Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis

Exploration of crop heterosis is crucial for increasing global agricultural production. However, the genetic basis of heterosis has not been solved quantitatively, and there is no effective prediction tool to optimize the cross combination. Here, 2,839 hybrid rice cultivars and 9,839 segregation individuals were re-sequenced and phenotypically investigated. We demonstrated that indica-indica hybrid improving breeding was a process to broaden genetic resource, pyramid breeding-favorable alleles through combination selection and collaboratively improve both parents to eliminate the inferior alleles of negative dominant loci. In addition, we revealed that widespread genetic complementarity contributed to indica-japonica interspecific heterosis for yield traits, and dominant effect loci had greater contribution to phenotypic variation than over-dominance effect loci. Furthermore, a genomic model applicable to diverse rice varieties was developed and optimized to predict the performance of hybrid combinations. Our data offer a valuable resource for advancing the understanding of rice heterosis and its applications.