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Heterosis has been widely applied in breeding, however, its mechanism remains unclear.In this study, we attempt to reveal the molecular mechanism of heterosis by comparing the transcriptional profiles between F1 hybrid and its parents of super hybrid rice via microarray technology, three combinations, LY2163 (SE21S × MH63), LY2186 (SE21S × MH86) and LYP9 (PA64S × 93-11) are used in this experiment.