Identification of drought-responsive microRNAs and their targets in Ammopiptanthus mongolicus by using high-throughput sequencing

Abstract

MicroRNAs (miRNAs) regulate target gene expression to modulate plant growth, development, and biotic and abiotic stress response at the post-transcriptional level. Ammopiptanthus mongolicus, an ecologically important desert plant, is increasingly used as a model for studying stress tolerance in plants. The miRNA-mediated gene regulatory network might remarkably contribute to the high stress tolerance of A. mongolicus. However, a genome-wide identification of miRNAs and their targets is still lacking in A. mongolicus. In this study, 170 conserved and 156 non-conserved miRNAs were identified in A. mongolicus. We experimentally identified 298 miRNA-target pairs from the degradome data. Quantitative real-time polymerase chain reaction analyses identified 28 drought-responsive miRNAs in leaves and 15 in roots. Some characteristics of the miRNA-mediated regulatory network were found in A. mongolicus. Multiple miRNAs, including 2 newly identified non-conserved miRNAs, miR-P11 and miR-P14, generated from the precursors of miR169, were found to be involved in drought stress response. Further, miR2118 and miR858 participated in drought stress response by up-regulating OZF1 gene and certain MYB genes that were involved in the regulation of flavonol biosynthesis in A. mongolicus. The findings of this study might provide new insights for understanding the functions of miRNA in stress response in plants.

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

“…Error bars represent SE (n = 3). This is consistent with previous work showing the root-specific up-regulation of this miRNA (Gao et al, 2016) and revealing its essential role in the adaptation of lateral root growth to DS . Additional evidence supporting the stress-mediated regulation of miR393 is the presence of specific drought-induced ciselements in the promoter region of the related MIR gene (Devi et al, 2013).…”

“…Only in the case of miRNA-specific cDNA was the retrotranscription protocol modified using a stem-loop primer (rather than random primers) specific for each of the target miRNAs. The use of stemloop primers in RT-qPCR experiments is an effective and well-developed strategy for the detection of miRNAs, first reported by Chen et al (2005) and Varkonyi-Gasic et al (2007) and applied successfully in many research experiments addressing the study of abiotic stress-responsive miRNAs (Shen et al, 2010;Eldem et al, 2012;Xie et al, 2014;Candar-Cakir et al, 2016;Gao et al, 2016;Yadav et al, 2016). A list of the stem-loop primers used in this study is given in Supplemental Table S1.…”

Tissue-specific transcriptional biomarkers in medicinal plants: Application of large-scale meta-analysis and computational systems biology

“…Interactions between the different treatments and miRNAs are also noticeable, namely for starvation exposure, drought, salt and oxidative stress ( Fig 5D). They involve in level of metabolites by coordinating the hormones and miRNAs (Gao et al, 2016). In addition, upstream microRNAs, including miR166, miR397, miR162 and miR169, in network are indicated involvement of these miRNAs in the several biological processes related to plant development and responses to stresses (Fig 5B).…”

Regulatory networks of gene expression in maize (Zea mays) under drought stress and re-watering

“…A transcriptional analysis of GRMZ2G026980 confirmed the stimulatory effect of nitrate on xyloglucan accumulation in cells of the transition zone of the root apex; GRMZ2G026980 encodes a cell wall extension protein related to cell wall synthesis (Manoli et al, 2015; Fry et al, 1992; Geilfus et al, 2011). The expression of GRMZM2G082184 (encoding aquaporin NIP) may be associated with self-protection of plant cells under salt stress (Gao et al, 2016). The proteins encoded by three DEGs, GRMZ2G112686 (target of miR5076-5p, miR5783-5p, novel-m0283-3p), GRMZ2G026980 (xyloglucan endo-transglycosylase xyloglucan endotransglucosylase/hydrolase protein 2, target of miR6214-3p,novel-m0611-5p,miR5783-5p) and GRMZ2G082184 (aquaporin NIP, target of miR9760-5p, 6214-3p, 5809-5p) are known to participate in secondary metabolite synthesis and influence the synthesis of the cell wall.…”