miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula

Identification and Network Construction of mRNAs, miRNAs, lncRNAs, and circRNAs in Sweetpotato (Ipomoea batatas L.) Adventitious Roots Under Salt Stress via Whole-Transcriptome RNA Sequencing

Sweetpotato is the seventh largest crop worldwide, and soil salinization is a major environmental stress limiting its yield. Recent studies have shown that noncoding RNAs (ncRNAs) play important regulatory roles in plant responses to abiotic stress. However, ncRNAs in sweetpotato remain largely unexplored. This study analyzed the characteristics of salt-responsive ncRNAs in sweetpotato adventitious roots under salt stress via whole-transcriptome RNA sequencing. The results revealed that 3175 messenger RNAs (mRNAs), 458 microRNAs (miRNAs), 544 long-chain ncRNAs (lncRNAs), and 23 circular RNAs (circRNAs) were differentially expressed. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that most differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) were enriched primarily in phenylpropanoid biosynthesis, starch and sucrose metabolism, the Mitogen-Activated Protein Kinase (MAPK) signaling pathway, plant hormone signal transduction, the mRNA surveillance pathway, and ATP-binding cassette (ABC) transporters. Gene Ontology (GO) enrichment analysis revealed that the majority of DEmRNAs, their target DEmiRNAs, and differentially expressed lncRNAs (DElncRNAs) were associated with the cell wall, oxidation-reduction, the plasma membrane, protein phosphorylation, metabolic processes, transcription factor activity, and the regulation of transcription. Additionally, based on the competitive endogenous RNA (ceRNA) hypothesis, we predicted interactions among different RNAs and constructed a salt-responsive ceRNA network comprising 22 DEmiRNAs, 42 DEmRNAs, 27 DElncRNAs, and 10 differentially expressed circRNAs (DEcircRNAs). Some miRNAs, such as miR408, miR169, miR160, miR5139, miR5368, and miR6179, were central to the network, suggesting their crucial roles in the sweetpotato salt response. Our findings provide a foundation for further research into the potential functions of ncRNAs and offer new targets for salt stress resistance improvement through the manipulation of ncRNAs.

Integrated analysis of transcriptome, sRNAome, and degradome involved in the drought-response of maize Zhengdan958

Drought is a major abiotic stress in restricting the growth, development, and yield of maize. As a significant epigenetic regulator, small RNA also functions in connecting the transcriptional and post-transcriptional regulatory network. Further to help comprehending the molecular mechanisms underlying drought adaptability and tolerance of maize, an integrated multi-omics analysis of transcriptome, sRNAome, and degradome was performed on the seedling roots of an elite hybrid Zhengdan958 under drought stress. In this study, 2,911 genes, 32 conserved miRNAs, and 12 novel miRNAs showed a significantly differential expression under drought stress. Moreover, 6,340 target genes of 445 miRNAs were validated using degradome sequencing, forming 281 miRNA-mRNA pairs in control (CK) and drought-stressed (DS) library. These target genes were mainly involved in the plant hormone signal transduction and phenylpropanoid biosynthesis pathways. The integrated multi-omics analysis revealed that five DEmiRNA-mRNA pairs displayed negatively correlated expression patterns, which were also verified by qRT-PCR. Tissue-specific expression profile and regulatory network analysis revealed that miR528a/b-Zm00001d021850, miR408a/b-Zm00001d020794, and miR164e-Zm00001d003414 might be essential in root-specific drought stress response of maize Zhengdan958 seedlings. These worthwhile will promote the functional characterization of miRNA-mRNA modules response to drought stress, and potentially contribute to drought-resistance breeding of maize.

Impact of water stress to plant epigenetic mechanisms in stress and adaptation

Water is the basic molecule in living beings, and it has a major impact on vital processes. Plants are sessile organisms with a sophisticated regulatory network that regulates how resources are distributed between developmental and adaptation processes. Drought-stressed plants can change their survival strategies to adapt to this unfavorable situation. Indeed, plants modify, change, and modulate gene expression when grown in a low-water environment. This adaptation occurs through several mechanisms that affect the expression of genes, allowing these plants to resist in dry regions. Epigenetic modulation has emerged as a major factor in the transcription regulation of drought stress-related genes. Moreover, specific molecular and epigenetic modifications in the expression of certain genetic networks lead to adapted responses that aid a plant's acclimatization and survival during repeated stress. Indeed, understanding plant responses to severe environmental stresses, including drought, is critical for biotechnological applications. Here, we first focused on drought stress in plants and their general adaptation mechanisms to this stress. We also discussed plant epigenetic regulation when exposed to water stress and how this adaptation can be passed down through generations.

The microRNA408-plantacyanin module balances plant growth and drought resistance by regulating reactive oxygen species homeostasis in guard cells

The conserved microRNA (miRNA) miR408 enhances photosynthesis and compromises stress tolerance in multiple plants, but the cellular mechanism underlying its function remains largely unclear. Here, we show that in Arabidopsis (Arabidopsis thaliana), the transcript encoding the blue copper protein PLANTACYANIN (PCY) is the primary target for miR408 in vegetative tissues. PCY is preferentially expressed in the guard cells, and PCY is associated with the endomembrane surrounding individual chloroplasts. We found that the MIR408 promoter is suppressed by multiple abscisic acid (ABA)-responsive transcription factors, thus allowing PCY to accumulate under stress conditions. Genetic analysis revealed that PCY elevates reactive oxygen species (ROS) levels in the guard cells, promotes stomatal closure, reduces photosynthetic gas exchange, and enhances drought resistance. Moreover, the miR408-PCY module is sufficient to rescue the growth and drought tolerance phenotypes caused by gain- and loss-of-function of MYB44, an established positive regulator of ABA responses, indicating that the miR408-PCY module relays ABA signaling for regulating ROS homeostasis and drought resistance. These results demonstrate that miR408 regulates stomatal movement to balance growth and drought resistance, providing a mechanistic understanding of why miR408 is selected during land plant evolution and insights into the long-pursued quest of breeding drought-tolerant and high-yielding crops.

Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures

The orthotospovirus capsicum chlorosis virus (CaCV) is an important pathogen affecting capsicum plants. Elevated temperatures may affect disease progression and pose a potential challenge to capsicum production. To date, CaCV-resistant capsicum breeding lines have been established; however, the impact of an elevated temperature of 35 °C on this genetic resistance remains unexplored. Thus, this study aimed to investigate how high temperature (HT) influences the response of CaCV-resistant capsicum to the virus. Phenotypic analysis revealed a compromised resistance in capsicum plants grown at HT, with systemic necrotic spots appearing in 8 out of 14 CaCV-infected plants. Molecular analysis through next-generation sequencing identified 105 known and 83 novel microRNAs (miRNAs) in CaCV-resistant capsicum plants. Gene ontology revealed that phenylpropanoid and lignin metabolic processes, regulated by Can-miR408a and Can- miR397, are likely involved in elevated-temperature-mediated resistance-breaking responses. Additionally, real-time PCR validated an upregulation of Can-miR408a and Can-miR397 by CaCV infection at HT; however, only the Laccase 4 transcript, targeted by Can-miR397, showed a tendency of negative correlation with this miRNA. Overall, this study provides the first molecular insights into how elevated temperature affects CaCV resistance in capsicum plants and reveals the potential role of miRNA in temperature-sensitive tospovirus resistance.

