Functions of microRNAs in plant stress responses

Unravelling the MicroRNA-Mediated Gene Regulation in Developing Pongamia Seeds by High-Throughput Small RNA Profiling

Pongamia (Millettia pinnata syn. Pongamia pinnata) is a multipurpose biofuel tree which can withstand a variety of abiotic stresses. Commercial applications of Pongamia trees may substantially benefit from improvements in their oil-seed productivity, which is governed by complex regulatory mechanisms underlying seed development. MicroRNAs (miRNAs) are important molecular regulators of plant development, while relatively little is known about their roles in seed development, especially for woody plants. In this study, we identified 236 conserved miRNAs within 49 families and 143 novel miRNAs via deep sequencing of Pongamia seeds sampled at three developmental phases. For these miRNAs, 1327 target genes were computationally predicted. Furthermore, 115 differentially expressed miRNAs (DEmiRs) between successive developmental phases were sorted out. The DEmiR-targeted genes were preferentially enriched in the functional categories associated with DNA damage repair and photosynthesis. The combined analyses of expression profiles for DEmiRs and functional annotations for their target genes revealed the involvements of both conserved and novel miRNA-target modules in Pongamia seed development. Quantitative Real-Time PCR validated the expression changes of 15 DEmiRs as well as the opposite expression changes of six targets. These results provide valuable miRNA candidates for further functional characterization and breeding practice in Pongamia and other oilseed plants.

Regulation of terpenoid biosynthesis by miRNA in Persicaria minor induced by Fusarium oxysporum

Background

Persicaria minor (kesum) is an herbaceous plant with a high level of secondary metabolite compounds, particularly terpenoids. These terpenoid compounds have well-established roles in the pharmaceutical and food industries. Although the terpenoids of P. minor have been studied thoroughly, the involvement of microRNA (miRNA) in terpenoid regulation remains poorly understood and needs to be explored. In this study, P. minor plants were inoculated with the pathogenic fungus Fusarium oxysporum for terpenoid induction.

Result

SPME GC-MS analysis showed the highest terpenoid accumulation on the 6th day post-inoculation (dpi) compared to the other treatment time points (0 dpi, 3 dpi, and 9 dpi). Among the increased terpenoid compounds, α-cedrene, valencene and β-bisabolene were prominent. P. minor inoculated for 6 days was selected for miRNA library construction using next generation sequencing. Differential gene expression analysis showed that 58 miRNAs belonging to 30 families had significantly altered regulation. Among these 58 differentially expressed genes (DEGs), 33 miRNAs were upregulated, whereas 25 miRNAs were downregulated. Two putative novel pre-miRNAs were identified and validated through reverse transcriptase PCR. Prediction of target transcripts potentially involved in the mevalonate pathway (MVA) was carried out by psRobot software, resulting in four miRNAs: pmi-miR530, pmi-miR6173, pmi-miR6300 and a novel miRNA, pmi-Nov_13. In addition, two miRNAs, miR396a and miR398f/g, were predicted to have their target transcripts in the non-mevalonate pathway (MEP). In addition, a novel miRNA, pmi-Nov_12, was identified to have a target gene involved in green leaf volatile (GLV) biosynthesis. RT-qPCR analysis showed that pmi-miR6173, pmi-miR6300 and pmi-nov_13 were downregulated, while miR396a and miR398f/g were upregulated. Pmi-miR530 showed upregulation at 9 dpi, and dynamic expression was observed for pmi-nov_12. Pmi-6300 and pmi-miR396a cleavage sites were detected through degradome sequence analysis. Furthermore, the relationship between miRNA metabolites and mRNA metabolites was validated using correlation analysis.

Conclusion

Our findings suggest that six studied miRNAs post-transcriptionally regulate terpenoid biosynthesis in P. minor. This regulatory behaviour of miRNAs has potential as a genetic tool to regulate terpenoid biosynthesis in P. minor.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5954-0) contains supplementary material, which is available to authorized users.

Identification of Differentially Expressed miRNAs between a Wheat K-type Cytoplasmic Male Sterility Line and Its Near-Isogenic Restorer Line

K-type cytoplasmic male sterility (KCMS) lines were ideal material for three-line hybrid wheat system due to the major role in hybrid wheat production. In this study, the morphology of developing microspore and mature pollen was compared between a KCMS line and its near-isogenic restorer line (KCMS-NIL). The most striking difference is that the microspore was unable to develop into tricellular pollen in the KCMS line. MicroRNA plays vital roles in flowering and gametophyte development. Small RNA sequencing identified a total of 274 known and 401 novel miRNAs differentially expressed between two lines or two developmental stages. Most of miRNAs with high abundance were differentially expressed at the uninucleate stage, and their expression level recovered or remained at the binucleate stage. Further degradome sequencing identified target genes which were mainly enriched in transcription regulation, phytohormone signaling and RNA degradation pathways. Combining with the transcriptome data, a correlation was found between the abnormal anther development, such as postmeiotic mitosis cessation, deformative pollen wall and the chromosome condensation of the vegetative cell, and the alterations in the related miRNA and their targets expression profiles. According to the correlation and pathway analysis, we propose a hypothetic miRNA-mediated network for the control of KCMS restoration.

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation

Abiotic stress is one of the major threats to plant crop yield and productivity. When plants are exposed to stress, production of reactive oxygen species (ROS) increases, which could lead to extensive cellular damage and hence crop loss. During evolution, plants have acquired antioxidant defense systems which can not only detoxify ROS but also adjust ROS levels required for proper cell signaling. Ascorbate peroxidase (APX), glutathione peroxidase (GPX), catalase (CAT) and superoxide dismutase (SOD) are crucial enzymes involved in ROS detoxification. In this study, 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginellamoellendorffii. Phylogenetic analyses classified the APX, GPX, and SOD proteins into five clades each, and CAT proteins into three clades. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems. The results suggest molecular pathways that regulate ROS in resurrection species and the role of APX, GPX, CAT and SOD genes in resurrection species during stress.

Determination of the MiRNAs Related to Bean Pyralid Larvae Resistance in Soybean Using Small RNA and Transcriptome Sequencing

Soybean is one of the most important oil crops in the world. Bean pyralid is a major leaf-feeding insect of soybean. In order to screen out the functional genes and regulatory pathways related to the resistance for bean pyralid larvae, the small RNA and transcriptome sequencing were performed based on the highly resistant material (Gantai-2-2) and highly susceptible material (Wan 82-178) of soybean. The results showed that, when comparing 48 h feeding with 0 h feeding, 55 differentially expressed miRNAs were identified in Gantai-2-2 and 58 differentially expressed miRNAs were identified in Wan82-178. When comparing Gantai-2-2 with Wan82-178, 77 differentially expressed miRNAs were identified at 0 h feeding, and 70 differentially expressed miRNAs were identified at 48 h feeding. The pathway analysis of the predicted target genes revealed that the plant hormone signal transduction, RNA transport, protein processing in the endoplasmic reticulum, zeatin biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, and isoquinoline alkaloid biosynthesis may play important roles in soybean's defense against the stress caused by bean pyralid larvae. According to conjoint analysis of the miRNA/mRNA, a total of 20 differentially expressed miRNAs were negatively correlated with 26 differentially expressed target genes. The qRT-PCR analysis verified that the small RNA sequencing results were credible. According to the analyses of the differentially expressed miRNAs, we speculated that miRNAs are more likely to play key roles in the resistance to insects. Gma-miR156q, Gma-miR166u, Gma-miR166b, Gma-miR166j-3p, Gma-miR319d, Gma-miR394a-3p, Gma-miR396e, and so on-as well as their negatively regulated differentially expressed target genes-may be involved in the regulation of soybean resistance to bean pyralid larvae. These results laid a foundation for further in-depth research regarding the action mechanisms of insect resistance.

