Phylogenetic tree of rice accessions. Green, black and orange branches refer to upland, irrigated and wild accessions respectively. Analysis showed that differentiation between Indica and Japonica has existed within the wild population, since there are strains of wild rice close to both Indica and Japonica respectively, supporting the double domestication model. The tree shows multiple origins for upland rice, though the upland japonicas may bear a single origin. Bootstrap values are indicated in some of the major internal nodes. Some of the leaf nodes are labeled with the sample number of the rice accessions. ‘ru’ refers to ‘rufipogon’, and ‘ni’ refers to ‘nivara’.