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The Han:SPRD strain is an SD-background strain known to be a model of polycystic kidney disease (PKD) expressed through an autosomal dominant gene (Cy). However, different genotypes of this strain cannot be identified in the neonatal period. First, to establish an accurate method of determining the genotypes (Cy/Cy, Cy/+, +/+) which cause different disease progressions, we used polymorphic markers on rat chromosome 5. PCR products of tissue DNA templated with D5Rat9 showed distinct patterns on electrophoresis indicating three genotypes. Second, to determine whether the same locus plays a major role in expressing PKD, we performed linkage analyses in a [BN x (BN x Han:SPRD)F1] backcross. Cy/Cy and Cy/+ also caused PKD in a BN background. In this backcross, we discovered that D5Rat11 is located closer to the Cy locus than D5Mgh10, which is regarded as one of the closest loci. We conclude that D5Rat9 and D5Rat11 are useful markers for determining the presence of the Cy allele, which is regarded as the gene responsible for PKD.