Genome-wide fungal stress responsive miRNA expression in wheat

İnal, Behçet; Türktaş, Mine; Eren, H.; İlhan, Emre; Okay, Sezer; Atak, Mehmet; Erayman, Mustafa; Ünver, Turgay

doi:10.1007/s00425-014-2153-8

Cited by 70 publications

(56 citation statements)

References 46 publications

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“…Several miRNA families have been reported to be differentially regulated in response to drought stress in various plant species, including rice (Zhao et al 2007), tomato (Solanum lycopersicum , Arabidopsis (Liu et al 2008), Medicago truncatula (Trindade et al 2010), peach (Eldem, et al 2012), barley (Kantar et al 2010), and wheat (Gupta, et al 2014;Pandey, et al 2014). There are several studies documenting expression levels of various miRNAs in T. aestivum L. (Xin, et al 2010;Inal et al 2014;Pandey, et al 2014), but none of these miRNAs are experimentally verified. Moreover, the biological functions of miRNAs upon drought stress have been identified experimentally in plants, but the number of studies is very limited.…”

Section: Introductionmentioning

confidence: 95%

miRNA-based drought regulation in wheat

Akdoğan

Tüfekçi

Uranbey

et al. 2015

Funct Integr Genomics

Self Cite

198

121

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MicroRNAs (miRNAs) are a class of small non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. Drought is a common environmental stress influencing crop growth and development. To date, it has been reported that a number of plant miRNA are involved in drought stress response. In this study, we comparatively investigated drought stress-responsive miRNAs in the root and leaf of bread wheat (Triticum aestivum cv. Sivas 111/33) by miRNA microarray screening. miRNA microarray analysis showed that 285 miRNAs (207 upregulated and 78 downregulated) and 244 miRNAs (115 upregulated and 129 downregulated) were differentially expressed in leaf and root tissues, respectively. Among the differentially expressed miRNAs, 23 miRNAs were only expressed in the leaf and 26 miRNAs were only expressed in the root of wheat growth under drought stress. Upon drought treatment, expression of miR159, miR160, miR166, miR169, miR172, miR395, miR396, miR408, miR472, miR477, miR482, miR1858, miR2118, and miR5049 were found to be significantly differentiated in bread wheat. The regulatory network analysis showed that miR395 has connections with a number of target transcripts, and miR159 and miR319 share a number of target genes. Drought-tolerant and drought-sensitive wheat cultivars showed altered expression pattern upon drought stress in terms of investigated miRNA and their target transcript expression level.

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Section: Introductionmentioning

confidence: 95%

miRNA-based drought regulation in wheat

Akdoğan

Tüfekçi

Uranbey

et al. 2015

Funct Integr Genomics

Self Cite

198

121

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“…However, there are several reports indicating that miRNAs from the MIR169 family are also involved in response to biotic and abiotic stresses (Sunkar et al 2012;Inal et al 2014;Luan et al 2015). Interestingly, under drought stress the wheat miR169 was highly downregulated in leaves but upregulated in roots (Akdogan et al 2016).…”

Section: Highly Conserved Wheat Mirnas Are Developmentally Regulatedmentioning

confidence: 99%

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

2017

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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 stemloop 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.

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“…It has been suggested that miR169-dependent NF-YA regulation can be involved in response to stresses in A. thaliana and maize (Leyva-Gonzalez et al 2012;Nelson et al 2007;Pant et al 2009). Its implications in fungal response in wheat (Inal et al 2014), as well as in drought tolerance and stem sugar content, were also described (Calvino and Messing 2013). Additionally, miR169 is involved in nodule development and nutritional balance in legume plants (Simon et al 2009).…”

Section: Target Predictionmentioning

confidence: 99%

Identification of apple miRNAs and their potential role in fire blight resistance

Kaja

Szcześniak

Jensen

et al. 2014

Tree Genetics & Genomes

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MicroRNAs (miRNAs) are key players in multiple biological processes; therefore, analysis and characterization of these small regulatory RNAs is a critical step toward a better understanding of animal and plant biology. In apple (Malus domestica), 200 microRNAs are known, which most probably represent only a fraction of miRNAome diversity. As a result, more effort is required to better annotate miRNAs and their functions in this economically important species. We performed deep sequencing of 12 small RNA libraries obtained for fire blight-resistant and fire blight-sensitive trees. In the sequencing results, we identified 116 novel microRNAs and confirmed a majority of previously reported apple miRNAs. We then experimentally verified selected candidates with RT-PCR and stem-loop quantitative PCR (qPCR) and performed differential expression analysis. Finally, we identified and characterized putative targets of all known apple miRNAs. The gene ontology (GO) enrichment analysis suggests prominent roles of miRNAs in response to stresses, including pathogen infection. In this study, we identified 116 new and confirmed the expression of 143 already known miRNAs. Moreover, our data suggests that apple microRNAs might be considered as regulators and markers of fire blight resistance. The analyses we performed allowed us to define four apple miRNAs potentially involved in fire blight resistance in apple trees: mdm-miR169a, mdm-miR160e, mdm-miR167b-g, and mdm-miR168a,b. These miRNAs are known to be involved in response to stresses across other plant species, usually by targeting stress response proteins. The relatively low number of candidates may result from the high variance of biological replicates and the fact that stress response miRNAs are usually induced by the stress factors and frequently expressed at a low level, or not expressed at all, in normal conditions. The results of our studies are freely available in an online database at

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Genome-wide fungal stress responsive miRNA expression in wheat

Cited by 70 publications

References 46 publications

miRNA-based drought regulation in wheat

miRNA-based drought regulation in wheat

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

Identification of apple miRNAs and their potential role in fire blight resistance

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