IDENTIFICATION AND CHARACTERIZATION OF 2 TANDEM REPEAT SEQUENCES (TRSB AND TRSC) AND A RETROTRANSPOSON (RIRE1) AS GENOME-GENERAL SEQUENCES IN RICE

Three kinds of DNA sequences (here called TrsB, TrsC and RIRE1) have b een previously reported to be those repeated in tandem specifically in the wild rice species with FF, CC or EE genome, respectively. To char acterize these genome type-specific sequences, we carried out PCR usin g a pair of primers, which hybridize to a restricted region in the rep eating unit sequence and prime DNA synthesis in both directions. Gel e lectrophoresis and DNA sequencing revealed that PCR using primers for TrsB (or TrsC) amplified the fragments with an integral series of a un it length not only from total DNA of the rice strain with FF (or CC) g enome, but also from those of the rice strains with non-FF (or non-CC) genome. TrsB or TrsC was, however, found to be repeated in an extraor dinary number of copies in the species with FF or CC genome, respectiv ely, in which the TrsB (or TrsC) sequence has been originally identifi ed. PCR using primers for RIRE1 produced various sizes of fragments fr om total DNA of the rice strains with EE genome. The fragments, howeve r, showed no progression at interval of the unit length characteristic for I tandem repeats. Nucleotide sequencing of the amplified fragment s revealed that they were not the sequences repeated in tandem, but we re those interspersed as an element having partial homology with the L TR sequences of retrotransposons, Wis-2-1A in wheat and BARE-1 in barl ey. RIRE1 was present in the rice species with any types of genomes, b ut in the species with EE genome in an extraordinary number of copies.