Conserved miR396b-GRF Regulation Is Involved in Abiotic Stress Responses in Pitaya (Hylocereus polyrhizus)

MicroRNA396 (miR396) is a conserved microRNA family that targets growth-regulating factors (GRFs), which play significant roles in plant growth and stress responses. Available evidence justifies the idea that miR396-targeted GRFs have important functions in many plant species; however, no genome-wide analysis of the pitaya (Hylocereus polyrhizus) miR396 gene has yet been reported. Further, its biological functions remain elusive. To uncover the regulatory roles of miR396 and its targets, the hairpin sequence of pitaya miR396b and the open reading frame (ORF) of its target, HpGRF6, were isolated from pitaya. Phylogenetic analysis showed that the precursor miR396b (MIR396b) gene of plants might be clustered into three major groups, and, generally, a more recent evolutionary relationship in the intra-family has been demonstrated. The sequence analysis indicated that the binding site of hpo-miR396b in HpGRF6 is located at the conserved motif which codes the conserved "RSRKPVE" amino acid in the Trp-Arg-Cys (WRC) region. In addition, degradome sequencing analysis confirmed that four GRFs (GRF1, c56908.graph_c0; GRF4, c52862.graph_c0; GRF6, c39378.graph_c0 and GRF9, c54658.graph_c0) are hpo-miR396b targets that are regulated by specific cleavage at the binding site between the 10th and 11th nucleotides from the 5' terminus of hpo-miR396b. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that hpo-miR396b is down-regulated when confronted with drought stress (15% polyethylene glycol, PEG), and its expression fluctuates under other abiotic stresses, i.e., low temperature (4 ± 1 °C), high temperature (42 ± 1 °C), NaCl (100 mM), and abscisic acid (ABA; 0.38 mM). Conversely, the expression of HpGRF6 showed the opposite trend to exposure to these abiotic stresses. Taken together, hpo-miR396b plays a regulatory role in the control of HpGRF6, which might influence the abiotic stress response of pitaya. This is the first documentation of this role in pitaya and improves the understanding of the molecular mechanisms underlying the tolerance to drought stress in this fruit.

Whirly (Why) transcription factors in tomato (Solanum lycopersicum L.): genome-wide identification and transcriptional profiling under drought and salt stresses

Whirly (Why) transcription factor (TFs) constitute one of the important TF families which plays essential roles in plant metabolism to cope with environmental stresses. In the present study, Why genes were identified at genome-wide scale in tomato (Solanum lycopersicum), and bioinformatics analyses were implemented. Validation of Why genes expressions under drought and salt stresses were also performed using RT-qPCR. The analyses revealed the presence of two Why genes in tomato genome, SlWhy1 (Solyc05g007100.2.1) and SlWhy2 (Solyc11g044750.1.1). Both genes contained Whirly transcription factor domain structure (PF08536), and Why proteins were in basic character (pI ≥ 7). While the lengths of the proteins ranged from 268 to 236 amino acid residues for SlWhy1 and SlWhy2 respectively, exon numbers identified in both genes were seven. According to the digital expression data, SlWhy genes are expressed at medium level in different anatomical parts and developmental stages. In the promotor sequence analysis, 13 types of putative TF binding sites were identified, and the highest motif number was 46, found for GATA TF. Gene co-expression analyses revealed that complex networks for SlWhy genes, which are connected with various metabolic pathways. Based on the RT-qPCR data, both SlWhy1 and SlWhy2 genes were up-regulated under salt and drought stresses. 3D structure analyses revealed that SlWhy1 protein had a more diverged structure than SlWhy2 protein, based on their comparisons in Arabidopsis and potato. The results obtained in the present study could be a useful scientific basis for understanding Why genes in tomato and their functions under abiotic stress conditions.

Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as "photosynthesis" and "starch and sucrose metabolism," were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

What Makes the Wood? Exploring the Molecular Mechanisms of Xylem Acclimation in Hardwoods to an Ever-Changing Environment

Wood, also designated as secondary xylem, is the major structure that gives trees and other woody plants stability for upright growth and maintains the water supply from the roots to all other plant tissues. Over recent decades, our understanding of the cellular processes of wood formation (xylogenesis) has substantially increased. Plants as sessile organisms face a multitude of abiotic stresses, e.g., heat, drought, salinity and limiting nutrient availability that require them to adjust their wood structure to maintain stability and water conductivity. Because of global climate change, more drastic and sudden changes in temperature and longer periods without precipitation are expected to impact tree productivity in the near future. Thus, it is essential to understand the process of wood formation in trees under stress. Many traits, such as vessel frequency and size, fiber thickness and density change in response to different environmental stimuli. Here, we provide an overview of our current understanding of how abiotic stress factors affect wood formation on the molecular level focussing on the genes that have been identified in these processes.

Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb

BACKGROUND

MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rosa rugosa Thunb. is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and their functions in R. rugosa.

RESULTS

We sequenced 10 samll RNA profiles from the roots, petals, pollens, stamens, and leaves and 4 RNA-seq profiles in leaves and petals to analysis miRNA, phasiRNAs and mRNAs in R. rugosa. In addition, we acquired a degradome sequencing profile from leaf of R. rugosa to identify miRNA and phasiRNA targets using the SeqTar algorithm. We have identified 321 conserved miRNA homologs including primary transcripts for 25 conserved miRNAs, and 22 novel miRNAs. We identified 592 putative targets of the conserved miRNAs or tasiRNAs that showed significant accumulations of degradome reads. We found differential expression patterns of conserved miRNAs in five different tissues of R. rugosa. We identified three hundred and thirty nine 21 nucleotide (nt) PHAS loci, and forty nine 24 nt PHAS loci, respectively. Our results suggest that miR482 triggers generations of phasiRNAs by targeting nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes in R. rugosa. Our results also suggest that the deregulated genes in leaves and petals are significantly enriched in GO terms and KEGG pathways related to metabolic processes and photosynthesis.

CONCLUSIONS

These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions, in R. rugosa.

Plant Hormones in Phytoplasma Infected Plants

Phytoplasmas are bacterial plant pathogens that need a plant host and an insect vector for their spread and survival. In plants, the physiological responses that phytoplasmas trigger result in symptom development through effects on hormonal, nutritional, and stress signaling pathways, and the interactions between these. In this review, recent advances on the involvement of plant hormones together with their known and deduced roles in plants infected with phytoplasmas are discussed. Several studies have directly, or in many cases indirectly, addressed plant hormone systems in phytoplasma-infected plants. These have provided accumulating evidence that phytoplasmas extensively affect plant hormone pathways. Phytoplasmas thus, with disturbing complex plant hormone networks, suppress plant immunity and modify plant structure, while optimizing their nutrient acquisition and facilitating their colonization of the plants, and their dissemination among plants by their insect vectors.