Redox regulation of epigenetic and epitranscriptomic gene regulatory pathways in plants

Developmental and environmental constraints influence genome expression through complex networks of regulatory mechanisms. Epigenetic modifications and remodelling of chromatin are some of the major actors regulating the dynamic of gene expression. Unravelling the factors relaying environmental signals that induce gene expression reprogramming under stress conditions is an important and fundamental question. Indeed, many enzymes involved in epigenetic and chromatin modifications are regulated by redox pathways, through post-translational modifications of proteins or by modifications of the flux of metabolic intermediates. Such modifications are potential hubs to relay developmental and environmental changes for gene expression reprogramming. In this review, we provide an update on the interaction between major redox mediators, such as reactive oxygen and nitrogen species and antioxidants, and epigenetic changes in plants. We detail how redox status alters post-translational modifications of proteins, intracellular epigenetic and epitranscriptional modifications, and how redox regulation interplays with DNA methylation, histone acetylation and methylation, miRNA biogenesis, and chromatin structure and remodelling to reprogram genome expression under environmental constraints.

Overlapping of copper-nanoparticles with microRNA reveals crippling of heat stress pathway in Solanum lycopersicum: Tomato case study

Despite the tangible benefits of copper nanoparticles (CuNPs) for plants, the increasing use of CuNPs poses a threat to plants and the environment. Although miRNAs have been shown to mediate heat shock and CuNPs by altering gene expression, no study has investigated how CuNPs in combination with heat shock (HS) affect the miRNA expression profile. Here, we exposed tomato plants to 0.01 CuONPs at 42 °C for 1 h after exposure. It was found that the expression levels of miR156a, miR159a and miR172a and their targets SPL3, MYB33 and AP2a were altered under CuNPs and HS + CuNPs. This alteration accelerated the change of vegetative phase and the process of leaf senescence. The overexpression of miR393 under CuNPs and HS + CuNPs could also be an indicator of the attenuation of leaf morphology. Interestingly, the down-regulation of Cu/ZnSOD1 and Cu/ZnSOD2 as target genes of miR398a, which showed strong abnormal expression, was replaced by FeSOD (FSD1), indicating the influence of CuNPs. In addition, CuNPs triggered the expression of some important genes of heat shock response, including HsFA2, HSP70-9 and HSP90-3, which showed lower expression compared to HS. Thus, CuNPs play an important role in altering the gene expression pathway during heat stress.

Genome-wide identification and evolutionary analysis of the AP2/EREBP, COX and LTP genes in Zea mays L. under drought stress

AP2 (APETALA2)/EREBP (ethylene-responsive element-binding protein), cytochrome c oxidase (COX) and nonspecific lipid transfer proteins (LTP) play important roles in the response to drought stress. This is the first study to identify the COX gene in Zea mays L. via genome-wide analysis. The qRT‒PCR results indicated that AP2/EREBP, COX and LTP were downregulated, with fold changes of 0.84, 0.53 and 0.31, respectively, after 12 h of drought stress. Genome-wide analysis identified 78 AP2/EREBP, 6 COX and 10 LTP genes in Z. mays L. Domain analysis confirmed the presence of the AP2 domain, Cyt_c_Oxidase_Vb domain and nsLTP1 in the AP2/EREBP, COX and LTP proteins, respectively. The AP2/EREBP protein family (AP2) includes five different domain types: the AP2/ERF domain, the EREBP-like factor (EREBP), the ethylene responsive factor (ERF), the dehydration responsive element binding protein (DREB) and the SHN SHINE. Synteny analysis of the AP2/EREBP, COX and LTP genes revealed collinearity orthologous relationships in O. sativa, H. vulgare and A. thaliana. AP2/EREBP genes were found on the 10 chromosomes of Z. mays L. COX genes were found on chromosomes 1, 3, 4, 5, 7 and 8. LTP genes were found on chromosomes 1, 3, 6, 8, 9 and 10. In the present study, the Ka/Ks ratios of the AP2/EREBP paralogous pairs indicated that the AP2/EREBP genes were influenced primarily by purifying selection, which indicated that the AP2/EREBP genes received strong environmental pressure during evolution. The Ka/Ks ratios of the COX-3/COX-4 paralogous pairs indicate that the COX-3/COX-4 genes were influenced primarily by Darwinian selection (driving change). For the LTP genes, the Ka/Ks ratios of the LTP-1/LTP-10, LTP-5/LTP-3 and LTP-4/LTP-8 paralogous pairs indicate that these genes were influenced primarily by purifying selection, while the Ka/Ks ratios of the LTP-2/LTP-6 paralogous pairs indicate that these genes were influenced primarily by Darwinian selection. The duplication time of the AP2/EREBP paralogous gene pairs in Z. mays L. ranged from approximately 9.364 to 100.935 Mya. The duplication time of the COX-3/COX-4 paralogous gene pair was approximately 5.217 Mya. The duplication time of the LTP paralogous gene pairs ranged from approximately 19.064 to 96.477 Mya. The major focus of research is to identify the genes that are responsible for drought stress tolerance to improve maize for drought stress tolerance. The results of the present study will improve the understanding of the functions of the AP2/EREBP, COX and LTP genes in response to drought stress.

Regulation of endogenous hormone and miRNA in leaves of alfalfa (Medicago sativa L.) seedlings under drought stress by endogenous nitric oxide

BACKGROUND

Alfalfa (Medicago sativa. L) is one of the best leguminous herbage in China and even in the world, with high nutritional and ecological value. However, one of the drawbacks of alfalfa is its sensitivity to dry conditions, which is a global agricultural problem. The objective of this study was to investigate the regulatory effects of endogenous nitric oxide (NO) on endogenous hormones and related miRNAs in alfalfa seedling leaves under drought stress. The effects of endogenous NO on endogenous hormones such as ABA, GA3, SA, and IAA in alfalfa leaves under drought stress were studied. In addition, high-throughput sequencing technology was used to identify drought-related miRNAs and endogenous NO-responsive miRNAs in alfalfa seedling leaves under drought stress.

RESULT

By measuring the contents of four endogenous hormones in alfalfa leaves, it was found that endogenous NO could regulate plant growth and stress resistance by inducing the metabolism levels of IAA, ABA, GA3, and SA in alfalfa, especially ABA and SA in alfalfa. In addition, small RNA sequencing technology and bioinformatics methods were used to analyze endogenous NO-responsive miRNAs under drought stress. It was found that most miRNAs were enriched in biological pathways and molecular functions related to hormones (ABA, ETH, and JA), phenylpropane metabolism, and plant stress tolerance.

CONCLUSION

In this study, the analysis of endogenous hormone signals and miRNAs in alfalfa leaves under PEG and PEG + cPTIO conditions provided an important basis for endogenous NO to improve the drought resistance of alfalfa at the physiological and molecular levels. It has important scientific value and practical significance for endogenous NO to improve plant drought resistance.

