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Link: Proposal for Discovering SNPs from Eight Commonly Used Inbred Rat Strains

Importance of the organism:

The importance of the laboratory rat in biomedical research is well established. Since 1966, there have been on average over 28,000 publications per year using rat (PubMed search, key word: rat); in the last eight years (1996-2003) there have been on average almost 37,000 publications annually. The initiation of the rat genome project has yielded a tremendous wealth of genomic resources including genetic maps; radiation hybrid (RH) cell lines and the associated RH maps (over 6,000 genetic markers and 16,000 genes and ESTs mapped); cDNA libraries generating more than 593,880 ESTs (with more being generated) clustered into over 63,000 UniGenes; over 10,033 genetic markers; and a published draft (~6.8 X) sequence of the genome based on the inbred BN (Brown Norway) strain. The physiology of the “sequenced” rat is being explored by placing each chromosome of the BN on to two genomic backgrounds (the SS and FHH strains) and then measuring over 200 phenotypes in each strain. The consomic rats and the data are available from the PhysGen Programs in Genomic Applications (PGA) project. The rat genome resources have also been expanded by three new BAC libraries (the F344, SS, and FHH) via the BAC resource White Paper proposal. Over 700 strains of rats, including over 200 transgenic lines, numerous congenics, advanced intercross lines, and recombinant inbred panels exist and are being actively used to advance the annotation of the human genome. This single nucleotide polymorphisms (SNP) project is needed to advance these studies. The rat is primarily known as a physiological model and there has been some question over the years about the likelihood that the rat genomic tools would be fully utilized. Figures 1 and 2 show the change in usage of the Rat Genome Database website (measured by number of pages accessed) and changes in the number of visits (defined as 30 minutes using the site without more than 5 minutes of inactivity), over the period 2000-2004. Recall that an advanced draft of the rat genomic sequence, together with an analysis and annotation, was published in April 2004 (Rat Genome Sequencing Project Consortium, 2004).

The full PDF text of this interesting article from genome.gov can be found at http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/RatSNPSeq.pdf.

 

Copyright © Authors Tim Aitman, Richard Gibbs, George Weinstock, Norbert Huebner, Michael JensenSeaman, Daniel Maloney, and Howard J. Jacob

 

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