Tissue-specific transcriptional regulation of seven heavy metal stress-responsive miRNAs and their putative targets in nickel indicator castor bean (R. communis L.) plants

R.communis L. has high capability to accumulate nickel which is a trace nutrient for higher plants and also an environmental contaminant causes toxicity related symptoms at higher concentrations. MicroRNAs (miRNAs) are known to be important modulators of responses against heavy metal stress for detoxification of the metal. In this study, we experimentally measured and validated the transcript levels of the seven heavy metal stress response-related miRNAs and the expression levels of target genes in both leaf and root tissues of R. communis L. subjected to three different concentrations of nickel stress via qRT-PCR quantification. The results demonstrated differential regulations of heavy metal stress-responsive miRNAs and their putative targets in both tissues in same stress treatments. This dynamic regulation suggest that regulatory processes differ between the tissues under nickel stress. Our data suggest that, miR838 was the most responsive to the Ni2+ stress. miR398 target gene Cu-Zn/SOD was found to be up-regulated in both root and leaf tissues. The relations between TCP and expression levels of miR159 and miR319 were also found statistically significant exclusive to leaf tissues. In leaf tissue, changes in miR395 level and its putative target genes, sulphate transporter and sulphate adenyltransferase gene were found in relation whereas, only expression level of sulphate transporter represented a statistically significant relation in root tissue. The sharp decrease in transcript levels of 2r3 myb gene at lower nickel dose suggest to investigate the role of r2r3 myb and the all MYB family members in primary and secondary metabolisms against nickel stress.

Quantitative expression of microRNAs in Brassica oleracea infected with Xanthomonas campestris pv. campestris

Brassica oleracea var. capitata (cabbage) is an economically important crop affected by black rot disease caused by Xanthomonas campestris pv. campestris (Xcc). MicroRNAs (miRNAs) play an important role in plant defense modulation and therefore the analysis of these molecules can help better understand plant-pathogen interactions. In this study, we report the differential expression of four miRNAs that seem to participate in the plant response to Xcc infection. Northern Blot and RT-qPCR techniques were used to measure miRNA expression in resistant (União) and susceptible (Kenzan) cultivars. From 6 miRNAs analyzed, 4 were detected and differentially expressed, showing a down- and upregulated expression profile in susceptible and resistant cultivars, respectively. These results suggest that miR156, miR167, miR169, and miR390 could play a role in B. oleracea resistance enhancement against Xcc and could be explored as potential resistance markers in B. oleracea-Xcc interaction.

Alfalfa response to heat stress is modulated by microRNA156

Heat stress and extreme temperatures negatively affect plant development by disrupting regular cellular and biochemical functions, ultimately leading to reduced crop production. Alfalfa (Medicago sativa) is an important forage crop grown worldwide as forage for livestock feed. Limiting the effects of abiotic stress by developing alfalfa cultivars that are stress tolerant would help mitigate losses to crop production. Members of the microRNA156 (miR156) family regulate the Squamosa Promoter-Binding Protein-Like (SPL) genes that in turn impact plant growth and development by regulating downstream genes in response to various abiotic stresses. In this study, alfalfa with miR156 overexpression and SPL13 RNAi knockdown show increased tolerance to heat stress (40°C). Transgenic plants show high water potential and increased non-enzymatic antioxidant content under heat stress. Moreover, anthocyanin content and chlorophyll abundance were increased under stress. Expression of some important transcription factors and downstream genes involved in abiotic stress response were altered in miR156-overexpressing genotypes under heat. Taken together, our results demonstrate that the miR156/SPL13 network contributes to improving heat stress tolerance in alfalfa.

The mitochondrial copper chaperone COX19 influences copper and iron homeostasis in arabidopsis

The mitochondrial metallochaperone COX19 influences iron and copper responses highlighting a role of mitochondria in modulating metal homeostasis in Arabidopsis. The mitochondrial copper chaperone COX19 participates in the biogenesis of cytochrome c oxidase (COX) in yeast and humans. In this work, we studied the function of COX19 in Arabidopsis thaliana, using plants with either decreased or increased COX19 levels. A fusion of COX19 to the red fluorescent protein localized to mitochondria in vivo, suggesting that Arabidopsis COX19 is a mitochondrial protein. Silencing of COX19 using an artificial miRNA did not cause changes in COX activity levels or respiration in plants grown under standard conditions. These amiCOX19 plants, however, showed decreased expression of the low-copper responsive miRNA gene MIR398b and an induction of the miR398 target CSD1 relative to wild-type plants. Plants with increased COX19 levels, instead, showed induction of MIR398b and other low-copper responsive genes. In addition, global transcriptional changes in rosettes of amiCOX19 plants resembled those observed under iron deficiency. Phenotypic analysis indicated that the roots of amiCOX19 plants show altered growth responses to copper excess and iron deficiency. COX activity levels and COX-dependent respiration were lower in amiCOX19 plants than in wild-type plants under iron deficiency conditions, suggesting that COX19 function is particularly important for COX assembly under iron deficiency. The results indicate that the mitochondrial copper chaperone COX19 has a role in regulating copper and iron homeostasis and responses in plants.

The Phosphoproteomic Response of Okra (Abelmoschus esculentus L.) Seedlings to Salt Stress

Soil salinization is a major environmental stresses that seriously threatens land use efficiency and crop yields worldwide. Although the overall response of plants to NaCl has been well studied, the contribution of protein phosphorylation to the detoxification and tolerance of NaCl in okra (Abelmoschus esculentus L.) seedlings is unclear. The molecular bases of okra seedlings’ responses to 300 mM NaCl stress are discussed in this study. Using a combination of affinity enrichment, tandem mass tag (TMT) labeling and high-performance liquid chromatography–tandem mass spectrometry analysis, a large-scale phosphoproteome analysis was performed in okra. A total of 4341 phosphorylation sites were identified on 2550 proteins, of which 3453 sites of 2268 proteins provided quantitative information. We found that 91 sites were upregulated and 307 sites were downregulated in the NaCl/control comparison group. Subsequently, we performed a systematic bioinformatics analysis including gene ontology annotation, domain annotation, subcellular localization, and Kyoto Encyclopedia of Genes and Genomes pathway annotation. The latter revealed that the differentially expressed proteins were most strongly associated with ‘photosynthesis antenna proteins’ and ‘RNA degradation’. These differentially expressed proteins probably play important roles in salt stress responses in okra. The results should help to increase our understanding of the molecular mechanisms of plant post-translational modifications in response to salt stress.

MicroRNAome Profile of Euphorbia kansui in Response to Methyl Jasmonate

miRNAs play vital regulatory roles in different plant developmental stages and in plant response to biotic and abiotic stresses. However, information is limited on the miRNA regulatory mechanism to methyl jasmonate (MeJA). In this study, we used the microRNAome profile to illustrate the relevant regulatory mechanisms of Euphorbia kansui in response to methyl jasmonate (MeJA) through Illumina RNA-Seq. As a result, we identified 875 miRNAs corresponding to 11,277 target mRNAs, among them, 168 known miRNA families representing 6019 target mRNAs sequences were obtained. 452 miRNA-mRNA pairs presented an anti-correlationship (Cor < −0.50 and p-value of correlation ≤ 0.05). The miRNA with a fold change ≥ 2 and a p (p-Value) < 0.05 in pairwise comparison were identified as significant differentially expressed miRNAs (DEMs). The DEMs in MeJA treatment of 0, 24, 36 and 48 h were compared by using Short Time Expression Miner (STEM) cluster and 4 significant gene profiles (p-value ≤ 0.02) were identified. Through the kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) enrichment analysis on all miRNA targets, we identified 33 mRNAs in terpenoid biosynthesis, which were regulated by miRNAs under MeJA treatment, so the miRNA maybe involved in the response of E. kansui plant to exogenous MeJA and the results would provide very useful information on illustrating the regulatory mechanism of E. kansui and also provide an overall view of the miRNAs response to MeJA stress of a non-model plant.

