DNA methylation mediated by a microRNA pathway

The regulatory roles of plant miRNAs in biotic stress responses

Throughout their life cycle, plants are inevitably confronted with various challenges imposed by adverse environmental conditions, including both biotic and abiotic stresses. To adapt to these environmental fluctuations, plants have evolved a highly efficient regulatory mechanism, in which microRNAs (miRNAs) play pivotal roles. miRNAs are a class of 20-24 nucleotide non-coding RNAs generated from MIR genes, which regulate gene expression at the post-transcriptional level through mRNA degradation or translational repression. Over the past decades, accumulating evidence has demonstrated that miRNAs serve as master regulators in plant responses to biotic stresses, such as those caused by bacteria, fungi, oomycetes, viruses, nematodes, and insects. In this review, we summarize recent advances in miRNA biogenesis and highlight the regulatory roles of plant miRNAs in biotic stress tolerance. Additionally, we discuss future directions of miRNA research.

A review of MicroRNAs and flavonoids: New insights into plant secondary metabolism

Flavonoids, essential plant secondary metabolites, play crucial roles in growth regulation, stress responses, and applications in medicine, agriculture, and industry. However, the complexity of their biosynthetic pathways and regulatory networks poses challenges for industrial-scale production. MicroRNAs (miRNAs), as pivotal post-transcriptional regulators, play significant roles in fine-tuning flavonoid metabolism by targeting key enzyme genes and transcription factors. This review provides a comprehensive analysis of miRNA biogenesis and their molecular mechanisms, emphasizing miRNA-mediated regulation of flavonoid biosynthesis. We introduce the concept of "miRNA-multifactorial synergistic networks", which elucidates the collaborative interactions between miRNAs, non-coding RNAs, transcription factors, and epigenetic regulators. The review explores emerging strategies, including artificial miRNA design and CRISPR/Cas technologies, to precisely manipulate miRNA activity for enhancing flavonoid production. Additionally, integrating CRISPR/Cas13, synthetic biology, and multi-omics technologies offers new opportunities to construct efficient flavonoid metabolic systems. Artificial intelligence (AI) is proposed as a powerful tool to analyze omics data, identify regulatory nodes, and simulate environmental impacts on miRNA networks, thereby optimizing metabolic pathways. By integrating these multidisciplinary approaches, this review provides a novel theoretical framework and technical roadmap for understanding and improving flavonoid metabolism. The insights presented here aim to facilitate breakthroughs in metabolic engineering, offering significant potential for practical applications in plant breeding, functional food production, and pharmaceutical development.

Classification of and detection techniques for RNAi-induced effects in GM plants

RNA interference (RNAi) is a biotechnological tool used for gene silencing in plants, with both endogenous and exogenous applications. Endogenous approaches, such as host-induced gene silencing (HIGS), involve genetically modified (GM) plants, while exogenous methods include spray-induced gene silencing (SIGS). The RNAi mechanism hinges on the introduction of double-stranded RNA (dsRNA), which is processed into short interfering RNAs (siRNAs) that degrade specific messenger RNAs (mRNAs). However, unintended effects on non-target organisms and GM plants are a concern due to sequence homologies or siRNA-induced epigenetic changes. Regulatory bodies such as the EPA and EFSA emphasize the need for comprehensive risk assessments. Detecting unintended effects is complex, often relying on bioinformatic tools and untargeted analyses like transcriptomics and metabolomics, though these methods require extensive genomic data. This review aims to classify mechanisms of RNAi effects induced by short interfering RNA from different sources in plants and to identify technologies that can be used to detect these effects. In addition, practical case studies are summarized and discussed in which previously unintended RNAi effects in genetically modified plants have been investigated. Current literature is limited but suggests RNAi is relatively specific, with few unintended effects observed in GM crops. However, further studies are needed to fully understand and mitigate potential risks, particularly those related to transcriptional gene silencing (TGS) mechanisms, which are less predictable than post-transcriptional gene silencing (PTGS). Particularly the application of untargeted approaches such as small RNA sequencing and transcriptomics is recommended for thorough and comprehensive risk assessments.

