TRANSPOSITION OF TNR1 IN RICE GENOMES TO 5'-PUTAPY-3' SITES, DUPLICATING THE TA SEQUENCE

Tnr1 is a repetitive sequence in rice with several features characteri stic of a transposable DNA element. Its copy number was estimated to b e about 3500 per haploid genome by slot-blot hybridization. We have is olated six members of Tnr1 located at different loci by PCR (polymeras e chain reaction) and determined their nucleotide sequences. The Tnr1 elements were similar in size and highly homologous (about 85%) to the Tnr1 sequence identified first in the Waxy gene in Oryza glaberrima. A consensus sequence of 235 bp could be derived from the nucleotide se quences of all the Tnr1 members. The consensus sequence showed that ba se substitutions occurred frequently in Tnr1 by transition, and that T nr1 has terminal inverted repeat sequences of 75 bp. Almost all the ch romosomal sequences that flank the Tnr1 members were 5'-PuTA-3' and 5' -TAPy-3', indicating that Tnr1 transposed to 5'-PuTAPy-3' sites, dupli cating the TA sequence. PCR-amplified fragments from some rice species did not contain the Tnr1 members at corresponding loci. Comparison of nucleotide sequences of the fragments with or without a Tnr1 member c onfirmed preferential transposition of Tnr1 to 5'-PuTAPy-3' sites, dup licating the TA sequence. One amplified sequence suggested that imprec ise excision had occurred to remove a DNA segment containing a Tnr1 me mber and its neighboring sequences at the Waxy locus of rice species w ith genome types other than AA. We also present data that may suggest that Tnr1 is a defective form of an autonomous transposable element.