MicroRNA Signatures of Drought Signaling in Rice Root

Oghan, Hassan Amiri; Fard, Ehsan Mohseni; Nikpay, Nava; Ebrahimi, Mohammad Ali; Bihamta, Mohammad Reza; Mardi, Mohsen; Salekdeh, Ghasem Hosseini

doi:10.1371/journal.pone.0156814

Cited by 55 publications

(40 citation statements)

References 80 publications

(115 reference statements)

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“…[65]. Bakhshi et al investigated the miRNA drought responsiveness in rice roots, and 9 miRNAs, including miR156, miR159, miR168, miR171, miR396, miR528, miR529, miR1861, and miR3979, participated in drought stress, drought signaling, and wet signaling [66]. These results are consistent with our study regarding the differentially expressed miRNAs that are drought-responsive in the root tissue (S3 File).…”

Section: Discussionsupporting

confidence: 90%

Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots

et al. 2017

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BackgroundDrought is the most important factor that limits rice production in drought-prone environments. Plant microRNAs (miRNAs) are involved in biotic and abiotic stress responses. Common wild rice (Oryza rufipogon Griff.) contains abundant drought-resistant genes, which provide an opportunity to explore these excellent resources as contributors to improve rice resistance, productivity, and quality.ResultsIn this study, we constructed four small RNA libraries, called CL and CR from PEG6000-free samples and DL and DR from PEG6000-treated samples, where ‘R’ indicates the root tissue and ‘L’ indicates the shoot tissue. A total of 200 miRNAs were identified to be differentially expressed under the drought-treated conditions (16% PEG6000 for 24 h), and the changes in the miRNA expression profile of the shoot were distinct from those of the root. At the miRNA level, 77 known miRNAs, which belong to 23 families, including 40 up-regulated and 37 down-regulated in the shoot, and 85 known miRNAs in 46 families, including 65 up-regulated and 20 down-regulated in the root, were identified as differentially expressed. In addition, we predicted 26 new miRNA candidates from the shoot and 43 from the root that were differentially expressed during the drought stress. The quantitative real-time PCR analysis results were consistent with high-throughput sequencing data. Moreover, 88 miRNAs that were differentially-expressed were predicted to match with 197 targets for drought-stress.ConclusionOur results suggest that the miRNAs of O. rufipogon are responsive to drought stress. The differentially expressed miRNAs that are tissue-specific under drought conditions could play different roles in the regulation of the auxin pathway, the flowering pathway, the drought pathway, and lateral root formation. Thus, the present study provides an account of tissue-specific miRNAs that are involved in the drought adaption of O. rufipogon.

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Section: Discussionsupporting

confidence: 90%

Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots

et al. 2017

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“…However, expression of miR166 is almost two fold greater in J. pentantha, compared to I. campanulata. miR166 is known to target HD-ZIP III transcription factor and regulate diverse facets of plant development such as leaf polarity, xylem differentiation in root, and modulation of lateral root growth under drought stress (Jung and Park 2007;Sakaguchi and Watanabe 2012;Bakhshi et al 2016). Differential abundances of miR166, observed in this study, could imply differential regulation of its target/s in wild and cultivated species studied here, impacting some of the targeted responses.…”

Section: Resultsmentioning

confidence: 99%

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

Ghorecha

Zheng

Liu

et al. 2017

Physiol Mol Biol Plants

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Agricultural productivity is severely hampered by drought in many parts of the globe. It is well-known that wild plant species can tolerate drought better when compared with their closely related cultivated plant species. Better drought adaptation of wild species over cultivated ones is accounted for their ability to differentially regulate gene expression. miRNAs, known to regulate gene expression at the post-transcriptional level, are admitted to play an important role in plant adaptation to stresses. This study aims at evaluating miRNA dynamics in a droughttolerant wild Ipomoea campanulata L. and drought-sensitive cultivated Jacquemontia pentantha (Jacq.) of the family Convolvulaceae under ex situ drought. Sequencing profiles revealed that 34 conserved miRNA families were analogous between the two species. Drought altered expression levels of several of these miRNAs in both the species. Drought-tolerant I. campanulata showed upregulation of miR398, miR168, miR858, miR162 and miR408, while miR394 and miR171 were downregulated. Droughtsensitive J. pentantha showed upregulation of miR394, miR156, miR160, miR164, miR167, miR172, miR319, miR395, miR396, miR403 and downregulation of miR157. Basal miRNA levels and their drought mediated regulation were very different between the two species. Differential drought sensitivities of these two plant species can be attributed to these innate variations in miRNA levels and their expression.

