|Budget Amount *help
¥2,200,000 (Direct Cost: ¥2,200,000)
Fiscal Year 1997: ¥700,000 (Direct Cost: ¥700,000)
Fiscal Year 1996: ¥1,500,000 (Direct Cost: ¥1,500,000)
There exist several kinds of mobile genetic elements in rice genomes. We have identified retroposon p-SINE1, a SINE (short interspersed element) in a japonica rice strain, Oryza sativa cv. Nipponbare, to be distributed in an average spacing of about one member per 70 kb. We have characterized 31 members of p-SINE1 located at different loci in Nipponbare and other rice strains, O.sativacv. IR36 and O.glaberrima.
Tnrl, 230 bp in size, is a rice transposable element with a long terminal inverted repeat (TIR) of 75 bp. We have identified and characterized six member of Tnrl located at different loci, where Tnrl transposes to the 5'-PuTAPy-3' sites, duplicating the TA sequence. Furthermore, we identified another rice transposable element Tnr2,157 bp in size, with the 56-bp TIR sequence and a tandem repeat of 20 bp long in the region between the TIR sequences, and characterized four Tnr2 members in IR36.
PCR using a pair of primers that hybridize to the sequences flanking each member of the th
ree elements revealed that many of them were present at the corresponding loci in the strains belonging to all the rice species with AA genome. Several of them were, however, present in the corresponding loci in the strains belonging to a limited number of species or in a limited number of the strains belonging to a rice species. These members were thus useful for identification and classification of various rice strains 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 seven groups and to infer their relationships : The japonica and javanica rice strains are most closely related to the indica rice strains, and the African cultivated rice strain (s) of O.glaberrima are more closely related to the African wild rice strains of O.barthii than to the Asian cultivated rice strains ; Asian wild rice strains of O.rufipogon are divided into three groups and found to be related to the strains belonging to either japonica, indica, or O.longistaminata (another African rice) strains ; the wild rice strains of O.glumaepatula (American rice), O.meridionalis (Oceanian rice), and O.barthiiare related more closely to indica rice than to japonica rice.
During the course of these works, we identified and characterized another category of transposable elements, called retrotransposons, which might be also useful for classification of various rice strains in the future. Less