Small RNA profiling in contrasting genotypes of chickpea through high-throughput sequencing in response to drought stress.

Global warming has reached an alarming situation, which led to altered climatic conditions. The irregular rainfalls and depletion of soil water level are the significant consequences of these climatic changes causing a decrease in water availability to the crop plants. Drought/water deficit is the most severe and the number one abiotic constraint to chickpea production throughout India, as the crop is largely grown as a rainfed crop during the post-rainy season. Root tissue is the primary organ involved in water uptake as well as water stress sensing and signaling. Deep sequencing was used for microRNA expression profiling in the root tissue of the chickpea (Cicer arietinum L.) in order to investigate post-transcriptional regulation of gene expression under drought stress. A total of 379 unique miRNA sequences including 224 conserved ones belonging to 51 families and 155 novel miRNAs were obtained from four small RNA libraries from two contrasting chickpea genotypes. 98 miRNAs were found to be differentially expressed between genotypes under water deficit stress. Poly(A)-based qRT-PCR (Quantitative real-time PCR) analysis revealed that miR159, miR171, and miR390 emerged as drought-responsive miRNAs in the tolerant genotype. More than one thousand mRNA targets involved in diverse cellular processes were predicted for all the miRNAs. The genomic locus distribution of identified miRNAs was mapped on eight chickpea chromosomes. Stress-responsive expression patterns of selected miRNAs, inverse expression patterns of their target genes, and the target-cleavage sites were validated by 5'RLM-RACE. This study will provide molecular insight into post-transcriptional gene regulation under water deficit stress mediated by small RNA and open a new avenue for crop improvement.