Fig. 2: Genetic analysis of superior indica hybrids.

a Population structure analysis of 1143 indica accessions. The results for K values from 2 to 6 are shown. When K = 2, two genetic groups match the IndII and IndI subgroups (see “Methods”). When K = 6, the six genetic groups generally correspond to GMS, restorer (3R + 2R), GR, IndII CR, IndI CR, and CMS lines, with some exceptions in each group. b, c Crossing patterns of the superior 3- (b) and 2-line (c) hybrids. The top curves connect two parents of superior hybrids: blue: IndII restorers crossed with IndI male sterile lines; green: IndII restorers crossed with IndII male sterile lines; red: IndI restorers crossed with IndI male sterile lines; yellow: IndII restorers crossed with IndII male sterile lines. A nuclear-genome phylogenetic tree in the horizontal format is shown below the curves in the same color schema as in Fig. 1. d Average nuclear-genome genetic distances between two parents for all 1143 accessions (n = 652,653) and superior 3- (n = 415) and 2-line (n = 136) hybrids (all: min = 0.001, max = 0.491; 3-line: min = 0.194, max = 0.420; 2-line: min = 0.253, max = 0.402). e Average mitochondrial genome genetic distances between two parents for all 1143 accessions (n = 652,653) and superior 3- (n = 415) and 2-line (n = 136) hybrids (all: min = 0.000, max = 0.438; 3-line: min = 0.001, max = 0.315; 2-line: min = 0.003, max = 0.242). In d, e, the p values by two-tailed unpaired Welch’s t-tests are shown on diagrams. Data representation: the middle line: median; the asterisk: mean; the lower and upper hinges: the first and third quartiles; the upper whisker extends from the hinge to the largest value no further than 1.5 × IQR (inter-quartile range) from the hinge. The lower whisker extends from the hinge to the smallest value at most 1.5 × IQR of the hinge. Data beyond the end of the whiskers, which were considered as the outlying points, are plotted individually. Source data underlying figures b–e are provided as a Source Data file.