Fig. 2

Population structure of 300 rice accessions inferred from 69,777 SNPs and 47,277 Indels. A Admixture plot of 300 rice accessions. The vertical axis represents an ancestry ratio of each accession. The horizontal axis represents individual accessions grouped by clustering analysis. Groups were assigned by clustering analysis on individual-admixture ratios. There are four ancestors (ancestor A–ancestor D) with five populations (POP1–POP5) inferred by clustering analysis. B The PCA scatter plot of first and second principal components (PCs) from a principal component analysis. C The PCA scatter plot of second and third PCs. Cluster colors were assigned according to ADMIXTURE clustering analysis results. The PC1 separates the japonica accessions (POP5) from the indica accessions. PC2 separates southern indica accessions (POP4) from central and northern accessions (POP1, POP2, and POP3). Lastly, PC3 separates central indica (POP1), from northern indica (POP3) with their admixture accessions appearing in between the two (POP2). D Phylogenetic tree of the 300 accessions, created by NJ tree, color coded according to the ADMIXTURE result