Sequencing of small RNA transcriptome demonstrates distinct temporal expression pattern of stress regulated miRNA in wheat

MicroRNAs (miRNAs) guided post-transcriptional regulation has emerged as an essential component of stress response in plants. Critical understanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. In the present study, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and, leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). A total of 72 small RNA libraries were sequenced on the Illumina platform, generating ~524 million reads corresponding to ~129 million distinct tags. The latter were mapped to previously annotated wheat miRNA precursor sequences and a total of 232 conserved miRNAs were identified. One, two and 79 miRNAs were differentially expressed following exposure to ultraviolet radiations, continuous light and heat stress, respectively. Approximately 55% of the differentially expressed miRNAs were downregulated in response to heat stress at 0 and 1 DAT. The differentially expressed miRNA were predicted to target more than 104 putative mRNAs. Members of miR398, miR528 and miR156 families were primarily downregulated in response to heat stress and were predicted to target mRNA involved in activation of signal transduction pathways, antioxidant activity and flowering. miRNAs induced in response to heat stress were associated with histone variant proteins, auxin response factors and nutrient transport and storage proteins. These results suggest a temporal miRNA-guided post-transcriptional regulation that enables wheat to respond to abiotic stresses, particularly heat. Designing novel wheat breeding strategies such as ‘regulatory gene based’-marker assisted selection depends on the accurate identification of stress induced miRNAs.