We analyzed the presence of p-SINE
1 members at five loci in the rice strains belonging to seven species with AA genome in the
Oryza genus by the methods including polymerase chain reaction (PCR). Four p-SINE
1 members (p-SINE
1-r3, r4, r5 and r7) were present at the corresponding loci in all the strains examined. One member (p-SINE
1-r6) was, however, not present at the corresponding locus in most of the African strains of
O. glaberrima and
O. barthii, but was in the other strains. The PCR-amplified fragments containing p-SINE
1-r4 in many strains were found to be larger due to insertion of either one of two transposable elements, named Tnr
2 and Ret
1, within or near p-SINE
1-r4, respectively: Tnr
2 is 157 bp in length with terminal inverted repeat sequences of about 56bp; Ret
1 is only 13 bp in length with a T stretch at its end. Tnr
2 was not present in the corresponding locus in all the strains belonging to
O. sativa Japonica and in some strains of
O. rufipogon and
O. longistaminata, while Ret
1 was present only in the two strains of
O. longistaminata. These results and previous ones obtained from the analysis of the other two p-SINE
1 members (p-SINE
1-r1 and r2) in the W
x gene indicate that the elements, such as p-SINE
1r6, Tnr
2, Ret
1 and p-SINE
1-r2, have been inserted into the respective loci during divergence of the rice species with AA genome. The patterns for the presence and absence of the transposable elements at the respective loci enabled us to classify the rice strains with AA genome into ten groups and to infer their relationships.
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