A 24-nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis

MicroRNAs (miRNAs) control gene expression in plant through transcript cleavage and translation inhibition. Recently, 24-nt miRNAs have been shown to direct DNA methylation at target sites, regulating the neighboring gene expression. Our study focused on miR9560, a 24-nt miRNA induced by cadmium (Cd) stress in Brassica rapa ssp. parachinensis (B. parachinensis). Phylogenetic analysis revealed miR9560 predominantly emerged in the Rosanae superorder and was conserved in Brassicaceae, with potential target sites adjacent to transporter family genes HMAs. RNA gel blotting showed that mature miR9560 was only detected in various Brassica crops roots after Cd stress. In B. parachinensis, miR9560's putative target site is upstream of BrpHMA2, an afflux-type Cd transporter. In a transient expression system of B. parachinensis protoplasts, the expression of miR9560 increased the DNA methylation upstream of BrpHMA2, reducing the transcription of BrpHMA2. This regulation was also observed in Arabidopsis wild-type protoplasts but not in the mutants dcl234 and ago4 with impairments in the RNA-dependent DNA methylation (RdDM) pathway. We deduced that miR9560 modulates BrpHMA2 expression via the RdDM pathway, potentially regulating Cd uptake and movement in B. parachinensis. Furthermore, this regulatory mechanism may extend to other Brassica plants. This study enhances our comprehension of 24-nt miRNAs role in regulating Cd accumulation within Brassica plants.

MicroRNA gatekeepers: Orchestrating rhizospheric dynamics

The rhizosphere plays a crucial role in plant growth and resilience to biotic and abiotic stresses, highlighting the complex communication between plants and their dynamic rhizosphere environment. Plants produce a wide range of signaling molecules that facilitate communication with various rhizosphere factors, yet our understanding of these mechanisms remains elusive. In addition to protein-coding genes, increasing evidence underscores the critical role of microRNAs (miRNAs), a class of non-coding single-stranded RNA molecules, in regulating plant growth, development, and responses to rhizosphere stresses under diverse biotic and abiotic factors. In this review, we explore the crosstalk between miRNAs and their target mRNAs, which influence the development of key plant structures shaped by the belowground environment. Moving forward, more focused studies are needed to clarify the functions and expression patterns of miRNAs, to uncover the common regulatory mechanisms that mediate plant tolerance to rhizosphere dynamics. Beyond that, we propose that using artificial miRNAs and manipulating the expression of miRNAs and their targets through overexpression or knockout/knockdown approaches could effectively investigate their roles in plant responses to rhizosphere stresses, offering significant potential for advancing crop engineering.

Epigenetics in the modern era of crop improvements

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

The Roles of MicroRNAs in the Regulation of Rice-Pathogen Interactions

Rice is exposed to attacks by the three most destructive pathogens, Magnaporthe oryzae (M. oryzae), Xanthomonas oryzae pv. oryzae (Xoo), and Rhizoctonia solani (R. solani), which cause substantial yield losses and severely threaten food security. To cope with pathogenic infections, rice has evolved diverse molecular mechanisms to respond to a wide range of pathogens. Among these strategies, plant microRNAs (miRNAs), endogenous single-stranded short non-coding RNA molecules, have emerged as promising candidates in coordinating plant-pathogen interactions. MiRNAs can modulate target gene expression at the post-transcriptional level through mRNA cleavage and/or translational inhibition. In rare instances, they also influence gene expression at the transcriptional level through DNA methylation. In recent years, substantial advancements have been achieved in the investigation of microRNA-mediated molecular mechanisms in rice immunity. Therefore, we attempt to summarize the current advances of immune signaling mechanisms in rice-pathogen interactions that are regulated by osa-miRNAs, including their functions and molecular mechanisms. We also focus on recent findings concerning the role of osa-miRNAs that respond to M. oryzae, Xoo, and R. solani, respectively. These insights enhance our understanding of how the mechanisms of osa-miRNAs mediate rice immunity and may facilitate the development of improved strategies for breeding pathogen-resistant rice varieties.