Identification and Validation of the miR156 Family Involved in Drought Responses and Tolerance in Tea Plants (Camellia sinensis (L.) O. Kuntze)

The microRNA156 (miR156) family, one of the first miRNA families discovered in plants, plays various important roles in plant growth and resistance to various abiotic stresses. Previously, miR156s were shown to respond to drought stress, but miR156s in tea plants (Camellia sinensis (L.) O. Kuntze) have not been comprehensively identified and analyzed. Herein, we identify 47 mature sequences and 28 precursor sequences in tea plants. Our evolutionary analysis and multiple sequence alignment revealed that csn-miR156s were highly conserved during evolution and that the rates of the csn-miR156 members' evolution were different. The precursor sequences formed typical and stable stem-loop structures. The prediction of cis-acting elements in the CsMIR156s promoter region showed that the CsMIR156s had diverse cis-acting elements; of these, 12 CsMIR156s were found to be drought-responsive elements. The results of reverse transcription quantitative PCR (RT-qPCR) testing showed that csn-miR156 family members respond to drought and demonstrate different expression patterns under the conditions of drought stress. This suggests that csn-miR156 family members may be significantly involved in the response of tea plants to drought stress. Csn-miR156f-2-5p knockdown significantly reduced the Fv/Fm value and chlorophyll content and led to the accumulation of more-reactive oxygen species and proline compared with the control. The results of target gene prediction showed that csn-miR156f-2-5p targeted SQUAMOSA promoter binding protein-like (SPL) genes. Further analyses showed that CsSPL14 was targeted by csn-miR156f-2-5p, as confirmed through RT-qPCR, 5' RLM-RACE, and antisense oligonucleotide validation. Our results demonstrate that csn-miR156f-2-5p and CsSPL14 are involved in drought response and represent a new strategy for increasing drought tolerance via the breeding of tea plants.

Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective

Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.

Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants

Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.

MicroRNA: A Dynamic Player from Signalling to Abiotic Tolerance in Plants

MicroRNAs (miRNAs) are a class of non-coding single-stranded RNA molecules composed of approximately 20-24 nucleotides in plants. They play an important regulatory role in plant growth and development and as a signal in abiotic tolerance. Some abiotic stresses include drought, salt, cold, high temperature, heavy metals and nutritional elements. miRNAs affect gene expression by manipulating the cleavage, translational expression or DNA methylation of target messenger RNAs (mRNAs). This review describes the current progress in the field considering two aspects: (i) the way miRNAs are produced and regulated and (ii) the way miRNA/target genes are used in plant responses to various abiotic stresses. Studying the molecular mechanism of action of miRNAs' downstream target genes could optimize the genetic manipulation of crop growth and development conditions to provide a more theoretically optimized basis for improving crop production. MicroRNA is a novel signalling mechanism in interplant communication relating to abiotic tolerance.

MicroRNA408 negatively regulates salt tolerance by affecting secondary cell wall development in maize

Although microRNA408 (miR408) is a highly conserved miRNA, the miR408 response to salt stress differs among plant species. Here, we show that miR408 transcripts are strongly repressed by salt stress and methyl viologen treatment in maize (Zea mays). Application of N, N1-dimethylthiourea partly relieved the NaCl-induced down-regulation of miR408. Transgenic maize overexpressing MIR408b is hypersensitive to salt stress. Overexpression of MIR408b enhanced the rate of net Na+ efflux, caused Na+ to locate in the inter-cellular space, reduced lignin accumulation, and reduced the number of cells in vascular bundles under salt stress. We further demonstrated that miR408 targets ZmLACCASE9 (ZmLAC9). Knockout of MIR408a or MIR408b or overexpression of ZmLAC9 increased the accumulation of lignin, thickened the walls of pavement cells, and improved salt tolerance of maize. Transcriptome profiles of the wild-type and MIR408b-overexpressing transgenic maize with or without salt stress indicated that miR408 negatively regulates the expression of cell wall biogenesis genes under salt conditions. These results indicate that miR408 negatively regulates salt tolerance by regulating secondary cell wall development in maize.

ASmiR: a machine learning framework for prediction of abiotic stress-specific miRNAs in plants

Abiotic stresses have become a major challenge in recent years due to their pervasive nature and shocking impacts on plant growth, development, and quality. MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of specific abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational model for prediction of miRNAs associated with four specific abiotic stresses such as cold, drought, heat and salt. The pseudo K-tuple nucleotide compositional features of Kmer size 1 to 5 were used to represent miRNAs in numeric form. Feature selection strategy was employed to select important features. With the selected feature sets, support vector machine (SVM) achieved the highest cross-validation accuracy in all four abiotic stress conditions. The highest cross-validated prediction accuracies in terms of area under precision-recall curve were found to be 90.15, 90.09, 87.71, and 89.25% for cold, drought, heat and salt respectively. Overall prediction accuracies for the independent dataset were respectively observed 84.57, 80.62, 80.38 and 82.78%, for the abiotic stresses. The SVM was also seen to outperform different deep learning models for prediction of abiotic stress-responsive miRNAs. To implement our method with ease, an online prediction server "ASmiR" has been established at https://iasri-sg.icar.gov.in/asmir/ . The proposed computational model and the developed prediction tool are believed to supplement the existing effort for identification of specific abiotic stress-responsive miRNAs in plants.

Genome-wide identification of germin-like proteins in peanut (Arachis hypogea L.) and expression analysis under different abiotic stresses

Peanut is an important food and feed crop, providing oil and protein nutrients. Germins and germin-like proteins (GLPs) are ubiquitously present in plants playing numerous roles in defense, growth and development, and different signaling pathways. However, the GLP members have not been comprehensively studied in peanut at the genome-wide scale. We carried out a genome-wide identification of the GLP genes in peanut genome. GLP members were identified comprehensively, and gene structure, genomic positions, motifs/domains distribution patterns, and phylogenetic history were studied in detail. Promoter Cis-elements, gene duplication, collinearity, miRNAs, protein-protein interactions, and expression were determined. A total of 84 GLPs (AhGLPs ) were found in the genome of cultivated peanut. These GLP genes were clustered into six groups. Segmental duplication events played a key role in the evolution of AhGLPs, and purifying selection pressure was underlying the duplication process. Most AhGLPs possessed a well-maintained gene structure and motif organization within the same group. The promoter regions of AhGLPs contained several key cis-elements responsive to 'phytohormones', 'growth and development', defense, and 'light induction'. Seven microRNAs (miRNAs) from six families were found targeting 25 AhGLPs. Gene Ontology (GO) enrichment analysis showed that AhGLPs are highly enriched in nutrient reservoir activity, aleurone grain, external encapsulating structure, multicellular organismal reproductive process, and response to acid chemicals, indicating their important biological roles. AhGLP14, AhGLP38, AhGLP54, and AhGLP76 were expressed in most tissues, while AhGLP26, AhGLP29, and AhGLP62 showed abundant expression in the pericarp. AhGLP7, AhGLP20, and AhGLP21, etc., showed specifically high expression in embryo, while AhGLP12, AhGLP18, AhGLP40, AhGLP78, and AhGLP82 were highly expressed under different hormones, water, and temperature stress. The qRT-PCR results were in accordance with the transcriptome expression data. In short, these findings provided a foundation for future functional investigations on the AhGLPs for peanut breeding programs.

