On the bases of archaeological discoveries, the earliest domestication of rice has been confirmed in the middle and lower Changjiang River basin, while in the region wild rice populations are found in shallow swamps under a climate with freezing winter cold. These findings lead us re-examine the past ideas about domestication and differentiation of rice. Historically, in 1930s two sub-species, indica and japonica, were proposed on the basis of sterility in F1 hybrids between them. Soon after that, the two types were classified by the associations of a number of genetically independent traits. The characteristic associations of traits have been explained by the hybrid sterility or reproductive barriers which were assumed to comprise a set of duplicate recessive lethal genes and to be an inner genetic mechanism to lead to the varietal differentiations. In 1980s, the hybrid sterility between Indica and Japonica types was analyzed, and Indica, Japonica, and wide-compatibility type which gives fertile hybrids when cross to Indica and Japonica types, are proved to contain an allele, S5 i, S5 j and S5 n, respectively at a locus on chromosome 6. And those gametes having S5 j allele are found to be partially aborted in the hybrid genotypes of S5 i/S5 j while no gamete abortion occurs in S5 i/S5 n and S5 j/S5 n genotypes. Since then, the gene S5 n has been used in hybrid rice breeding to obtain fertile and vigorous hybrids between subspecies, and the long-disputed problem of hybrid sterility has been solved. Also in such studies the characteristic association of traits found in each of varietal groups is better explained by founder effects. On the other hand, a large number of native cultivars of rice were surveyed with enzyme polymorphism in 1980s and later with molecular markers. As a result, profound genetic diversity is found in cultivated rice as well as in wild rice. These findings seem to lead us to the idea of multiple independent domestications of rice. However, before reaching such a conclusion, at least two factors, i.e., long-distance-dissemination of some genotypes and the possibilities of introgression by local wild rice to primitive cultivars need to be examined. Taking the two factors as well as the historical events into consideration, it is considered here that the perennial japonica cultivars which are close to wild rice in the Changjiang River basin were disseminated to East India through Assam or along the Bengal Bay, where they were transformed under the introgressions of local wild rice and formed a secondary center, from which some genotypes seem to be disseminated to colonies in Southeast Asia under the influence of Hinduism. Later some of the genotypes were introduced into China and constituted so called Indica type. This may be a reasonable picture for the varietal differentiation.
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