Identification and analysis of oxygen responsive microRNAs in the root of wild tomato (S. habrochaites)

BACKGROUND

MicroRNA (miRNA) are key players in regulating expression of target genes at post-transcriptional level. A number of miRNAs are implicated in modulating tolerance to various abiotic stresses. Waterlogging is an abiotic stress that deters plant growth and productivity by hypoxia. Dozens of reports mention about the miRNAs expressed in response to waterlogging and hypoxia. Despite the fact that tomato is a model vegetable but waterlogging sensitive crop, the role of miRNAs in hypoxia tolerance is poorly understood in tomato.

RESULTS

In this study, we investigated the differentially expressed miRNAs between hypoxia-treated and untreated wild tomato root by using high-throughput sequencing technology. A total of 33 known miRNAs were lowly expressed, whereas only 3 miRNAs showed higher expression in hypoxia-treated wild tomato root compared with untreated wild tomato root. Then two conserved and lowly expressed miRNAs, miR171 and miR390, were deactivated by Short Tandem Target Mimic (STTM) technology in Arabidopsis. As the results, the number and length of lateral roots were more in STTM171 and STTM390 transgenic lines compared with that of wild type plant, which partly phenocopy the increase root number and shortening the root length in hypoxia-treated wild tomato root.

CONCLUSIONS

The differentially expressed miRNAs between hypoxia-treated wild tomato and control root, which contribute to the auxin homeostasis, morphologic change, and stress response, might result in reduction in the biomass and length of the root in hypoxiated conditions.

Micromanagement of Developmental and Stress-Induced Senescence: The Emerging Role of MicroRNAs

MicroRNAs are short (19⁻24-nucleotide-long), non-coding RNA molecules. They downregulate gene expression by triggering the cleavage or translational inhibition of complementary mRNAs. Senescence is a stage of development following growth completion and is dependent on the expression of specific genes. MicroRNAs control the gene expression responsible for plant competence to answer senescence signals. Therefore, they coordinate the juvenile-to-adult phase transition of the whole plant, the growth and senescence phase of each leaf, age-related cellular structure changes during vessel formation, and remobilization of resources occurring during senescence. MicroRNAs are also engaged in the ripening and postharvest senescence of agronomically important fruits. Moreover, the hormonal regulation of senescence requires microRNA contribution. Environmental cues, such as darkness or drought, induce senescence-like processes in which microRNAs also play regulatory roles. In this review, we discuss recent findings concerning the role of microRNAs in the senescence of various plant species.

Identification of microRNAs and their targets responding to low-potassium stress in two barley genotypes differing in low-K tolerance

MicroRNAs (miRNAs) have diverse and crucial roles in plant growth and development, including in the response to abiotic stresses. Although plant responses to K deficiency are well documented at the physiological and transcriptional levels, the miRNA-mediated post-transcriptional pathways are still not clearly elucidated. In this study, high-throughput sequencing and degradome analysis were performed using two barley genotypes differing in low-K tolerance (XZ149, tolerant and ZD9, sensitive), to determine the genotypic difference in miRNAs profiling. A total of 270 miRNAs were detected in the roots of XZ149 and ZD9 at 2 d and 10 d after low-K treatment, of which 195 were commonly found in both genotypes. Their targets were further investigated by bioinformatics prediction and degradome sequencing approach. The results showed that ata-miR1432-5p might act as a regulator participating in Ca²⁺ signaling pathways in response to low-K stress. The difference in the miR444/MADS-box model as well as pathways mediated by miR319/TCP4 and miR396/GRF could be attributed to high tolerance to low-K stress in XZ149. In addition, other conserved and novel miRNAs families associated with low-K tolerance were also detected. The current results provide molecular evidence for understanding the possible involvement of miRNAs in the regulation of low-K tolerance.

MicroRNA414c affects salt tolerance of cotton by regulating reactive oxygen species metabolism under salinity stress

Salinity stress is a major abiotic stress affecting the productivity and fiber quality of cotton. Although reactive oxygen species (ROS) play critical roles in plant stress responses, their complex molecular regulatory mechanism under salinity stress is largely unknown in cotton, especially microRNA (miRNA)-mediated regulation of superoxide dismutase gene expression. Here, we report that a cotton iron superoxide dismutase gene GhFSD1 and the cotton miRNA ghr-miR414c work together in response to salinity stress. The miRNA ghr-miR414c targets the coding sequence region of GhFSD1, inhibiting expression of transcripts of this antioxidase gene, which represents the first line of defense against stress-induced ROS. Expression of GhFSD1 was induced by salinity stress. Under salinity stress, ghr-miR414c showed expression patterns opposite to those of GhFSD1. Ectopic expression of GhFSD1 in Arabidopsis conferred salinity stress tolerance by improving primary root growth and biomass, whereas Arabidopsis constitutively expressing ghr-miR414c showed hypersensitivity to salinity stress. Silencing GhFSD1 in cotton caused an excessive hypersensitive phenotype to salinity stress, whereas overexpressing miR414c decreased the expression of GhFSD1 and increased sensitivity to salinity stress, yielding a phenotype similar to that of GhFSD1-silenced cotton. Taken together, our results demonstrated that ghr-miR414c was involved in regulation of plant response to salinity stress by targeting GhFSD1 transcripts. This study provides a new strategy and method for plant breeding in order to improve plant salinity tolerance.

Identification and function analysis of drought-specific small RNAs in Gossypium hirsutum L

Cotton production is severely constrained by drought, especially if encountered during the seedling stage or the fiber initiation and elongation stage, but the regulatory mechanisms underlying the effects of drought remain unclear. Therefore, characterization and functional analysis of microRNA-mediated stress regulatory networks are critical to deciphering plant drought response. In this study, 357, 379 and 377 miRNAs with annotations were obtained using the drought-resistant cotton variety ZhongH177 under three treatments, CK, drought and re-watering, and divided into 73 miRNA families with varying copy numbers from 1 to 24. 136 differential expressed genes (DEGs) with significant expression changes were found, of which only 33 DEGs were upregulated, while 103 DEGs were downregulated under drought stress. However, most DEGs recovered their initial expression states when the plants were re-watered. In total, 2657 targets were identified and found to be mainly enriched in the pathways plant-pathogen interaction, plant hormone signal transduction and biosynthesis of amino acids. Drought tolerance was significantly enhanced in 2 transgenic Arabidopsis lines, showing that miRNAs were involved in cotton drought response. Analysis of the expression patterns of 2 miRNA precursors and methylation alterations of 2 targets suggested that these miRNAs or miRNA precursors may be involved in the regulation of target methylation states. Our study provides evidence of transcriptional responses to drought stress, which will be helpful for the research of drought-resistance mechanisms in the future.

The interaction between miR160 and miR165/166 in the control of leaf development and drought tolerance in Arabidopsis

MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development and abiotic stresses. To date, studies have mainly focused on the roles of individual miRNAs, however, a few have addressed the interactions among multiple miRNAs. In this study, we investigated the interplay and regulatory circuit between miR160 and miR165/166 and its effect on leaf development and drought tolerance in Arabidopsis using Short Tandem Target Mimic (STTM). By crossing STTM160 Arabidopsis with STTM165/166, we successfully generated a double mutant of miR160 and miR165/166. The double mutant plants exhibited a series of compromised phenotypes in leaf development and drought tolerance in comparison to phenotypic alterations in the single STTM lines. RNA-seq and qRT-PCR analyses suggested that the expression levels of auxin and ABA signaling genes in the STTM-directed double mutant were compromised compared to the two single mutants. Our results also suggested that miR160-directed regulation of auxin response factors (ARFs) contribute to leaf development via auxin signaling genes, whereas miR165/166- mediated HD-ZIP IIIs regulation confers drought tolerance through ABA signaling. Our studies further indicated that ARFs and HD-ZIP IIIs may play opposite roles in the regulation of leaf development and drought tolerance that can be further applied to other crops for agronomic traits improvement.

