Genome-wide profiling reveals extensive alterations in Pseudomonas putida-mediated miRNAs expression during drought stress in chickpea (Cicer arietinum L.)

Abstract

Pseudomonas putida strain MTCC5279 (RA) is a plant growth promoting rhizobacteria which improves growth and development of plants by colonizing their root surface and also confers drought stress tolerance. Further, along with several stress responsive genes, microRNAs are also well known for their crucial involvement in drought stress response. Considering the above, in this study, we performed identification and expression profiling of small RNAs in chickpea roots either uninoculated or inoculated with P. putida RA under drought stress through high-throughput sequencing. We identified 923 conserved and 216 novel miRNAs from all four libraries. Out of these, 431 and 332 conserved miRNAs; and 60 and 39 novel miRNAs were found to be differentially expressed in RA and drought with RA-inoculated plants, respectively. A total of 4647 and 551 target genes involved in various biological, cellular and molecular processes were predicted to be targets of conserved and novel miRNAs, respectively. Stem-loop quantitative real-time PCR analysis of selected nine miRNAs showed their expression patterns in consistence with those obtained from Illumina-sequencing. Besides, the expression patterns of miRNAs showed inverse correlation to that of their respective targets. Our results indicate that RA plays a very crucial role in regulating the expression of miRNAs and their targets during drought stress in chickpea paving the way for further characterization and utilization of miRNAs in crop improvement programmes.