Chaetomium globosum D5 confers salinity tolerance on Paeonia lactiflora Pall

Plants will interact with beneficial endophytic fungi to increase resistance under environmental stress. Among these stresses, salt stress poses one of the major threats to plant growth worldwide. We have studied the response mechanism of Chaetomium globosum D5, a salt-tolerant fungus isolated from the roots of Paeonia lactiflora under salt stress, and its mechanism of action in helping P. lactiflora alleviate salt stress. In our study, high levels of salt inhibit growth, whereas low levels promote the growth of C. globosum D5, which resists salt stress by forming dense hyphae and producing more pigments, soluble proteins, and antioxidants. Under salt stress, growth and photosynthesis of P. lactiflora are inhibited, and they are subjected to osmotic stress, oxidative stress, and ionic stress. C. globosum D5 could help P. lactiflora promote growth and photosynthesis by increasing the uptake of nitrogen and phosphorus and increasing the accumulation of the carbon and photosynthetic pigments, help P. lactiflora alleviate osmotic stress by increasing the accumulation of proline, help P. lactiflora alleviate ion stress by reducing Na⁺ and increasing K⁺/Na⁺, Ca2⁺/Na⁺ and Mg²⁺/Na ⁺ ratios in P. lactiflora roots and leaves. In summary, joint action between P. lactiflora and C. globosum D5 is responsible for mitigating damage caused by P. lactiflora under salt stress. We first investigate the interaction between the fungus and P. lactiflora under salt stress, providing a theoretical basis for further investigations into the mechanisms of P. lactiflora's response to salt stress and its promotion in coastal areas.

Plant responses to drought stress: microRNAs in action

Drought is common in most regions of the world, and it has a significant impact on plant growth and development. Plants, on the other hand, have evolved their own defense systems to deal with the extreme weather. The reprogramming of gene expression by microRNAs (miRNAs) is one of these defense mechanisms. miRNAs are short noncoding RNAs that have emerged as key post-transcriptional gene regulators in a variety of species. Drought stress modulates the expression of certain miRNAs that are functionally conserved across plant species. These characteristics imply that miRNA-based genetic changes might improve drought resistance in plants. This study highlights current knowledge of plant miRNA biogenesis, regulatory mechanisms and their role in drought stress responses. miRNAs functions and their adaptations by plants during drought stress has also been explained that can be exploited to promote drought-resistance among economically important crops.

Gma-miR408 Enhances Soybean Cyst Nematode Susceptibility by Suppressing Reactive Oxygen Species Accumulation

Soybean cyst nematode (SCN, Heterodera glycine) is a serious damaging disease in soybean worldwide, thus resulting in severe yield losses. MicroRNA408 (miR408) is an ancient and highly conserved miRNA involved in regulating plant growth, development, biotic and abiotic stress response. Here, we analyzed the evolution of miR408 in plants and verified four miR408 members in Glycine max. In the current research, highly upregulated gma-miR408 expressing was detected during nematode migration and syncytium formation response to soybean cyst nematode infection. Overexpressing and silencing miR408 vectors were transformed to soybean to confirm its potential role in plant and nematode interaction. Significant variations were observed in the MAPK signaling pathway with low OXI1, PR1, and wounding of the overexpressing lines. Overexpressing miR408 could negatively regulate soybean resistance to SCN by suppressing reactive oxygen species accumulation. Conversely, silencing miR408 positively regulates soybean resistance to SCN. Overall, gma-miR408 enhances soybean cyst nematode susceptibility by suppressing reactive oxygen species accumulation.

LncRNA-mediated ceRNA regulatory network provides new insight into chlorogenic acid synthesis in sweet potato

Sweet potato (Ipomoea batatas L.) is considered a highly nutritional and economical crop due to its high contents of bioactive substances, such as anthocyanin and chlorogenic acid (CGA), especially in leaves and stems. The roles of noncoding RNAs (ncRNA), including long noncoding RNA (lncRNA) and microRNA (miRNA), in CGA synthesis, are still unknown. In this study, the differentially expressed (DE) mRNAs, miRNAs, and lncRNAs in two leafy vegetable genotypes "FS7-6-14-7" (high CGA content) and "FS7-6" (low CGA content) were identified. The cis-regulation between lncRNA and mRNA was analyzed. Then, the CGA synthesis-related modules MEBlue and MEYellow were identified to detect trans-regulation mRNA-lncRNA pairs. The GO and KEGG annotations suggested that mRNA in these two modules was significantly enriched in the secondary metabolite synthesis biosynthesis category. A competing endogenous RNAs (ceRNA) network, including 8730 miRNA-mRNA and 444 miRNA-lncRNA pairs, was constructed by DEmiRNA target prediction. Then, a CGA synthesis-related ceRNA network was obtained with lncRNA and mRNA from MEBlue and MEYellow. Finally, one relational pair, MSTRG.47662.1/mes-miR398/itb04g00990, was selected for functional validation. Overexpression of lncRNA MSTRG.47662.1 and mRNA itb04g00990 increased CGA content in both tobacco and sweet potato callus, while overexpression of miRNA mes-miR398 decreased CGA content. Meanwhile, regression analysis of the expression patterns demonstrated that MSTRG.47662.1, acting as a ceRNA, promoted itb04g00990 expression by competitively binding mes-miR398 in CGA synthesis in sweet potato. Our results provide insights into how ncRNA-mediated ceRNA regulatory networks likely contribute to CGA synthesis in leafy sweet potato.

Screening of differentially expressed microRNAs and target genes in two potato varieties under nitrogen stress

BACKGROUND

A reasonable supply of nitrogen (N) fertilizer is essential for obtaining high-quality, high-level, and stable potato yields, and an improvement in the N utilization efficiency can effectively reduce N fertilizer use. It is important to use accurate, straightforward, and efficient transgenic breeding techniques for the identification of genes that can improve nitrogen use efficiency, thus enabling us to achieve the ultimate goal of breeding N-efficient potato varieties. In recent years, some of the mechanisms of miRNAs have been elucidated via the analysis of the correlation between the expression levels of potato miRNA target genes and regulated genes under conditions of stress, but the role of miRNAs in the inhibition/expression of key genes regulating N metabolism under N stress is still unclear. Our study aimed to identify the role played by specific enzymes and miRNAs in the responses of plants to N stress.

