INVOLVEMENT OF TRANSPOSITION IN DISPERSION OF TANDEM REPEAT SEQUENCES(TRSA) IN RICE GENOMES

We describe a method to identify and characterize DNA fragments contai ning the junction of AA genome-specific tandem repeat sequences (here called TrsA) with adjacent chromosomal sequences of rice by the polyme rase chain reaction (PCR) using a pair of primers that hybridize with TrsAs and a flanking non-TrsA sequence. With this method, we obtained results suggesting that TrsA sequences present at two loci (here calle d trsA1 and trsA2) are flanked by direct repeats of chromosomal sequen ces of 172 bp and about 440 bp in length, respectively. These results support the idea that the TrsA sequences have been inserted into each locus by transposition, resulting in duplication of the chromosomal se quence used as target. We also describe a method to identify and chara cterize TrsA sequences repeated in only a few copies in the rice genom e by PCR, using a pair of primers that hybridize with two different po rtions in the TrsA sequence, and demonstrate that TrsA sequences are p resent not only in rice strains with the AA genome, but also in those with non-AA genomes. The TrsA sequences were present at the trsA1 locu s in all the rice strains examined, indicating that TrsA was inserted and amplified at the locus before the divergence of the various specie s of rice in the Oryza genus. TrsA sequences were present at the trsA2 locus, however, only in an O. sativa IR36 strain, indicating that Trs A was inserted and amplified at this locus during divergence of rice s trains with the AA genome.