Classification and Relationships of Rice Strains with AA Genome by Identification of Transposable Elements at Nine Loci

Abstract

We analyzed the presence of p-SINEl 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-SINEl members (p-SINEl-r3, r4, r5 and r7) were present at the corresponding loci in all the strains examined. One member (p-SINEl-r6) was, however, not present at the corresponding locus in most of the African strains of 0. glaberrima and 0. barthii, but was in the other strains. The PCR-amplified fragments containing p-SINEl-r4 in many strains were found to be larger due to insertion of either one of two transposable elements, named Tnr2 and Retl, within or near p-SINEl-r4, respectively: Tnr2 is 157 bp in length with terminal inverted repeat sequences of about 56 bp; Retl is only 13 bp in length with a T stretch at its end. Tnr was not present in the corresponding locus in all the strains belonging to O. sativa Japonica and in some strains of 0. rufipogon and 0. longistaminata, while Retl was present only in the two strains of 0. longistaminata. These results and previous ones obtained from the analysis of the other two p-SINEl members (p-SINEl-rl and r2) in the Wx gene indicate that the elements, such as p-SINEl-r6, Tnr2, Retl and p-SINEl-r2, have been inserted into the respective loci during divergence of the rice species with A A 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. © 1993, The Genetics Society of Japan. All rights reserved.