Small RNA sequencing analysis provides novel insights into microRNA-mediated regulation of defense responses in chickpea against Fusarium wilt infection

MAIN CONCLUSION

Small RNA sequencing analysis in two chickpea genotypes, JG 62 (Fusarium wilt-susceptible) and WR 315 (Fusarium wilt-resistant), under Fusarium wilt stress led to identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 115 miRNAs showed differential expression in both the genotypes across different combinations. A miRNA, Car-miR398 targeted copper chaperone for superoxide dismutase (CCS) that, in turn, regulated superoxide dismutase (SOD) activity during chickpea-Foc interaction. Fusarium wilt (FW) of chickpea (Cicer arietinum L.) caused by Fusarium oxysporum f. sp. ciceris (Foc) is a destructive soil-borne disease that severely reduces the chickpea yield and quality globally. In the present study, we have investigated microRNAs and the microRNA/target gene crosstalk involved in chickpea resistance to FW. The control and stress samples from two genotypes, JG 62 (FW-susceptible) and WR 315 (FW-resistant), collected at 10 days post-inoculation (dpi), were selected for small RNA sequencing. A total of 12 libraries were constructed and sequenced using Illumina HiSeq 2500 platform. The sequencing and in silico analyses revealed the identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 50 miRNAs were physically co-localized with Foc-resistance QTLs present on chromosome 2 (also known as Foc hotspot). A total of 115 miRNAs showed differential expression in both the genotypes across different combinations. Prediction and functional annotation of miRNA targets revealed their role in transcription regulation, disease resistance, defense response, metabolism, etc. Ten miRNAs and their targets were validated using poly(A)-based qRT-PCR in two genotypes grown under lab and field conditions. Many miRNAs and their targets showed genotype-specific expression. The expression profiling also highlighted, both, similar and different expression patterns for the same sets of miRNA and mRNA at different stages of Foc infection. A high correlation in expression patterns of the miRNAs and their targets in lab- and field-grown plant samples was observed. Interestingly, Car-miR398 targeted copper chaperone for superoxide dismutase (CCS) that, in turn, regulated superoxide dismutase (SOD) activity during chickpea-Foc interaction. The cleavage site in targets was mapped for three miRNAs by analyzing publicly available degradome data for chickpea. The study, for the first time, provides novel insights into microRNA-mediated regulation of resistance and susceptibility mechanisms in chickpea against FW and opens up avenues for the development of the wilt-resistant cultivars in chickpea.

ARGONAUTE4 and the DNA demethylase REPRESSOR OF SILENCING 1C mediate dehydroascorbate-induced intergenerational nematode resistance in rice

Plants can transmit information to the next generation and modulate the phenotype of their offspring through epigenetic mechanisms. In this study, we demonstrate the activation of "intergenerational acquired resistance" (IAR) in the progeny of rice (Oryza sativa) plants exogenously treated with dehydroascorbate (DHA). The offspring of lifelong DHA-treated plants (DHA-IAR) were significantly less susceptible to the root-knot nematode Meloidogyne graminicola and partially inherited the DHA-induced transcriptional response found in the parental plants. Phytohormone analyses on the DHA-IAR plants unveiled higher basal abscisic acid levels and a primed induction of the jasmonic acid pathway. RNA-seq analysis on the embryonic tissues of immature seeds of DHA-treated plants revealed major shifts in the expression of genes associated with epigenetic pathways. We confirmed that DHA treatment leads to a significant but transient pattern of global DNA hypomethylation in the parental plants 12 to 24 h after treatment. The induction of resistance in the parental plants requires the DNA demethylase REPRESSOR OF SILENCING 1C (ROS1c) and ARGONAUTE 4, suggesting a role for DNA demethylation and subsequent remethylation in establishment of this phenotype. Confirming the transience of global hypomethylation upon DHA treatment, no significant change in global DNA methylation levels was observed in DHA-IAR versus naïve plants. Finally, DHA could not induce IAR in the ros1c mutant line and the ARGONAUTE 4 (ago4ab)-RNAi line. These data indicate that a controlled collaboration between transient DNA demethylation and remethylation underlies the induced resistance and IAR phenotypes upon DHA treatment.

