Identification and characterization of drought responsive miRNAs from a drought tolerant rice genotype of Assam

Abstract

Rice production is adversely constrained by drought especially if encountered during panicle initiation and flowering stage. Several traditional rice cultivars/landraces have inherent functioning mechanism of adaptation in diverse environmental adversities. The genetic and molecular characterization of these traditional tolerant germplasm at the omics level is critical to understand the schemas and molecular networks regulating stress tolerance and finally to identify candidate genes involved in stress tolerance. The current study attempts to unravel miRNA in response to drought stress in ARC-10372, a drought tolerant important rice genotype of Assam Rice Collection. Small RNA sequencing was performed that resulted a total of 45,742,638 good quality reads in both drought stressed and control samples. Upon annotation, 178 and 131 known miRNA were found to be expressed in control and drought samples, respectively. Out of these, 109 known miRNA belonging to 58 families were found to be differentially expressed. Nine (9) earlier reported drought responsive miRNAs were found to be expressed significantly in ARC-10372 and their expression pattern is similar to the earlier studies and, 10 miRNAs (miR531, miR827, miR8175 miR977, miR6300, miR1861, miR440, miR9773, miR3982 and miR1876) which were not reported earlier as drought responsive were found to be regulated significantly under drought stress in this local landrace. In silico identification revealed that target of most of these miRNAs are transcription factors such as NAC, MYB, MYC,ARF thereby further confirming their role in regulation during stress adaptation. Four new stress responsive miRNA targeted stress related transcript. The expression pattern of miRNA in sRNA sequencing data were validated by qPCR and most of them exhibited concordance with NGS data. In light of the reported studies, the present study for the first time gives a comparative aspect of drought regulated miRNome of leaf at panicle initiation stage in drought tolerant rice cultivar ARC-10372.