Abstract

BackgroundRice 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.ResultsOur 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.ConclusionDifferential 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 materialThe online version of this article (doi:10.1186/s12284-016-0082-9) contains supplementary material, which is available to authorized users.

Highlights

  • Rice exhibits a wide range of panicle structures

  • Panicle-associated small RNAs in African rice species To conduct a comprehensive survey of panicle-derived small RNAs in African rice and characterise qualitative and quantitative differences between the two species, we compared small RNA populations in panicles of O. glaberrima and O. barthii, using genome-wide small RNA-seq analysis

  • We provide evidence that the male-gametogenesisspecific 21-nt phasiRNA pathway triggered by miR2118 is conserved in both wild relative and domesticated African rice species

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Summary

Introduction

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. In O. sativa, phasiRNAs triggered by specific miRNAs and originating from non-coding loci, were shown to be involved in panicle development and in male gametogenesis (Arikit et al 2013; Johnson et al 2009; Komiya et al 2014; Song et al 2012a, b). Each phasiRNA type exhibits independent spatiotemporal regulation, with 21-nt premeiotic phasiRNAs dependent on stamen epidermal differentiation and 24-nt meiotic phasiRNAs dependent on tapetal cell differentiation (Zhai et al 2015) Their function during male gametogenesis remains unclear

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