Fingerprinting of Diverse Genomes Using PCR with Universal Rice Primers Generated from Repetitive Sequence of Korean Weedy Rice

Abstract

Twenty primers of 20 mer referred to universal rice primer (URP) were developed from a repetitive sequence of rice genome. URP-PCR protocol employed stringent PCR with high annealing temperature throughout the thermo-cycling reaction, giving high reproducibility. Under the PCR condition, each single URP primer produced characteristic fingerprints from diverse genomes containing 14 plants, 7 animals and 6 microbes, indicating its universal applicability. The generality of URP-PCR was demonstrated by applying it to 15 cultivars from five rice species, 23 isolates in four Alternaria species producing host-specific toxins on different host plants and 12 bacterial strains including Escherichia coli, Salmonella spp., and Blucella abortus. PCR approach using URP primers will be useful for studying DNA diversity of most eukaryotic or prokaryotic genomes, especially at inter- and intraspecies levels.