Identification of novel drought-responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis

Abstract

Small non-coding RNAs (sRNAs) namely microRNAs (miRNAs) and trans-acting small interfering RNAs (tasi-RNAs) play a crucial role in post-transcriptional regulation of gene expression and thus the control plant development and stress responses. In order to identify drought-responsive miRNAs and tasi-RNAs in sorghum, we constructed small RNA libraries from a drought tolerant (M35-1) and susceptible (C43) sorghum genotypes grown under control and drought stress conditions, and sequenced by Illumina Genome Analyzer IIx. Ninety seven conserved and 526 novel miRNAs representing 472 unique miRNA families were identified from sorghum. Ninety-six unique miRNAs were found to be regulated by drought stress, of which 32 were up- and 49 were down-regulated (fold change ≥ 2 or ≤ −2) at least in one genotype, while the remaining 15 miRNAs showed contrasting drought-regulated expression pattern between genotypes. A maximum of 17 and 18 miRNAs was differentially regulated under drought stress condition in the sensitive and tolerant genotypes, respectively. These results suggest that genotype dependent stress responsive regulation of miRNAs may contribute, at least in part, to the differential drought tolerance of sorghum genotypes. We also identified two miR390-directed TAS3 gene homologs and the auxin response factors as tasi-RNA targets. We predicted more than 1300 unique target genes for the novel and conserved miRNAs. These target genes were predicted to be involved in different cellular, metabolic, response to stimulus, biological regulation, and developmental processes. Genome-wide identification of stress-responsive miRNAs, tasi-RNAs and their targets identified in this study will be useful in unraveling the molecular mechanisms underlying drought stress responses and genetic improvement of biomass production and stress tolerance in sorghum.

Identification and Characterization of Stress-Responsive TAS3-Derived TasiRNAs in Melon

“…In line with a more general viewpoint, the incidence of environmental cues in the TAS3 processing reported herein agrees with previous results that have indicated a close interrelation between tasiARF accumulation and stress conditions in poplar (He et al 2018), arabidopsis (Moldovan et al 2009), and sorgum (Katiyar et al 2015). Interestingly, the observation that the general tendency of the alterations at the tasiARF level (down-regulation) observed in melon plants exposed to cold and HSVd was contradictory to that described for the TAS3 derived tasiRNAs in poplar plants exposed to saline conditions (where up-regulation of TAS3-derived tasiRNAs was reported).…”

“…According to our established filtering criteria (log2FC ≥1 or ≤-1, FDR value <0.05, and base mean ≥5), tasiARF accumulation was significantly reduced in the melon plants exposed to cold treatment (for both TAS3-L and TAS3-S derived tasiRNAs) and HSVd infection (for TAS3-S derived tasiRNA) ( Table 1 and Table S4). These results revealed that, in coincidence with the observed in other plants species (Moldovan et al 2009, Katiyar et al 2015, He et al 2018, the biogenesis of TAS3-derived tasiRNAs is a process susceptible to be altered by adverse environmental conditions. Quantitative RT-PCR (qRT-PCR) assays revealed that the accumulation of ARF2, ARF3 and ARF4 transcripts is significantly increased in cold-treated and HSVd-infected plants, as expected for the functional negative regulation of the TAS3-derived tasiARFs, whose accumulation decreases in the same conditions, on its predicted targets.…”

Deep sequencing identified potential miRNAs involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom

“…; Katiyar et al . ). The miRNAs identified from cardamom were diverse not only with respect to the number of miRNA families but also both location of mature miRNA sequences and length of precursor miRNAs.…”

Transcriptome analysis of drought-tolerant sorghum genotype SC56 in response to water stress reveals an oxidative stress defense strategy

“…In addition to the overall greater drought resistance of sorghum compared to other crops, certain sorghum genotypes that are more tolerant to drought than others exhibit a stay-green character that expresses post-anthesis and enables the continuation of photosynthesis and grain filling in dry conditions. These traits and the availability of its genome sequence have put sorghum in the forefront as a model system to elucidate the mechanisms of environmental stress tolerance, especially the response to drought [5,6].…”