A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains

Abstract

Background: 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. 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.

Results: The 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.

Conclusion: These 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.

Figure 1

A physical map of 357 rat SSLP markers. The blue lines represent the chromosomal physical map derived from the Rat Genome Browser [15][16] and the blue dots represent the physical position of SSLP markers along the chromosome. The right side graphs of the chromosome indicate the number of alleles among genotyped 122 strains as red dots.

Figure 2

A pedigree-like charting tool on the SSLP database. A pedigree-like charting tool that displays SSLP differences among the genotyped rat strains on the SSLP database [18]. Researchers can select a rat strain to instantly compare its genetic background against all rat strains typed at NBRP-Rat.

Figure 3

A graphical charting tool on the Phenome database. A graphical charting tool that displays phenotypic values for the deposited rat strains at NBRP-Rat on the Phenome database [13][24]. Various rat strains can be sorted according to their values for a selected parameter, such as body weight (A) and blood pressure (B). Column chart (C) or a scatter plot (D) are also two available options in case two parameters are selected to compare their correlation across all examined rat strains.

Figure 4

A family tree of 93 inbred rat strains. A phylogenetic tree was developed through a heuristic search for maximum parsimony implemented in PAUP 4.0b10 [25]. TreeView [32] was used to display the radial tree.