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Background  Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice  Oryza glaberrima  and its wild relative  Oryza barthii .    Results  Our RNA-seq analysis revealed a dramatic difference between the two species in the 21 nucleotide small RNA population, corresponding mainly to  miR2118 -triggered phased siRNAs. A detailed expression profiling during the panicle development of  O. glaberrima  and  O. barthii  using qRT-PCRs and  in situ  hybridization, confirmed a delayed expression of the phased siRNAs as well as their lncRNA precursors and regulators ( miR2118  and  MEL1  gene) in  O. glaberrima  compared to  O. barthii . We provide evidence that the 21-nt phasiRNA pathway in rice is associated with male-gametogenesis but is initiated in spikelet meristems.    Conclusion  Differential expression of the  miR2118 -triggered 21-nt phasiRNA pathway between the two African rice species reflects differential rates of determinate fate acquisition of panicle meristems between the two species.    Electronic supplementary material  The online version of this article (doi:10.1186/s12284-016-0082-9) contains supplementary material, which is available to authorized users.

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species