Quantitative Trait Loci (QTL). In the 1990s many reports were published on the construction of rat linkage maps that incorporated increasing numbers of markers and facilitated the localization of disease loci. Current genetic monitoring and linkage mapping relies on single nucleotide polymorphisms (SNPs). The Rat Genome Database collects information on genetic variation from the worldwide community of rat researchers and provides tools for searching and retrieving these data. As of today we show details about almost 605 million variants coming from many studies in our Variant Visualizer tool.

Integrated curation and data mining for disease and phenotype models at the Rat Genome Database.

Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, genome manipulation. Through the innovation of genome-editing technologies, genome-modified rats provide precision models of disease by disrupting or complementing targeted genes. To facilitate the use of these data produced from rat disease models, the Rat Genome Database (RGD) organizes rat strains and annotates these strains with disease and qualitative phenotype terms as well as quantitative phenotype measurements. From the curated quantitative data, the expected phenotype profile ranges were established through a meta-analysis pipeline using inbred rat strains in control conditions. The disease and qualitative phenotype annotations are propagated to their associated genes and alleles if applicable. Currently, RGD has curated nearly 1300 rat strains with disease/phenotype annotations and about 11% of them have known allele associations. All of the annotations (disease and phenotype) are integrated and displayed on the strain, gene and allele report pages. Finding disease and phenotype models at RGD can be done by searching for terms in the ontology browser, browsing the disease or phenotype ontology branches or entering keywords in the general search. Use cases are provided to show different targeted searches of rat strains at RGD.

Rat Genome Databases, Repositories, and Tools.

Resources for rat researchers are extensive, including strain repositories and databases all around the world. The Rat Genome Database (RGD) serves as the primary rat data repository, providing both manual and computationally collected data from other databases.