RFLP analysis of nuclear DNAs homologous with mitochondrial plasmid-like DNAs in cultivated rice

Novel DNA probes capable of discriminating indica and japonica rice cultivars

We obtained two DNA clones, G93 (1.6kb) and G318 (1.7kb) from indica rice (Oryza sativa L.) cultivar Culture 340. Southern hybridization analysis indicated that both DNA probes hybridized with DNA of indica cultivars but not with japonica cultivars. Some javanica cultivars DNAs did not hybridize with these probes. Nucleotide sequence (400bp) of a part of G93 showed a 65.8% G + C content. These novel DNA probes can be used for the study of evolutional fingerprinting of rice cultivars.

Polymorphic distribution and molecular diversification of mitochondrial plasmid-like DNAs in the genus Oryza

Four kinds of circular plasmid-like DNA, designated B1, B2, B3 and B4, have been found in the mitochondria of rice (Oryza sativa L.). We analyzed the distribution of families of plasmid-like DNAs homologous to those of O. sativa in 40 strains of the genus Oryza with AA, BB, BBCC, CC, CCDD and EE genomes. Plasmid-like DNAs were observed only strains having AA, CC and CCDD genomes. The distribution patterns of strains with AA genome were highly polymorphic. We amplified the plasmid-like DNAs from strains with the AA genome by PCR and examined restriction fragments length polymorphisms (RFLPs). RFLPs were detected among families of plasmid-like DNA amplified from different strains. This result indicated that some mutations, such as base substitutions and the insertion or deletion of a small fragment of DNA, had occurred and had accumulated during the differentiation of strains with an AA genome.

Restriction fragments homologous to mitochondrial plasmid-like DNAs are located within limited chromosomal regions on the rice nuclear genome

The chromosomal locations of restriction fragments of nuclear DNA that were homologous to four mitochondrial plasmid-like DNAs, namely, B1, B2, B3 and B4, were analyzed by restriction fragment length polymorphism (RFLP) analysis in cultivated rice. Nine kinds of fragments homologous to plasmidlike DNAs were analyzed for their segregation in three different F2 populations derived from intercrosses between rice subspecies; these were found to be localized in three chromosomal regions: three, one and five kinds of nuclear homologues were situated on chromosomes 1,3 and 8, respectively. Nuclear homologues on a given chromosome were tightly linked even though they were homologous to different plasmid-like DNAs. The loci of nuclear homologues found commonly in two or three cultivars were found to be highly conserved, a result that is consistent with their stable transmission. These results and those of the Southern analysis suggest the independent integration of these sequences during the varietal differentiation of rice. The concentration of loci for nuclear homologues on chromosomes 1 and 8 suggests that these sequences were integrated non-randomly into these chromosomal regions.

Linkage analysis of the nuclear homologues of mitochondrial plasmid-like DNAs in rice

A genetical study on the nucleotide sequences of the nuclear DNAs which share homology with rice mitochondrial plasmid-like DNAs, B1, B2, B3 and B4 was carried out. Restriction fragments of the nuclear DNAs hybridized with these plasmid-like DNAs showed polymorphisms in their length between Indica and Japonica rice cultivars. The hybridized signals found specifically in Indica or Japonica cultivars segregated in the F2 population derived from a cross between these two subspecies. The observed ratio of the nuclear homologues in the F2 population demonstrated that they were transmitted according to the Mendelian inheritance. The co-segregation of homologues was examined and the linkage was detected between the B1-nuclear homologue of Japonica and the B4-nuclear homologue of Indica, and also between the nuclear homologues of B2 and B3 of Indica. The linkage between the B1-nuclear homologue of Japonica and the B4-nuclear homologue of Indica was conserved in the different rice cultivars.