FINGERPRINTING GENOMES OF VARIOUS ORGANISMS USING PCR WITH URP PRIMERS DEVELOPED FROM REPETITIVE SEQUENCE OF RICE

¹National Institute of Agri. Science & Technology, Suwon 441-707, Korea
²Seoulin Research Institute of Life Science, Seoulin Scientific Co., Ltd, Seoul 134-030, Korea

A repetitive clone, pKRD was isolated from genomic DNA of weedy rice collected in Korea and was characterized at molecular level. Forty five oligonucleotides of 20-mer were randomly designed from the nucleotide sequence (1187 bp) of pKRD to generate reproducible PCR primers applicable to genomic fingerprints of different organisms. Each single primer was applied in PCR reaction as in the case of RAPD or AP-PCR. To improve PCR reproducibility, we employed a highly stringent PCR reaction with a high annealing temperature of more than 55 degrees. Interestingly, 12 primers produced reproducible PCR polymorphism with multiple bands on genomes of various organisms including other 15 genera of plants, 5 animals (mammals, bird, fish and insect) and 12 microorganisms (mushroom, fungi, bacteria) as well as rice and they were named as URP(universal rice primer) primer. We showed that species or strains of plants, animals and microorganisms can be distinguished by comparing PCR polymorphisms produced by URP primers. The generality of URP-PCR method is demonstrated by application to 32 isolates of five Alternaria species (fungi), 32 species in five genera of bacteria, 15 varieties of six rice species, 14 strains of three Pleurotus spp.(mushroom), 62 accessions of 27 Allium spp., and four strains of two Crassostrea spp (marine product). No prior sequence information is required for URP-PCR. In addition, the 12 URP primers were commercialized as SRILS UniPrimerTM Kit by Seoulin Research Institute of Life Science, Seoulin Scientific Co., Ltd, Korea.