Bioinformatic identification and expression analysis of new microRNAs from wheat (Triticum aestivum L.)

Sebastian Gasparis,Yuliya Yanushevska,Anna Nadolska-Orczyk

doi:10.1007/s11738-017-2530-6

Abstract

As an essential regulatory component in plants, microRNAs (miRNAs) have been intensively studied over the past decade. Although hundreds of miRNAs have been identified and analyzed in many important crops and model plants, very little is known about the function of common wheat (Triticum aestivum L.) miRNAs. In this study, we performed computational prediction of novel wheat miRNAs based on BLAST searches of the expressed sequence tag database. The expression profiles of all miRNAs were performed for both vegetative and reproductive tissues to identify developmentally regulated miRNAs. A total of 19 new miRNAs belonging to 12 MIR families were identified using stringent criteria for miRNA annotation. For all of the miRNAs, the secondary structures of their precursor sequences were predicted. Two pairs of distinct miRNAs were found to be located on the same precursor. The predicted miRNAs were experimentally verified by a stem-loop qRT-PCR-based assay. The expression profiles were performed in both vegetative and reproductive tissues to find the potential correlations between the developmental phase and miRNA activity. Thirteen out of 19 miRNAs were upregulated at certain phases of plant development, and three of them (miR319, miR395, and miR171) showed the greatest expression in young spikes during microsporogenesis. Our results provide useful information for future studies of miRNA-mediated regulation of flower and grain development in wheat.

Highlights

IntroductionSmall RNAs have become one of the major research topics in both animals and plants
For almost two decades, small RNAs have become one of the major research topics in both animals and plants
All of the tested miRNAs are constitutively expressed at a minimum level allowing their detection, and some of them are strongly upregulated at certain developmental stages, while the remaining are probably induced in response to stress factors

Summary

Introduction

Small RNAs have become one of the major research topics in both animals and plants. MIR genes are found mainly in intergenic regions and are transcribed by RNA polymerase II to primary transcripts (pri-miRNAs), which form an imperfect foldback structure. This structure is further processed to a stemloop precursor from which mature duplex miRNA is excised by a DLC-like protein (Voinnet 2009). The majority of plant miRNAs guide the RNA-induced silencing complex (RISC complex) to the target mRNA which is subsequently degraded (Bartel 2009); mRNA translation inhibition and direct

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Results

Discussion

Conclusion