Abstract
BackgroundThe National Bio Resource Project for the Rat in Japan (NBRP-Rat) is focusing on collecting, preserving and distributing various rat strains, including spontaneous mutant, transgenic, congenic, and recombinant inbred (RI) strains. To evaluate their value as models of human diseases, we are characterizing them using 109 phenotypic parameters, such as clinical measurements, internal anatomy, metabolic parameters, and behavioral tests, as part of the Rat Phenome Project. Here, we report on a set of 357 simple sequence length polymorphism (SSLP) markers and 122 rat strains, which were genotyped by the marker set.ResultsThe SSLP markers were selected according to their distribution patterns throughout the whole rat genome with an average spacing of 7.59 Mb. The average number of informative markers between all possible pairs of strains was 259 (72.5% of 357 markers), showing their high degree of polymorphism. From the genetic profile of these rat inbred strains, we constructed a rat family tree to clarify their genetic background.ConclusionThese highly informative SSLP markers as well as genetically and phenotypically defined rat strains are useful for designing experiments for quantitative trait loci (QTL) analysis and to choose strategies for developing new genetic resources. The data and resources are freely available at the NBRP-Rat web site [1].
Highlights
The National Bio Resource Project for the Rat in Japan (NBRP-Rat) is focusing on collecting, preserving and distributing various rat strains, including spontaneous mutant, transgenic, congenic, and recombinant inbred (RI) strains
A panel of 384 simple sequence length polymorphism (SSLP) markers was first selected from publicly available data in the Rat Genome Database [14] with two objectives: (1) to obtain the maximum polymorphisms among the listed rat inbred strains and (2) to cover the rat genome except for chromosome Y
Detailed information on the SSLP marker set used is available on our website [18]
Summary
The National Bio Resource Project for the Rat in Japan (NBRP-Rat) is focusing on collecting, preserving and distributing various rat strains, including spontaneous mutant, transgenic, congenic, and recombinant inbred (RI) strains. Several rat genetic markers, such as simple sequence length polymorphisms (SSLPs), expressed sequence tags (ESTs) and sequence-tagged sites (STSs), have been developed and integrated into a high-density rat radiation hybrid map [5], resulting in the comparative mapping of different species, such as between humans and mice. Such infrastructure development of rat genomic resources provides important inforPage 1 of 8. The right side graphs of the chromosome indicate the number of alleles among genotyped 122 strains as red dots
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