Extended Data Fig. 1: The analysis procedure and materials used in the study.

a, The experimental design and analysis procedure used in this study. b, Principal component analysis (PCA) for 2,839 rice hybrids used in this study. The first three PCs were used for plotting. Red, dark blue and yellow dots represent individuals from Y1, Y2 and Y3 breeding periods, respectively. For better demonstration, hybrids from three periods were separately highlighted in three panels. c, PCA plot for all materials used for genomic selection model construction. The first two PCs were used for plotting. Cyan-blue, blue, read and yellow dots represent 58,353 pseudo combinations, 2,839 cultivar rice hybrids, 5,342 segregating individuals from indica-japonica hybrids, and 4,497 segregating individuals from indica-indica hybrids. They were successively added to the plots to clearly demonstrate their distribution.