MicroRNA Signatures of Drought Signaling in Rice Root.

Behnam Bakhshi,Mohammad Reza Bihamta,Ehsan Mohseni Fard,Mohsen Mardi,Nava Nikpay,Mohammad Ali Ebrahimi,Ghasem Hosseini Salekdeh,Rogerio Margis

doi:10.1371/journal.pone.0156814

Abstract

BackgroundDrought stress is one of the most important abiotic stresses and the main constraint to rice agriculture. MicroRNA-mediated post-transcriptional gene regulation is one of the ways to establish drought stress tolerance in plants. MiRNAs are 20–24-nt regulatory RNAs that play an important role in regulating plant gene expression upon exposure to biotic and abiotic stresses.Methodology/Principal FindingsIn this study, we applied a partial root drying system as well as a complete root drying system to identify miRNAs involved in conditions of drought stress, drought signaling and wet signaling using high-throughput sequencing. To this end, we produced four small RNA libraries: (1) fully-watered (WW), (2) fully-droughted (WD), and split-root systems where (3) one-half was well watered (SpWW) and (4) the other half was water-deprived (SpWD). Our analysis revealed 10,671 and 783 unique known and novel miRNA reads in all libraries, respectively. We identified, 65 (52 known + 13 novel), 72 (61 known + 11 novel) and 51 (38 known + 13 novel) miRNAs that showed differential expression under conditions of drought stress, drought signaling and wet signaling, respectively. The results of quantitative real-time PCR showed expression patterns similar to the high-throughput sequencing results. Furthermore, our target prediction led to the identification of 244, 341 and 239 unique target genes for drought-stress-, drought-signaling- and wet-signaling-responsive miRNAs, respectively.Conclusions/SignificanceOur results suggest that miRNAs that are responsive under different conditions could play different roles in the regulation of abscisic acid signaling, calcium signaling, detoxification and lateral root formation.

Highlights

Drought stress is one of the major abiotic stresses that plants face
Our results indicate that down-regulation of a large numbers of drought-responsive miRNAs under drought stress probably cause the over-expression of their target genes which are involved in responses to stress, cell death and other biological processes
abscisic acid (ABA) signaling under drought stress conditions mediated by miRNA activity

Summary

Introduction

Drought stress is one of the major abiotic stresses that plants face. Response to this stress involves complex mechanisms of signal transduction. Since the first discovery of miRNAs in the form of Lin-4 and let-7 in Caenorhabditis elegans [3] and 16 miRNAs in Arabidopsis [4], miRNAs have been considered as important family of regulatory molecules in plants. These regulatory molecules usually target transcription factors and are involved in the control of several cellular processes, such as adaptation to biotic and abiotic stresses via their positive or negative regulatory roles [5,6]. MiRNAs are 20–24-nt regulatory RNAs that play an important role in regulating plant gene expression upon exposure to biotic and abiotic stresses.

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Discussion

Conclusion