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“…The gene family to which the target gene(s) of each of the 6 selected miRNAs belongs is indicated in the line immediately below the name of the targeting miRNA at the top of each column, more specifically MYB (MYELOBLASTOSIS), NAC (NAM/ATAF/CUC2), ARF (AUXIN RESPONSE FACTOR), AGO (ARGONAUTE), GRF (GROWTH REGULATING FACTOR) and LAC (LACCASE). The data used to construct Figure 1 was sourced from studies [23,68,[85][86][87][88][89][90][91][92][93][94][95][96][97][98][99][100][101][102][103].…”

Section: The Varying Responses Of Six Highly Conserved Micrornas To Dmentioning

confidence: 99%

Profiling of the Differential Abundance of Drought and Salt Stress-Responsive MicroRNAs Across Grass Crop and Genetic Model Plant Species

Pegler¹,

Grof²,

Eamens³

2018

Agronomy

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In recent years, it has become readily accepted among interdisciplinary agriculturalists that the current global crop yield to land capability ratio is significantly insufficient to achieve food security for the predicted population of 9.5 billion individuals by the year 2050. This issue is further compounded by the: (1) food versus biofuel debate; (2) decreasing availability of arable land; (3) required reductions to the extensive and ongoing environmental damage caused by either poor agricultural practices or agriculture expansion, and; (4) increasingly unfavorable (duration and severity) crop cultivation conditions that accompany man-made climate change, driven by ever-expanding urbanization and its associated industrial practices. Mounting studies are repeatedly highlighting the critical importance of linking genotypes to agronomically beneficial phenotypes and/or using a molecular approach to help address this global crisis, as "simply" clearing the remaining natural ecosystems of the globe for the cultivation of additional, non-modified crops is not efficient, nor is this practice sustainable. The majority of global food crop production is sourced from a small number of members of the Poaceae family of grasses, namely; maize (Zea mays L.), wheat (Triticum aestivum L.) and rice (Oryza sativa L.). It is, therefore, of significant concern that all three of these Poaceae grass species are susceptible to a range of abiotic stresses, including drought and salt stress. Highly conserved among monocotyledonous and dicotyledonous plant species, microRNAs (miRNAs) are now well-established master regulators of gene expression, influencing all aspects of plant development, mediating defense responses against pathogens and adaptation to environmental stress. Here we investigate the variation in the abundance profiles of six known abiotic stress-responsive miRNAs, following exposure to salt and drought stress across these three key Poaceae grass crop species as well as to compare these profiles to those obtained from the well-established genetic model plant species, Arabidopsis thaliana (L.) Heynh. Additionally, we outline the variables that are the most likely primary contributors to instances of differential miRNA abundance across the assessed species following drought or salt stress exposure, specifically; (1) identifying variations in the experimental conditions and/or methodology used to assess miRNA abundance, and; (2) the distribution of regulatory transcription factor binding sites within the putative promoter region of a MICRORNA (MIR) gene that encodes the highly conserved, stress-responsive miRNA. We also discuss the emerging role that non-conserved, species-specific miRNAs play in mediating a plant's response to drought or salt stress.

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MicroRNA Signatures of Drought Signaling in Rice Root

Cited by 55 publications

References 80 publications

Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots

Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

Profiling of the Differential Abundance of Drought and Salt Stress-Responsive MicroRNAs Across Grass Crop and Genetic Model Plant Species

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