RESULTS

The roots and leaves of the N-efficient potato variety, Yanshu4 ("Y"), and N-inefficient potato variety, Atlantic ("D"), were collected at the seedling and budding stages after they were exposed to different N fertilizer treatments. The miRNAs expressed differentially under the two types of N stress and their corresponding target genes were first predicted using miRNA and degradome analysis. Then, quantitative polymerase chain reaction (qRT-PCR) was performed to verify the expression of differential miRNAs that were closely related to N metabolism. Finally, the shearing relationship between stu-miR396-5p and its target gene StNiR was determined by analyzing luciferase activity levels. The results showed that NiR activity increased significantly with an increase in the applied N levels from the seedling stage to the budding stage, and NiR responded significantly to different N treatments. miRNA sequencing enabled us to predict 48 families with conserved miRNAs that were mainly involved in N metabolism, carbon metabolism, and amino acid biosynthesis. The differences in the expression of the following miRNAs were identified via screening (high expression levels and P < 0.05): stu-miR396-5p, stu-miR408b-3p_R-1, stu-miR3627-3p, stu-miR482a-3p, stu-miR8036-3p, stu-miR482a-5p, stu-miR827-5p, stu-miR156a_L-1, stu-miR827-3p, stu-miR172b-5p, stu-miR6022-p3_7, stu-miR398a-5p, and stu-miR166c-5p_L-3. Degradome analysis showed that most miRNAs had many-to-many relationships with target genes. The main target genes involved in N metabolism were NiR, NiR1, NRT2.5, and NRT2.7. qRT-PCR analysis showed that there were significant differences in the expression levels of stu-miR396-5p, stu-miR8036-3p, and stu-miR482a-3p in the leaves and roots of the Yanshu4 and Atlantic varieties at the seedling and budding stages under conditions that involved no N and excessive N application; the expression of these miRNAs was induced in response to N stress. The correlation between the differential expression of stu-miR396-5p and its corresponding target gene NiR was further verified by determining the luciferase activity level and was found to be strongly negative.

CONCLUSION

The activity of NiR was significantly positively correlated with N application from the seedling to the budding stage. Differential miRNAs and target genes showed a many-to-many relationship with each other. The expression of stu-miR396-5p, stu-miR482a-3p, and stu-miR8036-3p in the roots and leaves of the Yanshu4 and Atlantic varieties at the seedling and budding stages was notably different under two types of N stress. Under two types of N stress, stu-miR396-5p was down-regulated in Yanshu4 in the seedling-stage and shoot-stage roots, and up-regulated in seedling-stage roots and shoot-stage leaves; stu-miR482a-3p was up-regulated in the seedling and shoot stages. The expression of stu-miR8036-3p was up-regulated in the leaves and roots at the seedling and budding stages, and down-regulated in roots under both types of N stress. The gene expressing the key enzyme involved in N metabolism, StNiR, and the stu-miR396-5p luciferase assay reporter gene had a strong regulatory relationship with each other. This study provides candidate miRNAs related to nitrogen metabolism and highlights that differential miRNAs play a key role in nitrogen stress in potato, providing insights for future research on miRNAs and their target genes in nitrogen metabolic pathways and breeding nitrogen-efficient potatoes.

The early response of oil palm (Elaeis guineensis Jacq.) plants to water deprivation: Expression analysis of miRNAs and their putative target genes, and similarities with the response to salinity stress

Oil palm (Elaeis guineensis Jacq.) is a oilseed crop of great economic importance drastically affected by abiotic stresses. MicroRNAs (miRNAs) play crucial roles in transcription and post-transcription regulation of gene expression, being essential molecules in the response of plants to abiotic stress. To better understand the molecular mechanisms behind the response of young oil palm plants to drought stress, this study reports on the prediction and characterization of miRNAs and their putative target genes in the apical leaf of plants subjected to 14 days of water deprivation. Then, the data from this study were compared to the data from a similar study that focused on salinity stress. Both, the drought-and salt-responsive miRNAs and their putative target genes underwent correlation analysis to identify similarities and dissimilarities among them. Among the 81 identified miRNAs, 29 are specific for oil palm, including two (egu-miR28ds and egu-miR29ds) new ones - described for the first time. As for the expression profile, 62 miRNAs were significantly differentially expressed under drought stress, being five up-regulated (miR396e, miR159b, miR529b, egu-miR19sds, and egu-miR29ds) and 57 down-regulated. Transcription factors, such as MYBs, HOXs, and NF-Ys, were predicted as putative miRNA-target genes in oil palm under water deprivation; making them the most predominant group of such genes. Finally, the correlation analysis study revealed a group of putative target genes with similar behavior under salt and drought stresses. Those genes that are upregulated by these two abiotic stresses encode lncRNAs and proteins linked to stress tolerance, stress memory, modulation of ROS signaling, and defense response regulation to abiotic and biotic stresses. In summary, this study provides molecular evidence for the possible involvement of miRNAs in the drought stress response in oil palm. Besides, it shows that, at the molecular level, there are many similarities in the response of young oil palm plants to these two abiotic stresses.

MicroRNA398: A Master Regulator of Plant Development and Stress Responses

MicroRNAs (miRNAs) play crucial roles in plant development and stress responses, and a growing number of studies suggest that miRNAs are promising targets for crop improvement because they participate in the regulation of diverse, important agronomic traits. MicroRNA398 (miR398) is a conserved miRNA in plants and has been shown to control multiple stress responses and plant growth in a variety of species. There are many studies on the stress response and developmental regulation of miR398. To systematically understand its function, it is necessary to summarize the evolution and functional roles of miR398 and its target genes. In this review, we analyze the evolution of miR398 in plants and outline its involvement in abiotic and biotic stress responses, in growth and development and in model and non-model plants. We summarize recent functional analyses, highlighting the role of miR398 as a master regulator that coordinates growth and diverse responses to environmental factors. We also discuss the potential for fine-tuning miR398 to achieve the goal of simultaneously improving plant growth and stress tolerance.

Roles of microRNAs in abiotic stress response and characteristics regulation of plant

MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.

Molecular Aspects of MicroRNAs and Phytohormonal Signaling in Response to Drought Stress: A Review

Phytohormones play an essential role in plant growth and development in response to environmental stresses. However, plant hormones require a complex signaling network combined with other signaling pathways to perform their proper functions. Thus, multiple phytohormonal signaling pathways are a prerequisite for understanding plant defense mechanism against stressful conditions. MicroRNAs (miRNAs) are master regulators of eukaryotic gene expression and are also influenced by a wide range of plant development events by suppressing their target genes. In recent decades, the mechanisms of phytohormone biosynthesis, signaling, pathways of miRNA biosynthesis and regulation were profoundly characterized. Recent findings have shown that miRNAs and plant hormones are integrated with the regulation of environmental stress. miRNAs target several components of phytohormone pathways, and plant hormones also regulate the expression of miRNAs or their target genes inversely. In this article, recent developments related to molecular linkages between miRNAs and phytohormones were reviewed, focusing on drought stress.

Adaptative Mechanisms of Halophytic Eutrema salsugineum Encountering Saline Environment

Salt cress (Eutrema salsugineum), an Arabidopsis-related halophyte, can naturally adapt to various harsh climates and soil conditions; thus, it is considered a desirable model plant for deciphering mechanisms of salt and other abiotic stresses. Accumulating evidence has revealed that compared with Arabidopsis, salt cress possesses stomata that close more tightly and more succulent leaves during extreme salt stress, a noticeably higher level of proline, inositols, sugars, and organic acids, as well as stress-associated transcripts in unstressed plants, and they are induced rapidly under stress. In this review, we systematically summarize the research on the morphology, physiology, genome, gene expression and regulation, and protein and metabolite profile of salt cress under salt stress. We emphasize the latest advances in research on the genome adaptive evolution encountering saline environments, and epigenetic regulation, and discuss the mechanisms underlying salt tolerance in salt cress. Finally, we discuss the existing questions and opportunities for future research in halophytic Eutrema. Together, the review fosters a better understanding of the mechanism of plant salt tolerance and provides a reference for the research and utilization of Eutrema as a model extremophile in the future. Furthermore, the prospects for salt cress applied to explore the mechanism of salt tolerance provide a theoretical basis to develop new strategies for agricultural biotechnology.

