Identification of differentially expressed mungbean miRNAs and their targets in response to drought stress by small RNA deep sequencing

Abstract

MicroRNAs (miRNAs) are small, non-coding RNAs, 18–25 nt in length, that play a crucial role in regulating genes associated with the physiological processes and responses to various biotic and abiotic stresses. Different conserved and species-specific microRNAs and their functions have been identified, primarily in plants such as rice and Arabidopsis with sequenced genomes. Our present study identifies drought-responsive miRNAs and their potential targets from mungbean under three days of drought stress induced by PEG-6000. We constructed small RNA libraries from both control and drought-treated tolerant and susceptible mungbean genotypes and identified various miRNAs involved in drought stress regulation. Analysis of differentially expressed genes (DEGs) revealed 79 up-regulated and 158 down-regulated novel miRNAs and two up-and down-regulated known miRNAs under drought. Annotation of the miRNAs followed by target prediction and expression analysis revealed five miRNAs, Vra-miR160, Vra-miR164, Vra-miR167, Vra-miR394, and Vra-miR398, were potentially involved in the regulation of drought-responsive genes. Their predicted target genes were an Auxin response factor (ARF), a NAC (for petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) transcription factor, Serine acetyltransferase 1 , and Multicopper oxidase LPR2-like . The expression of drought-responsive miRNAs and their targets were validated by real-time PCR. Our data suggest that various known and novel microRNAs activated transcription factors, enzyme kinases, and hormone signaling pathways alleviate drought stress in the tolerant K-851 genotype of mungbean. • Our study identifies 79 novel up-regulated and 158 down-regulated miRNAs and their potential targets from mungbean under three days PEG induced drought stress using deep RNA sequencing. • The gene annotation of miRNAs followed by target prediction and their expression analysis revealed five miRNAs are likely to regulate drought-responsive genes, including various transcription factors, Serine acetyl transferases, and Multicopper oxidase LPR2-like genes. • This study shows that the expression of various novel microRNAs differs between the mungbean cv. K-851 (drought tolerant) and cv. PDM-139 (drought-sensitive) genotypes.