Progress Toward Deep Sequencing-Based Discovery of Stress-Related MicroRNA in Plants and Available Bioinformatics Tools

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression at the posttranscriptional level. Recently, studies have discovered that miRNAs are induced by various stresses, suggesting that miRNAs may be an efficient target to improve crop resilience. Studies that are more recent have demonstrated that the response of miRNAs to stresses stimuli depends on type and level of stress, tissue, and genotype. Stress conditions induce several miRNAs, which alter downstream signaling cascades by regulating target genes and lead to adaptive responses to stress. During the past decade, research was focused on identification of plant miRNAs in response to environmental stressors, dissecting their expression patterns and studying their role in plant stress responses and tolerance. This has been accomplished principally by using next-generation sequencing (NGS) technologies, which have proven to be a powerful tool for this purpose. Altering miRNAs expression resulted in changes in plant growth and development under abiotic stress including cold, drought, salinity, nutrient, high temperature, and heavy metal stress as well as biotic stress such as fungus, bacteria, and virus infection. These findings implicate potential targets for genetic manipulation to improve stress tolerance in plants. This review is aimed to provide updates on recent miRNA research in improving plant resistance to biotic and abiotic stress. Moreover, we discuss availability of computational tools and genomics platforms for identification of stress-related miRNAs in plants.