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MicroRNAs (miRNAs) are upstream gene regulators of plant development and hormone homeostasis through their directed cleavage or translational repression of the target mRNAs,which may play a crucial role in rice grain filling.In this study,high-throughput sequencing was performed to survey the dynamic expressions of miRNAs and their corresponding target genes in superior and inferior spikelets at five distinct developmental stages of grain filling.In total,457 known miRNAs and 76 novel miRNAs were detected with most of them expressed in a panicle location specific and/or developmental stage dependent manner,and the majority of known miRNAs increased gradually with rice grain filling,especially in inferior spikelets.Detailed expressional comparisons revealed a clear negative correlation between most miRNAs and their target genes.Given that specific miRNA cohorts are differentially expressed between superior and inferior spikelets during grain filling and the known functions of the miRNA target genes are revealed in plant hormone homeostasis and starch accumulation,we conclude a key role of distinct miRNA dynamics in grain filling for the development of superior and inferior spikelets,respectively.