Exploring miRNAs for developing climate-resilient crops: A perspective review

Climate changes and environmental stresses have significant implications on global crop production and necessitate developing crops that can withstand an array of climate changes and environmental perturbations such as irregular water-supplies leading to drought or water-logging, hyper soil-salinity, extreme and variable temperatures, ultraviolet radiations and metal stress. Plants have intricate molecular mechanisms to cope with these dynamic environmental changes, one of the most common and effective being the reprogramming of expression of stress-responsive genes. Plant microRNAs (miRNAs) have emerged as key post-transcriptional and translational regulators of gene-expression for modulation of stress implications. Recent reports are establishing their key roles in epigenetic regulations of stress/adaptive responses as well as in providing plants genome-stability. Several stress responsive miRNAs are being identified from different crop plants and miRNA-driven RNA-interference (RNAi) is turning into a technology of choice for improving crop traits and providing phenotypic plasticity in challenging environments. Here we presents a perspective review on exploration of miRNAs as potent targets for engineering crops that can withstand multi-stress environments via loss-/gain-of-function approaches. This review also shed a light on potential roles plant miRNAs play in genome-stability and their emergence as potent target for genome-editing. Current knowledge on plant miRNAs, their biogenesis, function, their targets, and latest developments in bioinformatics approaches for plant miRNAs are discussed. Though there are recent reviews discussing primarily the individual miRNAs responsive to single stress factors, however, considering practical limitation of this approach, special emphasis is given in this review on miRNAs involved in responses and adaptation of plants to multi-stress environments including at epigenetic and/or epigenomic levels.

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon

BACKGROUND

MiRNAs have emerged as key regulators of stress response in plants, suggesting their potential as candidates for knock-in/out to improve stress tolerance in agricultural crops. Although diverse assays have been performed, systematic and detailed studies of miRNA expression and function during exposure to multiple environments in crops are limited.

RESULTS

Here, we present such pioneering analysis in melon plants in response to seven biotic and abiotic stress conditions. Deep-sequencing and computational approaches have identified twenty-four known miRNAs whose expression was significantly altered under at least one stress condition, observing that down-regulation was preponderant. Additionally, miRNA function was characterized by high scale degradome assays and quantitative RNA measurements over the intended target mRNAs, providing mechanistic insight. Clustering analysis provided evidence that eight miRNAs showed a broad response range under the stress conditions analyzed, whereas another eight miRNAs displayed a narrow response range. Transcription factors were predominantly targeted by stress-responsive miRNAs in melon. Furthermore, our results show that the miRNAs that are down-regulated upon stress predominantly have as targets genes that are known to participate in the stress response by the plant, whereas the miRNAs that are up-regulated control genes linked to development.

CONCLUSION

Altogether, this high-resolution analysis of miRNA-target interactions, combining experimental and computational work, Illustrates the close interplay between miRNAs and the response to diverse environmental conditions, in melon.

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development

BACKGROUND

Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown.

RESULTS

By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5' RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse.

CONCLUSION

This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development.

Identification and Analysis of microRNAs in the SAM and Leaves of Populus tomentosa

The shoot apical meristem (SAM) is a crucial tissue located at the tops of plants which can continually grow and differentiate to develop into all aboveground parts. SAM development is controlled by a series of complicated molecular regulation networks, among which microRNAs (miRNAs) and their target genes play key roles. However, little is known about these miRNAs in woody plants. In this study, we used small RNA (sRNA) sequencing to build four libraries derived from shoot tips and mature leaf tissues of Populus tomentosa, and identified 99 known miRNA families. In addition, 193 known miRNAs, including phytohormone-, developmental-, and cellular process-related miRNAs, showed significant differential expression. Interestingly, quantitative real-time reverse transcription polymerase chain reaction (PCR) analysis of miR172, miR164, and miR393 expression showed marked changes in expression patterns during the development of shoot tips. The target genes of these miRNAs were involved in the regulation of hormone responses and stem cell function. In particular, the miR172 target APETALA2 (AP2), involved in the maintenance of stem cells in the shoot apex, was expressed specifically during the initial active stage of development. These findings provide new insights into the regulatory mechanisms of miRNAs involved in SAM development and differentiation in tree species.

Modulation of miRNA expression in natural populations of A. thaliana along a wide altitudinal gradient of Indian Himalayas

Plant populations growing along an altitudinal gradient are exposed to different environmental conditions. They are excellent resources to study regulatory mechanisms adopted by plants to respond to different environmental stresses. Regulation by miRNA is one of such strategies. Here, we report how different miRNAs are preferentially expressed in the three natural populations of A. thaliana originating from a wide altitudinal range. The expression level of miRNAs was mostly governed by temperature and radiation. Majority of the identified miRNAs expressed commonly in the three populations. However, 30 miRNAs expressed significantly at different level between the low and the high altitude populations. Most of these miRNAs regulate the genes associated with different developmental processes, abiotic stresses including UV, cold, secondary metabolites, etc. Further, the expression of miR397 and miR858 involved in lignin biosynthesis and regulation of secondary metabolites respectively, may be regulated by light intensity. A few miRNAs expressed at increasing level with the increase in the altitude of the site indicating environment driven tight regulation of these miRNAs. Further, several novel miRNAs and isomiR diversity specific to the Himalayas are reported which might have an adaptive advantage. To the best of our knowledge, this is the first report on miRNA expression from natural plant populations.

Target-mimicry based diminution of miRNA167 reinforced flowering-time phenotypes in tobacco via spatial-transcriptional biases of flowering-associated miRNAs

Evolutionarily conserved microRNAs such as miR156, miR159, miR167 and miR172 tightly regulate the extensive array of gene expression during flowering in plants, through instant and long-term alterations in the expression of their target genes. Here we employed a novel target-mimicry approach for the diminution of auxin signalling regulator miRNA167 by developing mimic-transgenic lines in tobacco, to investigate the transcriptional biases of flowering-associated miRNAs in apical and floral meristematic tissues and their phenotypic implications. Recorded morpho-alterations such as uneven flowering-time phenotypes, anomalous floral organ formation, and large variations in the seed forming characteristics permitted us to determine the consequence of the extent of miR167 expression diminution accompanying the transcriptional biases of interrelated miRNAs. We demonstrate that percent diminution of miR167 gene expression is proportionally associated with both early and late flowering-time phenotypes in mimic lines. Also, the associated miRNAs, miR156, miR159, and miR172 showed >90% transcriptional diminution in at least 'early-flowering' miR167 mimic lines. On contrary, low percentages of their respective diminution were recorded in 'late-flowering' lines. Evidently, the misexpression of miR156, miR159, and miR172 led to the over-expression of their respective target genes SPL9, AtMYB33-like and AP2 genes in mimic lines which resulted in assorted phenotypes. We describe the scope of spatial regulation of these microRNAs in floral bud tissues of mimic lines which showed negative- or very low (<25%) misexpression levels in early/late-flowering lines highlighting their roles in the acquisition of flowering mechanism. To our knowledge, this study represents the first characterization of transcriptional biases of flowering associated miRNAs in miR167-mimic lines and certainly augments our understanding of the importance of microRNA-mediated regulation of flowering in plants.

Banana sRNAome and degradome identify microRNAs functioning in differential responses to temperature stress

Background

Temperature stress is a major environmental factor affecting not only plant growth and development, but also fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in various biological processes. Harvested banana fruit can exhibit distinct symptoms in response to different temperature stresses, but the underlying miRNA-mediated regulatory mechanisms remained unknown.

