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BackgroundMicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that down-regulate target genes by mRNA degradation or translational repression. Numerous plant miRNAs have been identified. Evidence is increasing for their crucial roles during plant development. In the globally important crop of wheat (Triticum aestivum L.), the process by which grains are formed determines yield and end-use quality. However, little is known about miRNA-mediated developmental regulation of grain production. Here, we applied high-throughput sRNA sequencing and genome-wide mining to identify miRNAs potentially involved in the developmental regulation of wheat grains.ResultsFour sRNA libraries were generated and sequenced from developing grains sampled at 5, 15, 25, and 30 days after pollination (DAP). Through integrative analysis, we identified 605 miRNAs (representing 540 families) and found that 86 are possibly involved in the control of grain-filling. Additionally, 268 novel miRNAs (182 families) were identified, with 18 of them also potentially related to that maturation process. Our target predictions indicated that the 104 grain filling-associated miRNAs might target a set of wheat genes involved in various biological processes, including the metabolism of carbohydrates and proteins, transcription, cellular transport, cell organization and biogenesis, stress responses, signal transduction, and phytohormone signaling. Together, these results demonstrate that the developmental steps by which wheat grains are filled is correlated with miRNA-mediated gene regulatory networks.ConclusionsWe identified 605 conserved and 268 novel miRNAs from wheat grains. Of these, 104 are potentially involved in the regulation of grain-filling. Our dataset provides a useful resource for investigating miRNA-mediated regulatory mechanisms in cereal grains, and our results suggest that miRNAs contribute to this regulation during a crucial phase in determining grain yield and flour quality.

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microRNAs (miRNAs) are endogenous small non-coding RNAs that bind to mRNAs and target them for cleavage and/or translational repression, leading to gene silencing. We previously developed short tandem target mimic (STTM) technology to deactivate endogenous miRNAs in Arabidopsis. Here, we created hundreds of STTMs that target both conserved and species-specific miRNAs in Arabidopsis, tomato, rice, and maize, providing a resource for the functional interrogation of miRNAs. We not only revealed the functions of several miRNAs in plant development, but also demonstrated that tissue-specific inactivation of a few miRNAs in rice leads to an increase in grain size without adversely affecting overall plant growth and development. RNA-seq and small RNA-seq analyses of STTM156/157 and STTM165/166 transgenic plants revealed the roles of these miRNAs in plant hormone biosynthesis and activation, secondary metabolism, and ion-channel activity-associated electrophysiology, demonstrating that STTM technology is an effective approach for studying miRNA functions. To facilitate the study and application of STTM transgenic plants and to provide a useful platform for storing and sharing of information about miRNA-regulated gene networks, we have established an online Genome Browser (https://blossom.ffr.mtu.edu/designindex2.php) to display the transcriptomic and miRNAomic changes in STTM-induced miRNA knockdown plants.