Studies on transposition and dispersion of tandem repeat sequences (TrsA) in rice genome

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Our final goal of this project is to elucidate the dispersion mechanism of the tandem repeat sequences, TrsA,on rice chromosomes. The results we obtained in the past two years can be summarized as follows :(1) Involvement of transposition in dispersion of tandem repeat sequences (TrsA) in rice genome.We carried out PCR using a pair of primers that hybridize to TrsAs and flanking non-TrsA sequences, and obtained the results suggesting that TrsA sequences present at two independent loci, trsAl and trsA2, are flanked by long direct repeats of chromosomal sequences. These results may support the idea that the TrsA sequences have been inserted into each locus by transposition, resulting in duplication of chromosomal sequence used as target. We also found that the target sequence at trsA2 was present specifically in the indica rice chromosomes. Cloning and sequencing the target site of 440 bp at trsA2 revealed that this sequence was an LTR sequence of a novel retrotransposon repeated in rice … More chromosomes(2) Mapping of TrsA sequences on rice chromosomes by FISH.We mapped the TrsA sequences on the somatic prometaphase chromosomes of two O.sativa cultivars by using an improved FISH method. The FISH signals were detected at the distal ends of long arms of chromosome 6 and 12 in the japonica rice and at the distal ends of long arms of chromosome 5,7,8,9,10, and 11 in indica rice. In O.glaberrima, an African cultivated rice, the FISH signals were detected at the distal ends of long arms of chromosome 5,6 and 7. It has been known that the copy numbers of TrsA in O.meridionalis, a wild type rice, are almost ten times higher than those in O.sativa. FISH analysis showed that the hybridization signals were detected at the distal ends of long arms of all the chromosomes except 12. These results suggest that the numbers and locations of the TrsA on the chromosomes are characteristic to each rice species. It should be noticed that all the signals were detected at the distal ends of long arms of chromosomes except one (chromosome 4 to O.meridionalis). These results indicate that chromosomes have polarity which may play an important role in gathering chromosomes. Less