Integrated Expression Analysis of Small RNA, Degradome and Microarray Reveals Complex Regulatory Action of miRNA during Prolonged Shade in Swarnaprabha Rice

Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be miR5493-OsSLAC and miR5144-OsLOG1 for enhanced panicle size, miR5493-OsBRITTLE1-1 for grain formation, miR6245-OsCsIF9 for decreased stem mechanical strength, miR5487-OsGns9 and miR168b-OsCP1 for better pollen development, and miR172b-OsbHLH153 for hyponasty under shade.

ASRmiRNA: Abiotic Stress-Responsive miRNA Prediction in Plants by Using Machine Learning Algorithms with Pseudo K-Tuple Nucleotide Compositional Features

MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational method for prediction of miRNAs associated with abiotic stresses. Three types of datasets were used for prediction, i.e., miRNA, Pre-miRNA, and Pre-miRNA + miRNA. The pseudo K-tuple nucleotide compositional features were generated for each sequence to transform the sequence data into numeric feature vectors. Support vector machine (SVM) was employed for prediction. The area under receiver operating characteristics curve (auROC) of 70.21, 69.71, 77.94 and area under precision-recall curve (auPRC) of 69.96, 65.64, 77.32 percentages were obtained for miRNA, Pre-miRNA, and Pre-miRNA + miRNA datasets, respectively. Overall prediction accuracies for the independent test set were 62.33, 64.85, 69.21 percentages, respectively, for the three datasets. The SVM also achieved higher accuracy than other learning methods such as random forest, extreme gradient boosting, and adaptive boosting. To implement our method with ease, an online prediction server “ASRmiRNA” has been developed. The proposed approach is believed to supplement the existing effort for identification of abiotic stress-responsive miRNAs and Pre-miRNAs.

The Evolution and Functional Roles of miR408 and Its Targets in Plants

MicroRNA408 (miR408) is an ancient and highly conserved miRNA, which is involved in the regulation of plant growth, development and stress response. However, previous research results on the evolution and functional roles of miR408 and its targets are relatively scattered, and there is a lack of a systematic comparison and comprehensive summary of the detailed evolutionary pathways and regulatory mechanisms of miR408 and its targets in plants. Here, we analyzed the evolutionary pathway of miR408 in plants, and summarized the functions of miR408 and its targets in regulating plant growth and development and plant responses to various abiotic and biotic stresses. The evolutionary analysis shows that miR408 is an ancient and highly conserved microRNA, which is widely distributed in different plants. miR408 regulates the growth and development of different plants by down-regulating its targets, encoding blue copper (Cu) proteins, and by transporting Cu to plastocyanin (PC), which affects photosynthesis and ultimately promotes grain yield. In addition, miR408 improves tolerance to stress by down-regulating target genes and enhancing cellular antioxidants, thereby increasing the antioxidant capacity of plants. This review expands and promotes an in-depth understanding of the evolutionary and regulatory roles of miR408 and its targets in plants.

Integrative small RNA and transcriptome analysis provides insight into key role of miR408 towards drought tolerance response in cowpea

Drought stress response studies and overexpression of vun-miR408 proved it to be essential for abiotic stress tolerance in cowpea. Small RNA and transcriptome sequencing of an elite high-yielding drought-tolerant Indian cowpea cultivar, Pusa Komal revealed a differential expression of 198 highly conserved, 21 legume-specific, 14 less-conserved, and 10 novel drought-responsive microRNAs (miRNAs) along with 3391 (up-regulated) and 3799 (down-regulated) genes, respectively, in the leaf and root libraries. Among the differentially expressed miRNAs, vun-miR408-3p, showed an up-regulation of 3.53-log₂-fold change under drought stress. Furthermore, laccase 12 (LAC 12) was identified as the potential target of vun-miR408-3p using 5' RNA ligase-mediated rapid amplification of cDNA ends. The stable transgenic cowpea lines overexpressing artificial vun-miR408-3p (OX-amiR408) displayed enhanced drought and salinity tolerance as compared to the wild-type plants. An average increase of 30.17% in chlorophyll, 26.57% in proline, and 27.62% in relative water content along with lesser cellular H₂O₂ level was observed in the transgenic lines in comparison with the wild-type plants under drought stress. Additionally, the scanning electron microscopic study revealed a decrease in the stomatal aperture and an increase in the trichome density in the transgenic lines. The expression levels of laccase 3 and laccase 12, the potential targets of miR408, related to lipid catabolic processes showed a significant reduction in the wild-type plants under drought stress and the transgenic lines, indicating the regulation of lignin content as a plausibly essential trait related to the drought tolerance in cowpea. Taken together, this study primarily focused on identification of drought-responsive miRNAs and genes in cowpea, and functional validation of role of miR408 towards drought stress response in cowpea.

De novo transcriptome sequencing, assembly, and gene expression profiling of a salt-stressed halophyte (Salsola drummondii) from a saline habitat

Salsola drummondii is a perennial habitat-indifferent halophyte growing in saline and nonsaline habitats of the Arabian hyperarid deserts. It offers an invaluable opportunity to examine the molecular mechanisms of salt tolerance. The present study was conducted to elucidate these mechanisms through transcriptome profiling of seedlings grown from seeds collected in a saline habitat. The Illumina Hiseq 2500 platform was employed to sequence cDNA libraries prepared from shoots and roots of nonsaline-treated plants (controls) and plants treated with 1200 mM NaCl. Transcriptomic comparison between salt-treated and control samples resulted in 17,363 differentially expressed genes (DEGs), including 12,000 upregulated genes (7870 in roots, 4130 in shoots) and 5363 downregulated genes (4258 in roots and 1105 in shoots). The majority of identified DEGs are known to be involved in transcription regulation (79), signal transduction (82), defense metabolism (101), transportation (410), cell wall metabolism (27), regulatory processes (392), respiration (85), chaperoning (9), and ubiquitination (98) during salt tolerance. This study identified potential genes associated with the salt tolerance of S. drummondii and demonstrated that this tolerance may depend on the induction of certain genes in shoot and root tissues. These gene expressions were validated using reverse-transcription quantitative PCR, the results of which were consistent with transcriptomics results. To the best of our knowledge, this is the first study providing genetic information on salt tolerance mechanisms in S. drummondii.

Non-Coding RNAs in Response to Drought Stress

Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.

Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development

Gene silencing is a negative feedback mechanism that regulates gene expression to define cell fate and also regulates metabolism and gene expression throughout the life of an organism. In plants, gene silencing occurs via transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). TGS obscures transcription via the methylation of 5' untranslated region (5'UTR), whereas PTGS causes the methylation of a coding region to result in transcript degradation. In this review, we summarized the history and molecular mechanisms of gene silencing and underlined its specific role in plant growth and crop production.

