Fig. 1

Sequence and structure analysis of USDA mini core collection. a Distribution of SNPs on the rice chromosomes. Number of SNPs per 0.1 Mb window was shown as a color index (bottom right), b Ancestries analysis for each individual was inferred using admixture, c Cross-validation error (CV) score across different K value. The best K value (K = 4) was chosen according to the lowest CV score for the admixture analysis, d Phylogenetic tree of 191 rice accessions. Green indicated Indica (IND) rice, Red indicated Aus (AUS) rice, Purple represented Tropical Japonica (TRJ) rice; Blue represented Temperate Japonica (TEJ) rice, e PCA showing genetic variation in the rice accessions with first and second PCs, the color was defined by current Admixture analysis. f PCA showing genetic variation in the rice accessions with second and third PCs, the color was defined by current Admixture analysis. g Genome-wide average LD decay estimated from the whole population and each subpopulation