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Heterosis, which describes the superior vigor and yield of F1 hybrids with respect to their parents, is observed in many rice hybrid crosses. The exploitation of heterosis is a great leap in the history of rice breeding. With advances in genomics and genetics, high-resolution mapping and functional identification of heterosis-associated loci have been performed in rice. Here we summarize advances in understanding the genetic basis of grain yield heterosis in hybrid rice and provide a vision for the genetic study and breeding application of rice heterosis in the future.