Unlocking the small RNAs: local and systemic modulators for advancing agronomic enhancement

Small regulatory RNAs (sRNAs) are essential regulators of gene expression across a wide range of organisms to precisely modulate gene activity based on sequence-specific recognition. In model plants like Arabidopsis thaliana, extensive research has primarily concentrated on 21 to 24-nucleotide (nt) sRNAs, particularly microRNAs (miRNAs). Recent advancements in cell and tissue isolation techniques, coupled with advanced sequencing technologies, are revealing a diverse array of preciously uncharacterized sRNA species. These include previously novel structural RNA fragments as well as numerous cell- and tissue-specific sRNAs that are active during distinct developmental stages, thereby enhancing our understanding of the precise and dynamic regulatory roles of sRNAs in plant development regulation. Additionally, a notable feature of sRNAs is their capacity for amplification and movement between cells and tissues, which facilitates long-distance communication-an adaptation critical to plants due to their sessile nature. In this review, we will discuss the classification and mechanisms of action of sRNAs, using legumes as a primary example due to their essential engagement for the unique organ establishment of root nodules and long-distance signaling, and further illustrating the potential applications of sRNAs in modern agricultural breeding and environmentally sustainable plant protection strategies.

Advantage looping: Gene regulatory circuits between microRNAs and their target transcription factors in plants

The 20 to 24 nucleotide microRNAs (miRNAs) and their target transcription factors (TF) have emerged as key regulators of diverse processes in plants, including organ development and environmental resilience. In several instances, the mature miRNAs degrade the TF-encoding transcripts, while their protein products in turn bind to the promoters of the respective miRNA-encoding genes and regulate their expression, thus forming feedback loops (FBLs) or feedforward loops (FFLs). Computational analysis suggested that such miRNA-TF loops are recurrent motifs in gene regulatory networks (GRNs) in plants as well as animals. In recent years, modeling and experimental studies have suggested that plant miRNA-TF loops in GRNs play critical roles in driving organ development and abiotic stress responses. Here, we discuss the miRNA-TF FBLs and FFLs that have been identified and studied in plants over the past decade. We then provide some insights into the possible roles of such motifs within GRNs. Lastly, we provide perspectives on future directions for dissecting the functions of miRNA-centric GRNs in plants.

Enjoy the silence: Canonical and non-canonical RNA silencing activity during plant sexual reproduction

Plants produce small RNAs that accomplish a surprisingly versatile number of functions. The heterogeneity of functions of plant small RNAs is evident at the tissue-specific level. In particular, in the last years, the study of their activity in reproductive tissues has unmasked an unexpected diversity in their biogenesis and roles. Here, we review recent findings about the biogenesis pathways and roles of small RNAs during plant sexual reproduction.

Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass

BACKGROUND

Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) are essential components of RNA silencing pathways in plants. These components are crucial for the generation and regulatory functions of small RNAs, especially in plant development and response to environmental stresses. Despite their well-characterized functions in other plant species, there is limited information about these genes and their stress responses in centipedegrass (Eremochloa ophiuroides), a key turfgrass species.

