Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens.

miRNAs are non-coding small RNAs that involve diverse biological processes. Until now, little is known about their roles in plant drought resistance. Physcomitrella patens is highly tolerant to drought; however, it is not clear about the basic biology of the traits that contribute P. patens this important character. In this work, we discovered 16 drought stress-associated miRNA (DsAmR) families in P. patens through computational analysis. Due to the possible discrepancy of expression periods and tissue distributions between potential DsAmRs and their targeting genes, and the existence of false positive results in computational identification, the prediction results should be examined with further experimental validation. We also constructed an miRNA co-regulation network, and identified two network hubs, miR902a-5p and miR414, which may play important roles in regulating drought-resistance traits. We distributed our results through an online database named ppt-miRBase, which can be accessed at http://bioinfor.cnu.edu.cn/ppt_miRBase/index.php. Our methods in finding DsAmR and miRNA co-regulation network showed a new direction for identifying miRNA functions

Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s

Identity between pre-miR166s in soybean. (TIF 5906 kb

microRNA Utilization as a Potential Tool for Stress Tolerance in Plants

This chapter describe the possibilities of MicroRNAs (miRNAs) in crop plants gene expression regulation in different metabolic pathways. Several current researches have shown different environmental stresses induce abnormal expression of miRNA, thus signifying that miRNAs may be an appropriate tool for genetical improvement in plant for stress tolerance. These miRNAs mainly control gene expression through translational inhibition. Generally, stress induce miRNAs-based inhibition of their target mRNAs, however, positive transcription factors accumulated and become more active after mRNA inhibition. Initially, researchers were mainly focused on miRNA identification, appropriate to specific or multiple environmental condition, expression profiling and recognize their roles in stress tolerance. Transformed miRNA expression studied in some plant species for better understanding of plant development and stress tolerance such as heavy metal, salinity, temperature, drought and nutrient deficiency. All these findings indicate that miRNAs act as a potential tool for genetic engineering and to enhance stress tolerance in crop plants

MicroRNA and cDNA-Microarray as Potential Targets against Abiotic Stress Response in Plants: Advances and Prospects

Abiotic stresses, such as temperature (heat and cold), salinity, and drought negatively affect plant productivity; hence, the molecular responses of abiotic stresses need to be investigated. Numerous molecular and genetic engineering studies have made substantial contributions and revealed that abiotic stresses are the key factors associated with production losses in plants. In response to abiotic stresses, altered expression patterns of miRNAs have been reported, and, as a result, cDNA-microarray and microRNA (miRNA) have been used to identify genes and their expression patterns against environmental adversities in plants. MicroRNA plays a significant role in environmental stresses, plant growth and development, and regulation of various biological and metabolic activities. MicroRNAs have been studied for over a decade to identify those susceptible to environmental stimuli, characterize expression patterns, and recognize their involvement in stress responses and tolerance. Recent findings have been reported that plants assign miRNAs as critical post-transcriptional regulators of gene expression in a sequence-specific manner to adapt to multiple abiotic stresses during their growth and developmental cycle. In this study, we reviewed the current status and described the application of cDNA-microarray and miRNA to understand the abiotic stress responses and different approaches used in plants to survive against different stresses. Despite the accessibility to suitable miRNAs, there is a lack of simple ways to identify miRNA and the application of cDNA-microarray. The elucidation of miRNA responses to abiotic stresses may lead to developing technologies for the early detection of plant environmental stressors. The miRNAs and cDNA-microarrays are powerful tools to enhance abiotic stress tolerance in plants through multiple advanced sequencing and bioinformatics techniques, including miRNA-regulated network, miRNA target prediction, miRNA identification, expression profile, features (disease or stress, biomarkers) association, tools based on machine learning algorithms, NGS, and tools specific for plants. Such technologies were established to identify miRNA and their target gene network prediction, emphasizing current achievements, impediments, and future perspectives. Furthermore, there is also a need to identify and classify new functional genes that may play a role in stress resistance, since many plant genes constitute an unexplained fraction

The Molecular Mechanism for Vegetative Phase Change: Regulation Ff Mir156 Expression and Action

The timing of the transitions between the juvenile and adult vegetative stages (vegetative phase change) is important for shoot maturation in plants. The juvenile and adult vegetative stages are defined by a difference in reproductive competence (incompetent versus competent), but they are also associated with a variety of other morphological and physiological differences. An evolutionarily conserved microRNA, miR156, plays a central role in promoting the juvenile phase through its repression of ten adult-phase-inducing SPL family transcription factors. A decrease in miR156 abundance and a concomitant increase in SPL expression are correlated with the onset of adult traits. However, despite the importance of miR156 in regulating vegetative phase change, very little is known about the regulation of miR156 itself at either transcriptional or posttranscriptional levels. The aim of this work is to further the understanding of the factors that contribute to the regulation of miR156. To identify the source of signals that repress miR156 and promote vegetative phase change, I performed organ ablation experiments in Arabidopsis. I discovered that defoliation, but not root or cotyledon ablation, delayed phase change, and this effect was attributable to an increase in the expression of MIR156. Defoliation also delayed phase change in Nicotiana benthamiana, Zea mays (maize), and Acacia mangium. Based on these results, I concluded that vegetative phase change is mediated by a leaf-derived signal that represses the transcription of MIR156. Furthermore, the possibility that sugar is the leaf signal was explored. Exogenous sugar repressed the expression of MIR156, resulting in an increase in SPL expression and early phase change. Consistent with this observation, mutants with reduced abundance of endogenous sugars had elevated miR156 expression and delayed phase change. This sugar response was dependent on the signaling function of the glucose sensor HXK1. To identify additional modifiers of the miR156 pathway, I performed a genetic screen using an SPL3-GFP translational reporter, identifying mutants that have either higher or lower GFP expression. This screen produced mutations in SUO, a BAH domain containing protein. SUO is a Processing-body (P-body) component and is specifically required for miR156-mediated translational repression, but not for miR156-mediated transcript cleavage. These results indicate that miR156-mediated translational repression plays an important role in regulating vegetative phase change