Results

Here, we profiled temperature-responsive miRNAs in banana, using deep sequencing and computational and molecular analyses. In total 113 known miRNAs and 26 novel banana-specific miRNAs were identified. Of these miRNAs, 42 miRNAs were expressed differentially under cold and heat stresses. Degradome sequencing identified 60 target genes regulated by known miRNAs and half of these targets were regulated by 15 temperature-responsive miRNAs. The correlative expression patterns between several miRNAs and their target genes were further validated via qRT-PCR. Our data showed that miR535 and miR156 families may derive from a common ancestor during evolution and jointly play a role in fine-tuning SPL gene expression in banana. We also identified the miRNA-triggered phased secondary siRNAs in banana and found miR393-TIR1/AFB phasiRNA production displaying cold stress-specific enrichment.

Conclusions

Our results provide a foundation for understanding the miRNA-dependent temperature stress response in banana. The characterized correlations between miRNAs and their response to temperature stress could serve as markers in the breeding programs or tools for improving temperature tolerance of banana.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5395-1) contains supplementary material, which is available to authorized users.

An Introduction to Methods for Discovery and Functional Analysis of MicroRNAs in Plants

MicroRNAs play important roles in posttranscriptional regulation of plant development, metabolism, and abiotic stress responses. The recent generation of massive amounts of small RNA sequence data, along with development of bioinformatic tools to identify miRNAs and their mRNA targets, has led to an explosion of newly identified putative miRNAs in plants. Genome editing techniques like CRISPR-Cas9 will allow us to study the biological role of these potential novel miRNAs by efficiently targeting both the miRNA and its mRNA target. In this chapter, we review bioinformatic tools and experimental methods for the identification and functional characterization of miRNAs and their target mRNAs in plants.

miR824/AGAMOUS-LIKE16 Module Integrates Recurring Environmental Heat Stress Changes to Fine-Tune Poststress Development

Plant development is continually fine-tuned based on environmental factors. How environmental perturbations are integrated into the developmental programs and how poststress adaptation is regulated remains an important topic to dissect. Vegetative to reproductive phase change is a very important developmental transition that is complexly regulated based on endogenous and exogenous cues. Proper timing of flowering is vital for reproductive success. It has been shown previously that AGAMOUS LIKE 16 (AGL16), a MADS-box transcription factor negatively regulates flowering time transition through FLOWERING LOCUS T (FT), a central downstream floral integrator. AGL16 itself is negatively regulated by the microRNA miR824. Here we present a comprehensive molecular analysis of miR824/AGL16 module changes in response to mild and recurring heat stress. We show that miR824 accumulates gradually in response to heat due to the combination of transient transcriptional induction and posttranscriptional stability. miR824 induction requires heat shock cis-elements and activity of the HSFA1 family and HSFA2 transcription factors. Parallel to miR824 induction, its target AGL16 is decreased, implying direct causality. AGL16 posttranscriptional repression during heat stress, however, is more complex, comprising of a miRNA-independent, and a miR824-dependent pathway. We also show that AGL16 expression is leaf vein-specific and overlaps with miR824 (and FT) expression. AGL16 downregulation in response to heat leads to a mild derepression of FT. Finally, we present evidence showing that heat stress regulation of miR824/AGL16 is conserved within Brassicaceae. In conclusion, due to the enhanced post-transcriptional stability of miR824, stable repression of AGL16 is achieved following heat stress. This may serve to fine-tune FT levels and alter flowering time transition. Stress-induced miR824, therefore, can act as a "posttranscriptional memory factor" to extend the acute impact of environmental fluctuations in the poststress period.

Cre-miR914-regulated RPL18 is involved with UV-B adaptation in Chlamydomonas reinhardtii

UV radiation is a serious threat to life, and algae have developed highly efficient adaptations to UV radiation through the course of evolution. To date, studies investigating the mechanisms of UV adaptation in algae have focused on physiological regulation and associated protein coding genes, with only a few reports on associated protein non-coding genes. In a previous study, we found that Cre-miR914 was significantly down-regulated in Chlamydomonas reinhardtii in response to heat shock. In the present study, we aimed to determine whether Cre-miR914 plays a role in response to UV-B radiation. Our bioinformatics analysis indicated that the potential target gene of Cre-miR914 is ribosomal protein L18 (RPL18). We also measured the expression of Cre-miR914 and RPL18 in response to UV-B radiation through qPCR analysis. Then, we constructed cell lines overexpressing Cre-miR914 or RPL18, and performed survival experiments under UV-B stress. The results showed that Cre-miR914 overexpression decreased resistance while RPL18 overexpression enhanced tolerance to UV-B radiation. These results indicate that Cre-miR914 and its potential target gene RPL18 are involved in the adaptation to UV-B in C. reinhardtii.

The Altered Expression of microRNA408 Influences the Arabidopsis Response to Iron Deficiency

MicroRNAs contribute to the adaptation of plants to varying environmental conditions by affecting systemic mineral nutrient homeostasis. Copper and iron deficiencies antagonistically control the expression of Arabidopsis thaliana microRNA408 (miR408), which post-transcriptionally regulates laccase-like multicopper oxidase family members LAC3, LAC12, and LAC13. In this work, we used miR408 T-DNA insertion mutants (408-KO1 and 408-KO2) and a previously characterized transgenic line overexpressing miR408 (35S:408-14) to explore how miR408 influences copper- and iron-dependent metabolism. We observed that the altered expression of miR408 diminished plant performance and the activation of the iron-regulated genes under iron-deficient conditions. Consistently with the low expression of the miR408-target laccases, we showed that the vascular bundle lignification of the 35S:408-14 plants diminished. The decrease in the phenoloxidase and ferroxidase activities exhibited by wild-type plants under iron deficiency did not occur in the 408-KO1 plants, probably due to the higher expression of laccases. Finally, we observed that the hydrogen peroxide levels under iron starvation were altered in both the 408-KO1 and 35S:408-14 lines. Taken together, these results suggest that Arabidopsis plants with modified miR408 levels undergo multiple deregulations under iron-deficient conditions.

Analyses of MiRNA Functions in Maize Using a Newly Developed ZMBJ-CMV-2bN81-STTM Vector

Endogenous microRNAs (miRNAs) play pivotal roles in plant development and responses to various biotic or abiotic stresses. Up to now, more than 500 maize miRNAs have been identified. However, functions of these identified miRNAs remained largely unknown due mainly to the lack of rapid and reliable tools. We previously reported a cucumber mosaic virus strain ZMBJ (ZMBJ-CMV)-based gene silencing vector for rapid and efficient gene function studies in maize lines with agronomical importance. Because ZMBJ-CMV induces very mild disease symptoms but strong gene silencing in maize, we decided to further modify this vector to suppress miRNA expressions in maize. The newly developed ZMBJ-CMV-2b_N81-STTM vector expresses a short tandem target mimic (STTM) containing two target-mimic sequences separated by a short spacer sequence. Our results showed that ZMBJ-CMV-2b_N81-STTM can be used to investigate miRNA function in Nicotiana benthamiana and maize seedlings. The ZMBJ-CMV-2b_N81-STTM-based downregulation of Nbe-miR165/166 or Nbe-miR159 induced specific and strong miRNA-sequestering phenotypes, and increased the expressions of their predicted target genes. For maize, the ZMBJ-CMV-2b_N81-STTM based downregulation of zma-miR167 or zma-miR482 caused a decrease of lateral roots growth and a plant stunting phenotypes, respectively. In both cases, the target genes of zma-miR167- or zma-miR482 were increased significantly. Thus, we consider ZMBJ-CMV based VbMS system as a useful tool for high-throughput investigations of miRNA functions in maize.

