Fig. 5

Analysis of the 48 KASP markers in hybrid varieties. a–c The phylogenetic tree, population structure and PCA of the hybrid varieties using 48 KASP markers. d The heterozygous rate of each chromosome. e The heterozygous rate of japonica hybrid variety. The blue star indicated three sites with higher heterozygous rate. The brown indicated the japonica varieties while light red represented the indica varieties in b. The blue indicated that the varieties with the classification of the phylogenetic tree different from the original annotation coming from the breeding institutes in b. The brown indicated the subpopulation 1while light red represented subpopulation 2 in c