RESULTS

Using genome-wide analysis we identified 20 AGO, 6 DCL, and 10 RDR members in centipedegrass and provided a comprehensive overview of their characteristics. We performed the chromosomal location, gene duplication, syntenic analysis, conserve motif, gene structure, and cis-acting elements analysis. And conducted phylogenetic analyses to clarify the evolutionary relationships among the EoAGO, EoDCL, and EoRDR gene families. Three-dimensional modeling prediction of EoAGO, EoDCL, and EoRDR proteins supported the phylogenetic classification. Furthermore, we examined the expression patterns of these genes in different tissues (spike, stem, leaf, root, and flower) and under different stress conditions (cold, salt, drought, aluminum, and herbicide) using RT-qPCR. The results revealed that most of EoAGO, EoDCL, and EoRDR genes were upregulated in response to multiple abiotic stresses, while some exhibited unique responses, suggesting potential specialized regulatory functions.

CONCLUSION

In this study, we performed a comprehensive genome‑wide identification, and phylogenetic and expression pattern analyses of the EoAGO, EoDCL and EoRDR gene families. Our analysis provides a foundation for future research on the RNA silence elements of turfgrass, and affords scientific basis and insights for clarifying the expression patterns of EoAGO, EoDCL and EoRDR genes under adversity stress. Further functional validation and molecular breeding of these genes can be carried out for enhancing the stress resistance of centipedegrass.

Variations in DNA methylation and the role of regulatory factors in rice (Oryza sativa) response to lunar orbit stressors

Deep space flight imposes higher levels of damage on biological organisms; however, its specific effects on rice remain unclear. To investigate the variations in DNA methylation under deep space flight conditions, this study examined rice seeds carried by Chang'e-5. After 23 days of lunar orbital flight, the samples were planted in an artificial climate chamber and subjected to transcriptome and DNA methylation sequencing during the tillering and heading stages. The methylation patterns in the rice genome exhibited variability in response to lunar orbital stressors. DNA methylation alters the expression and interaction patterns of functional genes, involving biological processes such as metabolism and defense. Furthermore, we employed single-sample analysis methods to assess the gene expression and interaction patterns of different rice individuals. The genes exhibiting changes at the transcriptional and methylation levels varied among the different plants; however, these genes regulate consistent biological functions, primarily emphasizing metabolic processes. Finally, through single-sample analysis, we identified a set of miRNAs induced by lunar orbital stressors that potentially target DNA methylation regulatory factors. The findings of this study broaden the understanding of space biological effects and lay a foundation for further exploration of the mechanisms by which deep space flight impacts plants.

The OsAGO2-OsNAC300-OsNAP module regulates leaf senescence in rice

Leaves play a crucial role in the growth and development of rice (Oryza sativa) as sites for the production of photosynthesis. Early leaf senescence leads to substantial drops in rice yields. Whether and how DNA methylation regulates gene expression and affects leaf senescence remains elusive. Here, we demonstrate that mutations in rice ARGONAUTE 2 (OsAGO2) lead to premature leaf senescence, with chloroplasts in Osago2 having lower chlorophyll content and an abnormal thylakoid structure compared with those from wild-type plants. We show that OsAGO2 associates with a 24-nt microRNA and binds to the promoter region of OsNAC300, which causes DNA methylation and suppressed expression of OsNAC300. Overexpressing OsNAC300 causes the similar premature leaf senescence as Osago2 mutants and knocking out OsNAC300 in the Osago2 mutant background suppresses the early senescence of Osago2 mutants. Based on yeast one-hybrid, dual-luciferase, and electrophoresis mobility shift assays, we propose that OsNAC300 directly regulates transcription of the key rice aging gene NAC-like, activated by APETALA3/PISTILLATA (OsNAP) to control leaf senescence. Our results unravel a previously unknown epigenetic regulatory mechanism underlying leaf senescence in which OsAGO2-OsNAC300-OsNAP acts as a key regulatory module of leaf senescence to maintain leaf function.

