Fig. 1

Population genomic analyses in rice. a. Geographic distribution of 140 wild and 868 cultivated rice accessions. Darkred, blue, lightblue, purple, lightgreen, darkgreen, red, yellow and gold dots on the world map represent the deepwater rice (DW), irrigated rice (IR), rainfed lowland (RL), tidal wetland rice (TW), swamp rice (SW), upland rice (UP), Oryza rufipogon (Or), Oryza nivara (On) and Oryza barthii (Ob), respectively. b. Phylogenetic tree of all accessions inferred from whole-genome SNPs. The major clades are indicated in the outer. The colors were same as the geographic distribution. In addition, magenta, darkorange, darkmagenta, orange and cyan represent the aus, Oryza longistaminata (Ol), Oryza meridionalis (Om), Oryza glumaepatula (Oglu) and Oryza glaberrima (Ogla). The green, red, magenta and orange lines indicate groups of XI, GJ, aus and wild rice accessions. c. ADMIXTURE plot for all rice accessions assuming K = 2–6 and K = 10. The values of K represent the number of clusters. At K = 10, nine subgroups of domesticated rice and three subgroups of wild rice are identified