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

Cardamom has long been used as a food flavouring agent and in ayurvedic medicines for mouth ulcers, digestive problems and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reductions in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses. In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using an Ion Proton sequencer. We identified 161 potential miRNAs representing 42 families, including monocot/tissue-specific and 14 novel miRNAs in both genotypes. Significant differences in miRNA family abundance between the libraries were observed in read frequencies. A total of 19 miRNAs (from known miRNAs) displayed a twofold difference in expression between wild and cultivar genotypes. We found 1168 unique potential targets for 40 known miRNA families in wild and 1025 potential targets for 42 known miRNA families in cultivar genotypes. The differential expression analysis revealed that most miRNAs identified were highly expressed in cultivars and, furthermore, lower expression of miR169 and higher expression of miR529 in wild cardamom proved evidence that wild genotypes have stronger drought stress tolerance and floral development than cultivars. Potential targets predicted for the newly identified miRNAs from the miRNA libraries of wild and cultivar cardamom genotypes involved in metabolic and developmental processes and in response to various stimuli. qRT-PCR confirmed miRNAs were differentially expressed between wild and cultivar genotypes. Furthermore, four target genes were validated experimentally to confirm miRNA-mRNA target pairing using RNA ligase-mediated 5' Rapid Amplification of cDNA Ends (5'RLM-RACE) PCR.

Genome-wide identification of drought-responsive microRNAs in two sets of Malus from interspecific hybrid progenies

Drought stress can negatively impact apple fruit quality and yield. Apple microRNAs (miRNAs) participate in apple tree and fruit development, as well as in biotic stress tolerance; however, it is largely unknown whether these molecules are involved in the drought response. To identify drought-responsive miRNAs in Malus, we first examined the drought stress tolerance of ten F₁ progenies of R3 (M. × domestica) × M. sieversii. We performed Illumina sequencing on pooled total RNA from both drought-tolerant and drought-sensitive plants. The sequencing results identified a total of 206 known miRNAs and 253 candidate novel miRNAs from drought-tolerant plants and drought-sensitive plants under control or drought conditions. We identified 67 miRNAs that were differentially expressed in drought-tolerant plants compared with drought-sensitive plants under drought conditions. Under drought stress, 61 and 35 miRNAs were differentially expressed in drought-tolerant and drought-sensitive plants, respectively. We determined the expression levels of seven out of eight miRNAs by stem-loop qPCR analysis. We also predicted the target genes of all differentially expressed miRNAs and identified the expression of some genes. Gene Ontology analyses indicated that the target genes were mainly involved in stimulus response and cellular and metabolic processes. Finally, we confirmed roles of two miRNAs in apple response to mannitol. Our results reveal candidate miRNAs and their associated mRNAs that could be targeted for improving drought tolerance in Malus species, thus providing a foundation for understanding the molecular networks involved in the response of apple trees to drought stress.

Genotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypes

BACKGROUND

Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially regulate many aspects of plant growth and development. Although miRNAs were reported in alfalfa, their expression profiles in different tissues and the discovery of novel miRNAs as well as their targets have not been described in this plant species.

RESULTS

To identify tissue-specific miRNA profiles in whole plants, shoots and roots of three different alfalfa genotypes (Altet-4, NECS-141and NF08ALF06) were used. Small RNA libraries were generated and sequenced using a high-throughput sequencing platform. Analysis of these libraries enabled identification of100 miRNA families; 21 of them belong to the highly conserved families while the remaining 79 families are conserved at the minimum between M. sativa and the model legume and close relative, M. truncatula. The profiles of the six abundantly expressed miRNA families (miR156, miR159, miR166, miR319, miR396 and miR398) were relatively similar between the whole plants, roots and shoots of these three alfalfa genotypes. In contrast, robust differences between shoots and roots for miR160 and miR408 levels were evident, and their expression was more abundant in the shoots. Additionally, 17 novel miRNAs were identified and the relative abundance of some of these differed between tissue types. Further, the generation and analysis of degradome libraries from the three alfalfa genotypes enabled confirmation of 69 genes as targets for 31 miRNA families in alfalfa.

CONCLUSIONS

The miRNA profiles revealed both similarities and differences in the expression profiles between tissues within a genotype as well as between the genotypes. Among the highly conserved miRNA families, miR166 was the most abundantly expressed in almost all tissues from the three genotypes. The identification of conserved and novel miRNAs as well as their targets in different tissues of multiple genotypes increased our understanding of miRNA-mediated gene regulation in alfalfa and could provide valuable insights for practical research and plant improvement applications in alfalfa and related legume species.

miRNomes involved in imparting thermotolerance to crop plants

Thermal stress is one of the challenges to crop plants that negatively impacts crop yield. To overcome this ever-growing problem, utilization of regulatory mechanisms, especially microRNAs (miRNAs), that provide efficient and precise regulation in a targeted manner have been found to play determining roles. Besides their roles in plant growth and development, many recent studies have shown differential regulation of several miRNAs during abiotic stresses including heat stress (HS). Thus, understanding the underlying mechanism of miRNA-mediated gene expression during HS will enable researchers to exploit this regulatory mechanism to address HS responses. This review focuses on the miRNAs and regulatory networks that were involved in physiological, metabolic and morphological adaptations during HS in plant, specifically in crops. Illustrated examples including, the miR156-SPL, miR169-NF-YA5, miR395-APS/AST, miR396-WRKY, etc., have been discussed in specific relation to the crop plants. Further, we have also discussed the available plant miRNA databases and bioinformatics tools useful for miRNA identification and study of their regulatory role in response to HS. Finally, we have briefly discussed the future prospects about the miRNA-related mechanisms of HS for improving thermotolerance in crop plants.

N⁶-methyladenosine (m⁶A): Revisiting the Old with Focus on New, an Arabidopsis thaliana Centered Review

N⁶-methyladenosine (m⁶A) is known to occur in plant and animal messenger RNAs (mRNAs) since the 1970s. However, the scope and function of this modification remained un-explored till very recently. Since the beginning of this decade, owing to major technological breakthroughs, the interest in m⁶A has peaked again. Similar to animal mRNAs, plant mRNAs are also m⁶A methylated, within a specific sequence motif which is conserved across these kingdoms. m⁶A has been found to be pivotal for plant development and necessary for processes ranging from seed germination to floral development. A wide range of proteins involved in methylation of adenosine have been identified alongside proteins that remove or identify m⁶A. This review aims to put together the current knowledge regarding m⁶A in Arabidopsis thaliana.

High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

BACKGROUND

Cold stress is one of the most severe abiotic stresses affecting the banana production. Although some miRNAs have been identified, little is known about the role of miRNAs in response to cold stress in banana, and up to date, there is no report about the role of miRNAs in the response to cold stress in the plants of the cultivated or wild bananas.

RESULT

Here, a cold-resistant line wild banana (Musa itinerans) from China was used to profile the cold-responsive miRNAs by RNA-seq during cold stress. Totally, 265 known mature miRNAs and 41 novel miRNAs were obtained. Cluster analysis of differentially expressed (DE) miRNAs indicated that some miRNAs were specific for chilling or 0 °C treated responses, and most of them were reported to be cold-responsive; however, some were seldom reported to be cold-responsive in response to cold stress, e.g., miR395, miR408, miR172, suggesting that they maybe play key roles in response to cold stress. The GO and KEGG pathway enrichment analysis of DE miRNAs targets indicated that there existed diversified cold-responsive pathways, and miR172 was found likely to play a central coordinating role in response to cold stress, especially in the regulation of CK2 and the circadian rhythm. Finally, qPCR assays indicated the related targets were negatively regulated by the tested DE miRNAs during cold stress in the wild banana.