Bioengineering for robust tolerance against cold and drought stresses via co-overexpressing three Cu-miRNAs in major food crops

Environmental stresses threaten global food security by reducing major crop productivity. MicroRNAs (miRNAs), a class of small non-coding RNAs, function as master regulators of gene expression in plants. In this study, we co-overexpressed three copper-miRNAs (miR397, miR408, and miR528) in three major food crops (referred to as 3miR-OE), which simultaneously silenced several target laccase genes, resulting in reduced lignin contents but increased flavonoid metabolites. Importantly, we observed that, compared to wild-type and single miRNA overexpression lines, the 3miR-OE transgenic Japonica and Indica rice exhibited significantly enhanced tolerance against cold and drought stresses throughout the growth period. In addition, 3miR-OE transgenic maize and wheat also exhibited robust resistance to cold and water-deficit conditions, suggesting that co-overexpressing three Cu-miRNAs is a powerful tool for improving resilience to abiotic stresses across diverse crops. Altogether, we have developed a bioengineering strategy to maintain crop growth and yield under unfavorable environmental conditions.

Advances in RNA Interference for Plant Functional Genomics: Unveiling Traits, Mechanisms, and Future Directions

RNA interference (RNAi) is a conserved molecular mechanism that plays a critical role in post-transcriptional gene silencing across diverse organisms. This review delves into the role of RNAi in plant functional genomics and its applications in crop improvement, highlighting its mechanistic insights and practical implications. The review begins with the foundational discovery of RNAi's mechanism, tracing its origins from petunias to its widespread presence in various organisms. Various classes of regulatory non-coding small RNAs, including siRNAs, miRNAs, and phasiRNAs, have been uncovered, expanding the scope of RNAi-mediated gene regulation beyond conventional understanding. These RNA classes participate in intricate post-transcriptional and epigenetic processes that influence gene expression. In the context of crop enhancement, RNAi has emerged as a powerful tool for understanding gene functions. It has proven effective in deciphering gene roles related to stress resistance, metabolic pathways, and more. Additionally, RNAi-based approaches hold promise for integrated pest management and sustainable agriculture, contributing to global efforts in food security. This review discusses RNAi's diverse applications, such as modifying plant architecture, extending shelf life, and enhancing nutritional content in crops. The challenges and future prospects of RNAi technology, including delivery methods and biosafety concerns, are also explored. The global landscape of RNAi research is highlighted, with significant contributions from regions such as China, Europe, and North America. In conclusion, RNAi remains a versatile and pivotal tool in modern plant research, offering novel avenues for understanding gene functions and improving crop traits. Its integration with other biotechnological approaches such as gene editing holds the potential to shape the future of agriculture and sustainable food production.

Analysis of the miR482 Gene Family in Plants

MicroRNA482 (miR482) is a conserved microRNA family in plants, playing critical regulatory roles in different biological activities. Though the members of the miR482 gene family have been identified in plants, a systematic study has not been reported yet. In the present research, 140 mature sequences generated by 106 precursors were used for molecular characterization, phylogenetic analysis, and target gene prediction, and the competing endogenous RNA (ceRNA) network mediated by miR482 was summarized. The length of mature sequences ranged from 17 nt to 25 nt, with 22 nt being the most abundant, and the start and end of the mature sequences had a preference for uracil (U). By sequence multiplex comparison, it was found that the mature sequences of 5p were clustered into one group, and others were clustered into the other group. Phylogenetic analysis revealed that the 140 mature sequences were categorized into six groups. Meanwhile, all the precursor sequences formed a stable hairpin structure, and the 106 precursors were divided into five groups. However, the expression of miR482 varied significantly between different species and tissues. In total, 149 target genes were predicted and their functions focused on single-organism process, cellular process, and cell and cell part. The ceRNA network of miR482 in tomato, cotton, and peanut was summarized based on related publications. In conclusion, this research will provide a foundation for further understanding of the miR482 gene family.

