Comparative study on the chloroplast, mitochondrial and nuclear genome differentiation in two cultivated rice species, Oryza sativa and O. glaberrima, by RFLP analyses.

Restriction fragment length polymorphisms of chloroplast (ct), mitochondrial (mt) and nuclear DNA were investigated using eight cultivars of Oryza sativa and two cultivars of O. glaberrima. Relative variability in the nuclear and cytoplasmic genomes was estimated by a common measure, genetic distance. Based on the average genetic distances among ten cultivars for each genome, the evolutionary variabilities of the mitochondrial and nuclear genomes were found to be almost the same, whereas the variability of the chloroplast genome was less than half that of the other two genomes. Cluster analyses on ct and mt DNA variations revealed that chloroplast and mitochondrial genomes were conservative within a taxon and that their differentiations were well-paralleled with respect to each other. For nuclear DNA variation, an array of different degrees of differentiation was observed in O. sativa, in contrast with little variation in O. glaberrima. As a whole, differentiation between O. sativa and O. glaberrima was clearly observed in all three genomes. In O. sativa, no notable difference was found between the cultivars 'Japonica' and 'Javanica', whereas a large differentiation was noticed between 'Japonica' (including 'Javanica') and 'Indica'. In all three genomes, the average genetic distances within 'Indica' were much larger than those within 'Japonica' (including 'Javanica'), and almost similar between 'Japonica' (including 'Javanica') and 'Indica'. These facts indicate that differentiation in O. sativa was due mainly to 'Indica'.