CONCLUSIONS

In this study, the profiling of miRNAs by RNA-seq in response to cold stress in the plants of the wild banana (Musa itinerans) was reported for the first time. The results showed that there existed diversified cold-responsive pathways, which provided insight into the roles of miRNAs during cold stress, and would be helpful for alleviating cold stress and cold-resistant breeding in bananas.

Preharvest Ultraviolet C Treatment Affected Senescence of Stored Strawberry Fruit with a Potential Role of MicroRNAs in the Activation of the Antioxidant System

Recent studies presented preharvest ultraviolet C (UV-C) as an environmentally friendly approach for the management of horticultural crop diseases. The effect of this approach on quality preservation during postharvest storage has not yet been investigated. Strawberry fruit harvested from plants grown with supplemental UV-C were stored at room temperature for 72 h, and their postharvest shelf-life biochemical indicators were evaluated. The involvement of microRNAs (miRNAs) in the activation of UV-C-induced antioxidant systems was investigated. Preharvest UV-C contributed to the preservation of sugar and organic acid and reduced overall lipid peroxidation in strawberry fruit during storage. We found that miR159 and miR398 were downregulated by preharvest UV-C and that their respective targets were upregulated at the early stage of storage with enhancement of the activity of antioxidant enzymes. The initial burst of H₂O₂ and O₂^• - suggested that preharvest UV-C primed the fruit in an antioxidative activated state via reactive-oxygen-species-mediated feedback control with post-transcriptional involvement of miRNAs.

Circulating miRNA measurements are reflective of cholesterol-based changes in rainbow trout (Oncorhynchus mykiss)

MicroRNAs (miRNAs) are a class of small non-coding RNAs which are known to posttranscriptionally regulate the expression of most genes in both animals and plants. Meanwhile, studies have shown that numbers of miRNAs are present in body fluids including the plasma. Despite the mode of action of these circulating miRNAs still remains unknown, they have been found to be promising biomarkers for disease diagnosis, prognosis and response to treatment. In order to evaluate the potential of miRNAs as non-invasive biomarkers in aquaculture, a time-course experiment was implemented to investigate the postprandial regulation of miRNAs levels in liver and plasma as well as the hepatic expression of genes involved in cholesterol metabolism. We showed that miR-1, miR-33a, miR-122, miR-128 and miR-223 were expressed in the liver of rainbow trout and present at detectable level in the plasma. We also demonstrated that hepatic expression of miR-1, miR-122 and miR-128 were regulated by feed intake and reached their highest levels 12 hours after the meal. Interestingly, we observed that circulating levels of miR-128 and miR-223 are subjected to postprandial regulations similar to that observed in their hepatic counterparts. Statistical correlations were observed between liver and plasma for miR-128 and miR-223 and between hepatic and circulating miR-122, miR-128 and miR-223 and expression of genes related to cholesterol synthesis and efflux or glucose phosphorylation. These results demonstrated that circulating miR-122, miR-128 and miR-223 are potential biomarkers of cholesterol metabolism in rainbow trout.

Physiological studies and genome-wide microRNA profiling of cold-stressed Brassica napus

Temperature extremes, including cold, adversely impact plant growth and development. Plant responses to cold stress (CS) are regulated at both transcriptional and post-transcriptional levels. MicroRNAs (miRNAs), small non-coding RNAs, are known to be involved in post-transcriptional regulation of various developmental processes and metal stress in Brassica napus L. (canola), however, their role in response to CS is largely unknown. In this study, changes in various physiological parameters and endogenous abundance of miRNAs were characterized in spring canola seedlings (DH12075) exposed to 4 °C for 0-48 h. Cold stress induced electrolyte leakage, increased the levels of malondialdheyde and antioxidant enzymes and reduced photosynthetic efficiency. Using small RNA sequencing, 70 known and 126 novel miRNAs were identified in CS leaf tissues and among these, 25 known and 104 novel miRNAs were differentially expressed. Quantitative real-time (qRT) PCR analysis of eight selected miRNAs confirmed their CS responsiveness. Furthermore, the expression of six out of eight miRNAs exhibited an opposite trend in a winter variety of canola, 'Mendel', when compared to 'DH12075'. This first study on the B. napus miRNAome provides a framework for further functional analysis of these miRNAs and their targets in response to CS which may contribute towards the future development of cold resilient crops.

Comparative profiling of microRNAs and their effects on abiotic stress in wild-type and dark green leaf color mutant plants of Anthurium andraeanum 'Sonate'

MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including Anthurium andraeanum. To identify miRNAs and their target genes in A. andraeanum and study their responses to abiotic stresses, we conducted deep-sequencing of two small RNA (sRNA) libraries prepared from young leaves of wild-type (WT) and dark green (dg) leaf color mutant plants of A. andraeanum 'Sonate'. A total of 53 novel miRNAs were identified, 32 of which have been annotated to 18 miRNA families. 10 putative miRNAs were found to be differentially expressed in WT and dg, among which two miRNAs were significantly up-regulated and eight down-regulated in dg relative to WT. One differentially expressed miRNA, Aa-miR408, was dramatically up-regulated in dg. qRT-PCR analysis and heterologous expression of Aa-miR408 in Arabidopsis under different stress treatments suggest that Aa-miR408 is involved in abiotic stress responses in A. andraeanum. Our results provide a foundation for further dissecting the roles of miRNAs and their targets in regulating abiotic stress tolerance in A. andraeanum.

State-Dependent Memory: Neurobiological Advances and Prospects for Translation to Dissociative Amnesia

In susceptible individuals, overwhelming traumatic stress often results in severe abnormalities of memory processing, manifested either as the uncontrollable emergence of memories (flashbacks) or as an inability to remember events (dissociative amnesia, DA) that are usually, but not necessarily, related to the stressful experience. These memory abnormalities are often the source of debilitating psychopathologies such as anxiety, depression and social dysfunction. The question of why memory for some traumatic experiences is compromised while other comparably traumatic experiences are remembered perfectly well, both within and across individuals, has puzzled clinicians for decades. In this article, we present clinical, cognitive, and neurobiological perspectives on memory research relevant to DA. In particular, we examine the role of state dependent memory (wherein memories are difficult to recall unless the conditions at encoding and recall are similar), and discuss how advances in the neurobiology of state-dependent memory (SDM) gleaned from animal studies might be translated to humans.

Ambient Temperature-Responsive Mechanisms Coordinate Regulation of Flowering Time

In plants, environmental conditions such as temperature affect survival, growth, and fitness, particularly during key stages such as seedling growth and reproduction. To survive and thrive in changing conditions, plants have evolved adaptive responses that tightly regulate developmental processes such as hypocotyl elongation and flowering time in response to environmental temperature changes. Increases in temperature, coupled with increasing fluctuations in local climate and weather, severely affect our agricultural systems; therefore, understanding the mechanisms by which plants perceive and respond to temperature is critical for agricultural sustainability. In this review, we summarize recent findings on the molecular mechanisms of ambient temperature perception as well as possible temperature sensing components in plants. Based on recent publications, we highlight several temperature response mechanisms, including the deposition and eviction of histone variants, DNA methylation, alternative splicing, protein degradation, and protein localization. We discuss roles of each proposed temperature-sensing mechanism that affects plant development, with an emphasis on flowering time. Studies of plant ambient temperature responses are advancing rapidly, and this review provides insights for future research aimed at understanding the mechanisms of temperature perception and responses in plants.