Fig. 1

Population structure of 259 rice accessions. (A) Neighbor-joining phylogenetic tree generated using 2,888,332 high-quality SNPs; (B) Individual ancestry coefficients of 259 rice accessions determined using ADMIXTURE with the number of ancestry kinships (K) set to 2 or 3. Each accession is denoted by a vertical bar; the proportion of different colors in each bar indicates the proportion of genetic from each of the ancestral populations; (C) Principal component analysis (PCA) plot of 259 rice accessions. (D) Genome-wide average linkage disequilibrium (LD) decay rate of 259 rice accessions and three different subgroups