Extended Data Fig. 6: Identification and quantitative analysis of breeding signatures based on genome-wide association analysis.

a, The distribution of the count of pyramiding breeding-favorable alleles in indica-indica hybrid from three breeding periods. The top-100 GWAS signals in indica-indica rice hybrid population were applied for analysis. b, The d/a index (dominance-effect/additive-effect) and PVE (phenotypic variance explained) for candidate genes involved in improvement breeding. c, Allelic frequency change for candidate genes involved in improvement breeding within three subgroups of indica-indica hybrids. Because most BT hybrids were indica-japonica or japonica-japonica hybrids, they were not discussed here. For morphological characteristics, grain yield-related and quality-related traits, symbol ‘+’ denotes breeding-favorable alleles and ‘-’ indicates breeding-unfavorable alleles. As for heading date, symbol ‘+’ represents alleles associated with longer heading date and ‘-’ indicates alleles with shorter heading date.