Genome-wide analysis of the Universal stress protein A gene family in Vitis and expression in response to abiotic stress

Universal Stress Protein A (USPA) plays critical roles in the regulation of growth, development and response to abiotic stress in plants. To date, most research related to the role of USPA in plants has been carried out in herbaceous models such as Arabidopsis, rice and soybean. Here, we used bioinformatics approaches to identify 21 USPA genes in the genome of Vitis vinifera L. Phylogenetic analysis revealed that VvUSPAs could be divided into eight clades. Based on predicted chromosomal locations, we identified 16 pairs of syntenic, orthologous genes between A. thaliana and V. vinifera. Further promoter cis-elements analysis, together with identification of potential microRNA (miRNA) binding sites, suggested that at least some of the VvUSPAs participate in response to phytohormones and abiotic stress. To add support for this, we analyzed the developmental and stress-responsive expression patterns of the homologous USPA genes in the drought-resistant wild Vitis yeshanensis accession 'Yanshan-1' and the drought-sensitive Vitis riparia accession 'He'an'. Most of the USPA genes were upregulated in different degrees in the two genotypes after drought stress and exposure to ethephon (ETH), abscisic acid (ABA) and methyl jasmonate (MeJA). Individual USPA genes showed various tissue-specific expression patterns. Heterologous expression of five selected genes (VvUSPA2, VvUSPA3, VvUSPA11, VvUSPA13 and VvUSPA16) in Escherichia coli (E. coli) enhanced resistance to drought stress. Our study provides a model for mapping gene function in response to abiotic stress and identified three candidate genes, VvUSPA3, VvUSPA11 and VvUSPA16, as regulators of drought response in V. vinifera.

MiR408-SmLAC3 Module Participates in Salvianolic Acid B Synthesis in Salvia miltiorrhiza

MicroRNAs (miRNAs) are important regulators of gene expression involved in plant development and abiotic stress responses. Recently, miRNAs have also been reported to be engaged in the regulation of secondary plant metabolism. However, there are few functional studies of miRNAs in medicinal plants. For this study, we obtained Sm-miR408 interference lines to investigate the function of Sm-miR408 in a medicinal model plant (Salvia miltiorrhiza). It was found that inhibiting the expression of Sm-miR408 could increase the content of salvianolic acid B and rosmarinic acid in the roots. The SmLAC3 and Sm-miR408 expression patterns were analyzed by qRT-PCR. A 5’ RLM-RACE assay confirmed that Sm-miR408 targets and negatively regulates SmLAC3. Moreover, the overexpression of SmLAC3 in S. miltiorrhiza promoted the accumulation of salvianolic acids in the roots. Furthermore, the lignin content of the roots in overexpressed SmLAC3 lines was decreased. Taken together, these findings indicated that Sm-miR408 modulates the accumulation of phenolic acids in S. miltiorrhiza by targeting SmLAC3 expression levels.

Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development

Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.

Root-omics for drought tolerance in cool-season grain legumes

Root traits can be exploited to increase the physiological efficiency of crop water use under drought. Root length, root hairs, root branching, root diameter, and root proliferation rate are genetically defined traits that can help to improve the water productivity potential of crops. Recently, high-throughput phenotyping techniques/platforms have been used to screen the germplasm of major cool-season grain legumes for root traits and their impact on different physiological processes, including nutrient uptake and yield potential. Advances in omics approaches have led to the dissection of genomic, proteomic, and metabolomic structures of these traits. This knowledge facilitates breeders to improve the water productivity and nutrient uptake of cultivars under limited soil moisture conditions in major cool-season grain legumes that usually face terminal drought. This review discusses the advances in root traits and their potential for developing drought-tolerant cultivars in cool-season grain legumes.

Coping with low moisture stress: Remembering and responding

Low-moisture stress, also referred to as drought, is one of the major factors that negatively impact the agricultural yield. The present scenario of climate change is expected to aggravate it further. Considering the extended time required to develop resistant crops, it is important to prioritize research efforts for coping with low moisture, prevalent in arid and semi-arid regions of the world. While agricultural yield is a tradeoff between many choices, tolerance to biotic and abiotic stresses comes with yield penalties. To balance the tradeoffs and maximize productivity, the use of region-specific cultivars and/or introgression of precise genetic proportions in an elite variety may prove useful. Stress memory is an emerging approach that helps plants to record and respond to repeated stress in an effective manner. In this context, we discuss the role of "stress memory" in imparting drought tolerance in plants. Future research efforts for its effective deployment for "drought hardening" in agricultural settings, along with a discussion on the yield tradeoff involved, is implicated.

Overexpression of Os-microRNA408 enhances drought tolerance in perennial ryegrass

As a conserved microRNA (miRNA) family in plants, miR408 is known to be involved in different abiotic stress responses, including drought. Interestingly, some studies indicated a species- and/or cultivar-specific drought-responsive characteristic of miR408 in plant drought stress. Moreover, the functions of miR408 in perennial grass species are unknown. In this study, we investigated the role of miR408 in perennial ryegrass (Lolium perenne L.) by withholding water for 10 days for both wild type and transgenic plants with heterologous expression of rice (Oryza sativa L.) miR408 gene, Os-miR408. The results showed that transgenic perennial ryegrass plants displayed morphological changes under normal growth conditions, such as curl leaves and sunken stomata, which could be related to decreased leaf water loss. Moreover, transgenic perennial ryegrass exhibited improved drought tolerance, as demonstrated by maintaining higher leaf relative water content (RWC), lower electrolyte leakage (EL), and less lipid peroxidation compared to WT plants under drought stress. Furthermore, the transgenic plants showed higher antioxidative capacity under drought. These results showed that the improved drought tolerance in Os-miR408 transgenic plants could be due to leaf morphological changes favoring the maintenance of water status and to increased antioxidative capacity protecting against the reactive oxygen species damages under stress. These findings implied that miR408 could serve as a potential target for genetic manipulations to engineer perennial grass plants for improved water stress tolerance.

Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica

Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica (M. ruthenica) is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, microRNAs (miRNAs), and key miRNA-target pairs in M. ruthenica under drought and rewatering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed in three test conditions (CK: control, DS: plants under drought stress, and RW: plants rewatering after drought stress). The degradome sequencing (AllenScore < 4) analysis revealed that 104 miRNAs (11 novel and 93 conserved miRNAs) were identified with 263 target transcripts, forming 296 miRNA-target pairs in three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21, 18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.

Physiological, Transcriptomic, and Metabolic Responses of Ginkgo biloba L. to Drought, Salt, and Heat Stresses

Ginkgo biloba L. is highly adaptable and resistant to a range of abiotic stressors, allowing its growth in various environments. However, it is unclear how G. biloba responds to common environmental stresses. We explored the physiological, transcriptomic, and metabolic responses of G. biloba to short-term drought, salt, and heat stresses. Proline, H2O2, and ABA contents, along with CAT activity, increased under all three types of stress. SOD activity increased under salt and heat stresses, while soluble protein and IAA contents decreased under drought and salt stresses. With respect to metabolites, D-glyceric acid increased in response to drought and salt stresses, whereas isomaltose 1, oxalamide, and threonine 2 increased under drought. Piceatannol 2,4-hydroxybutyrate and 1,3-diaminopropane increased under salt stress, whereas 4-aminobutyric acid 1 and galactonic acid increased in response to heat stress. Genes regulating nitrogen assimilation were upregulated only under drought, while the GRAS gene was upregulated under all three types of stressors. ARF genes were downregulated under heat stress, whereas genes encoding HSF and SPL were upregulated. Additionally, we predicted that miR156, miR160, miR172, and their target genes participate in stress responses. Our study provides valuable data for studying the multilevel response to drought, salinity, and heat in G. biloba.

