Fig. 4

Analysis of the 48 KASP markers in conventional varieties. a–c The phylogenetic tree, population structure and PCA of the conventional varieties using 48 KASP markers. d The difference of reference allele frequency between japonica and indica. The blue star indicated the sites which showed almost completely different alleles. 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 1 while light red represented subpopulation 2 in c