Population structure estimation. PCA analysis was conducted with the top four components shown in (a) and (b). The four components together explain about 65% of the genetic variance. (a), Principal component 1 distinguishes the type japonica from the type indica. Both types include two ecotypes (upland and irrigated ones). The ecotype differentiation in Japonica is clear-cut. (b), principal components 3 and 4. (c), the population structure reported by FRAPPE. Results were shown from K = 2 to K = 5. When K = 2, there is only division of Indica and Japonica. Then wild rice is separated when K = 3. When K = 4, the ecotype differentiation in Japonica emerges, i.e. upland japonica begins to differ from irrigated japonica. Our results show that upland-irrigated ecotype differentiation is genetically lower than the Indica-Japonica differentiation. The red rectangle indicates the six upland accessions, which were previously classified as upland indica accessions but are genetically more close to the upland japonica group. The blue arrows in K = 5 panel indicates the two upland indica, GS215 and GS233, which have a large genomic proportion close to upland japonica. The red arrow indicates upland indica, GS224, which is close to wild rice.