While the source of O. japonica rice strains has been pinpointed to southern China’s Pearl River Delta’s middle reaches, Japanese cultivars are likely the offspring of crosses between local wild rice and the initial japonica rice cultivars that spread into Southeast Asia according to a 2012 paper:
See Huang X., et al., A map of rice genome variation reveals the origin of cultivated rice Nature. 2012 Oct 25;490(7421):497-501. doi: 10.1038/nature11532. Epub 2012 Oct 3. Full pdf text link
In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.
Figure 1: Genetic structure and association analysis in the wild rice population.
Heritage of Japan 