Understanding of the postgerminative development response to salinity and drought stresses in cucumber seeds by integrated proteomics and transcriptomics analysis

The postgerminative development is a complex, genetically programmed process, and also the most dangerous period before the developing seedlings reach the autotrophy state. To obtain a comprehensive understanding of postgerminative development mechanism, the study focuses on an integrative analysis on transcriptome, proteome, and microRNA in cucumber seeds under drought and salt stress. Drought and salt stress caused differential expression of 4197 mRNAs, 36 microRNAs and 768 proteins compared with the control, and 827 mRNAs, 364 proteins, and 12 microRNAs were shared by the two stresses. Numerous common differentially expressed genes and proteins participated the signal transduction of plant hormone, photosynthesis, and argine and proline metabolism. We noted the correlation among nitric oxide, polyamine, proline, and ethylene metabolism, thereby helping to elucidate the role of these substances, which are derived either directly or indirectly from arginine, in the regulation of abiotic stress and provide a basis for building better network-based molecular models in further research. Above findings contribute to new and useful information regarding the common molecular mechanisms during cucumber seedling development under drought and salt stress. SIGNIFICANCE: Water scarcity and high salt are two of the most destructive and wide stress factors which limit the growth and progression of plants by affecting a variety of vital physiological and biochemical processes. Our study focuses on an integrative analysis on transcriptome, proteome, and microRNA for confirming the essential regulators as well as pathways using cucumber postgerminative development under drought and salt stress. Arginine metabolism is a vital response to abiotic stress during cucumber seed germination.

Global identification and characterization of miRNA family members responsive to potassium deprivation in wheat (Triticum aestivum L.)

Potassium (K) is essential for plant growth and stress responses. MicroRNAs (miRNAs) are involved in adaptation to nutrient deprivation through modulating gene expression. Here, we identified the miRNAs responsive to K deficiency in Triticum aestivum based on high-throughput small RNA sequencing analyses. Eighty-nine miRNAs, including 68 previously reported ones and 21 novel ones, displayed differential expression under K deficiency. In Gene Ontology and Kyoto Encyclopedia and Genome analyses, the putative target genes of the differentially expressed miRNAs were categorized into functional groups associated with ADP-binding activity, secondary metabolic pathways, and biosynthesis and metabolism. Functional characterization of tae-miR408, an miRNA significantly down-regulated under K deficiency, revealed its important role in mediating low-K tolerance. Compared with wild type, transgenic tobacco lines overexpressing tae-miR408 showed significantly improved K uptake, biomass, photosynthesis, and reactive oxygen species scavenging under K deficiency. These results show that distinct miRNAs function in the plant response to K deficiency through regulating target genes involved in energy metabolism and various secondary metabolic pathways. Our findings shed light on the plant response to K deficiency mediated by miRNAs in T. aestivum. Distinct miRNAs, such as tae-miR408, are valuable targets for generating crop varieties with improved K-use efficiency.

Characterization of microRNA genes from Pigeonpea (Cajanus cajan L.) and understanding their involvement in drought stress

MicroRNAs (miRNA) are non-coding 20-24 nucleotide long RNAs regulating gene expression. In this study, we have characterized and analysed expression of miRNAs in Pigeonpea by using bioinformatics and experimental tools. We identified 116 miRNAs belonging to 32 phylogenetic families. Further, transcription start sites of miRNA genes revealed abundance and unique arrangement of adenine at +1 and thymine at -1 position. Promoter analysis exhibited presence of 19 most prevalent motifs which comprises majorly of TATA box and MYC domains. In total, 252 miRNA-targets were identified and found to be involved in various developmental processes and stress responses. Moreover, genome-wide localization studies demonstrated clustering of cca-miRNA 395 and 169 genes. The tandem and segmental duplication events were observed suggesting miRNA genes have been originated parallelly with protein coding genes. The expression analysis revealed induction of cca-miR169a, 398a and 408 miRNAs under drought stress highlighting their involvement. Conversely, down-regulation of their putative targets (NFYA, SOD, and UCLA, respectively) confirmed regulatory role of miRNAs in their expression emphasising the negative relationship between these miRNAs and targets in Pigeonpea. This study reports vast repertoire of miRNA genes which further can be experimentally characterized to elucidate their functions in various biological processes and can be recommended for Pigeonpea improvement programs.

Epigenetics: possible applications in climate-smart crop breeding

To better adapt transiently or lastingly to stimuli from the surrounding environment, the chromatin states in plant cells vary to allow the cells to fine-tune their transcriptional profiles. Modifications of chromatin states involve a wide range of post-transcriptional histone modifications, histone variants, DNA methylation, and activity of non-coding RNAs, which can epigenetically determine specific transcriptional outputs. Recent advances in the area of '-omics' of major crops have facilitated identification of epigenetic marks and their effect on plant response to environmental stresses. As most epigenetic mechanisms are known from studies in model plants, we summarize in this review recent epigenetic studies that may be important for improvement of crop adaptation and resilience to environmental changes, ultimately leading to the generation of stable climate-smart crops. This has paved the way for exploitation of epigenetic variation in crop breeding.

Identification of candidate miRNAs related in storage root development of sweet potato by high throughput sequencing

Sweet potato (Ipomoea batatas L.) is a food consumed worldwide, an industrial raw material and new energy crop. The storage root is the most economical part of the crop. However, the mechanism of storage root initiation and development is still unclear. In this study, conserved and novel miRNAs during storage root development were identified by high-throughput sequencing technology by constructing small RNA libraries from sweet potato fibrous roots (F) and storage roots at four different developmental stages (storage roots with different diameters: 1 cm, D1; 3 cm, D3; 5 cm, D5 and 10 cm, D10). A total of 61 known miRNAs and 471 novel miRNAs were identified. In addition, 145 differentially expressed miRNAs were identified in the F library compared with the four storage root libraries, with 30 known miRNAs and 115 novel miRNAs. Moreover, the targets of the differentially expressed miRNAs were predicted and their network was further investigated by GO analysis using our previous transcriptome data. The GO analysis revealed that antioxidant activity and binding process were the most enriched terms of the target genes. The secondary structure and expression of six candidate miRNAs including three conserved miRNAs and three novel miRNAs were investigated and their predicted targets were validated by qRT-PCR. The results showed that the expression levels of the miRNAs were all consistent with the sequencing data. Most of the miRNAs and their corresponding targets had obvious negative correlations. This study contributed to elucidating the potential miRNA mediated regulatory mechanism of storage root development in sweet potato. The specific differentially expressed miRNAs in sweet potato storage roots can be used to breed high-yield sweet potatoes and other tuberous root crops.