Different maternal origins of Japanese lowland and upland rice populations

Plastid subtype ID (PS-ID) sequences were determined from sequence data based on CA repeats between genes rpl16 and rpl14 in Japanese lowland and upland cultivars. The PS-ID sequences of Japanese rice cultivars showed that there are different maternal origins between lowland and upland cultivars. One subtype, 6C7A, of PS-ID sequences was predominant in all but one Japanese lowland cultivar and carried a combination of the indica-specific subtype 8C8A and japonica-specific nuclear markers for the isozyme genotype. It is probably a nuclear-cytoplasmic recombinant resulting from natural out-crossing and succeeding self-pollination. The origin of the plastid was re-confirmed by the existence of an indica-specific deletion in the plastid genome. In contrast, the Japanese upland cultivars showed two subtypes, 7C6A and 6C7A, of PS-ID sequences. An upland-specific isozyme allele as a nuclear marker was equally predominant in cultivars carrying each subtype. The existence of these particular upland-specific nuclear and cytoplasmic genotypes suggests that the origin of Japanese upland cultivars is different from that of Japanese lowland cultivars. Cultivars carrying the upland-specific nuclear genotype are common in Southeast Asia, but the combination of the upland-specific nuclear and cytoplasmic genotypes which is the same as the Japanese upland predominant type was found in cultivars only in Taiwan and Indonesia. Japanese upland cultivars are closely related to those cultivars.