Identification of miRNA-mediated drought responsive multi-tiered regulatory network in drought tolerant rice, Nagina 22

Abstract

Comparative characterization of microRNA-mediated stress regulatory networks in contrasting rice cultivars is critical to decipher plant stress response. Consequently, a multi-level comparative analysis, using sRNA sequencing, degradome analysis, enzymatic and metabolite assays and metal ion analysis, in drought tolerant and sensitive rice cultivars was conducted. The study identified a group of miRNAs “Cultivar-specific drought responsive” (CSDR)-miRNAs (osa-miR159f, osa-miR1871, osa-miR398b, osa-miR408-3p, osa-miR2878-5p, osa-miR528-5p and osa-miR397a) that were up-regulated in the flag-leaves of tolerant cultivar, Nagina 22 (N22) and Vandana, but down-regulated in the sensitive cultivar, Pusa Basmati 1 (PB1) and IR64, during drought. Interestingly, CSDR-miRNAs target several copper-protein coding transcripts like plantacyanins, laccases and Copper/Zinc superoxide dismutases (Cu/Zn SODs) and are themselves found to be similarly induced under simulated copper-starvation in both N22 and PB1. Transcription factor OsSPL9, implicated in Cu-homeostasis also interacted with osa-miR408-3p and osa-miR528-5p promoters. Further, N22 flag leaves showed lower SOD activity, accumulated ROS and had a higher stomata closure. Interestingly, compared to PB1, internal Cu levels significantly decreased in the N22 flag-leaves, during drought. Thus, the study identifies the unique drought mediated dynamism and interplay of Cu and ROS homeostasis, in the flag leaves of drought tolerant rice, wherein CSDR-miRNAs play a pivotal role.

Temporal responses of conserved miRNAs to drought and their associations with drought tolerance and productivity in rice

“…Time course of the regulation of miRNAs under drought conditions provides key information to identify miRNAs associated with DT miRNAs are in the response to drought stress and play essential roles in rice DT [7,49]. Many previous studies have described responses of miRNAs to drought in different rice genotypes [3,5,6] and tissues [2,18]. The common design of these experiments is to generate drought-responsive miRNAs from a single genotype [2,6,56] or a pair of genotypes with contrasting tolerance [3,5].…”

“…Recently, attentions have been focused on the importance of posttranscriptional regulation by miRNAs in drought tolerance (DT) due to their central roles in the regulatory network [7,38]. With the fast development of next-generation sequencing, drought-responsive miRNAs (DRMs) have been identified in diverse crops, including cotton [48], rapeseed [21], maize [1], tomato [28], and rice (Oryza sativa) [3,5,6]. Many DRMs have been characterized as important modulators in DT via regulating the expression of drought-responsive genes [7].…”

“…There have been 604 pre-miRNAs, which encode 738 mature miRNAs, identified in rice and recorded in miRBase (release 22.1, [22]). Hundreds of miRNAs have been determined as DRMs by several genome-wide investigations in different genotypes or tissues [2,3,6,56]. However, there is still a large knowledge gap between the identification of DRMs and the characterization of their associations with DT [17].…”

“…Many former studies have typically investigated a single genotype [3,6,56] or two rice genotypes of contrasting DT [5] to identify DRMs. A miRNA that is differentially regulated in response to environmental stress is not necessarily associated with stress tolerance [17].…”

Human Genes AreIn SilicoPotential Targets For Rice miRNA

“…For example, developed rice lines overexpressing MIR529a have been shown to have increased resistance to oxidative stress (Chen & Li, 2018; Cimini et al, 2019). The participation of osa-miR159f, osa-miR1871, osa-miR398b, osa-miR408-3p, osa-miR2878-5p, osa-miR528-5p and osa-miR397a in the regulation of a number of physiological processes of rice has been established (Balyan et al, 2017). The expression of miRNA of Setaria italica (sit) changed many times: sit-miR1432-3p, sit-miR156a-5p, sit-miR156b-5p, sit-miR164a-5p, sit-miR167b-5p, sit-miR171c-3p, sit-miR2118-3p, sit-miR390-5p, sit-miR394-5p, sit-miR395-3p, sit-miR408-3p, sit-miR529a-3p, sit-miR529b-3p, and sit-miR827, sit-miR159b-3p, sit-miR319c-5p, sit-miR528-5p and sit-miR535-5p under various stresses (Wang et al, 2016).…”