HYL1's multiverse: A journey through miRNA biogenesis and beyond canonical and non-canonical functions of HYL1

A delicate balance in gene expression, a process highly controlled by post-transcriptional gene silencing mediated by miRNAs, is vital during plant growth and responses to stress. Within the miRNA biogenesis pathway, HYL1 is one of the most important proteins, initially recognized for its role as a cofactor of DCL1. Yet, HYL1's functions extend beyond miRNA processing, encompassing transcriptional regulation and protein translation between other recently discovered functions. This review comprehensively examines our current knowledge of HYL1 functions in plants, looking at its structure, the complex biochemistry behind it, and its involvement in a variety of cellular processes. We also explored the most compelling open questions regarding HYL1 biology and the further perspectives in its study. Unraveling HYL1 functional details could better understand how plants grow, face environmental stresses, and how the miRNA pathway adapts its outcome to the plant growing conditions.

Participation of miR165a in the Phytochrome Signal Transduction in Maize (Zea mays L.) Leaves under Changing Light Conditions

The involvement of the microRNA miR165a in the light-dependent mechanisms of regulation of target genes in maize (Zea mays) has been studied. The light-induced change in the content of free miR165a was associated with its binding by the AGO10 protein and not with a change in the rate of its synthesis from the precursor. The use of knockout Arabidopsis plants for the phytochrome A and B genes demonstrated that the presence of an active form of phytochrome B causes an increase in the level of the RNA-induced silencing miR165a complex, which triggers the degradation of target mRNAs. The two fractions of vesicles from maize leaves, P40 and P100 that bind miR165a, were isolated by ultracentrifugation. The P40 fraction consisted of larger vesicles of the size >0.170 µm, while the P100 fraction vesicles were <0.147 µm. Based on the quantitative PCR data, the predominant location of miR165a on the surface of extracellular vesicles of both fractions was established. The formation of the active form of phytochrome upon the irradiation of maize plants with red light led to a redistribution of miR165a, resulting in an increase in its proportion inside P40 vesicles and a decrease in P100 vesicles.

Multiomics analysis of a resistant European turnip ECD04 during clubroot infection reveals key hub genes underlying resistance mechanism

The clubroot disease has become a worldwide threat for crucifer crop production, due to its soil-borne nature and difficulty to eradicate completely from contaminated field. In this study we used an elite resistant European fodder turnip ECD04 and investigated its resistance mechanism using transcriptome, sRNA-seq, degradome and gene editing. A total of 1751 DEGs were identified from three time points after infection, among which 7 hub genes including XTH23 for cell wall assembly and two CPK28 genes in PTI pathways. On microRNA, we identified 17 DEMs and predicted 15 miRNA-target pairs (DEM-DEG). We validated two pairs (miR395-APS4 and miR160-ARF) by degradome sequencing. We investigated the miR395-APS4 pair by CRISPR-Cas9 mediated gene editing, the result showed that knocking-out APS4 could lead to elevated clubroot resistance in B. napus. In summary, the data acquired on transcriptional response and microRNA as well as target genes provide future direction especially gene candidates for genetic improvement of clubroot resistance on Brassica species.

Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops

As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.

Complexity of responses to ionizing radiation in plants, and the impact on interacting biotic factors

In nature, plants are simultaneously exposed to different abiotic (e.g., heat, drought, and salinity) and biotic (e.g., bacteria, fungi, and insects) stresses. Climate change and anthropogenic pressure are expected to intensify the frequency of stress factors. Although plants are well equipped with unique and common defense systems protecting against stressors, they may compromise their growth and development for survival in such challenging environments. Ionizing radiation is a peculiar stress factor capable of causing clustered damage. Radionuclides are both naturally present on the planet and produced by human activities. Natural and artificial radioactivity affects plants on molecular, biochemical, cellular, physiological, populational, and transgenerational levels. Moreover, the fitness of pests, pathogens, and symbionts is concomitantly challenged in radiologically contaminated areas. Plant responses to artificial acute ionizing radiation exposure and laboratory-simulated or field chronic exposure are often discordant. Acute or chronic ionizing radiation exposure may occasionally prime the defense system of plants to better tolerate the biotic stress or could often exhaust their metabolic reserves, making plants more susceptible to pests and pathogens. Currently, these alternatives are only marginally explored. Our review summarizes the available literature on the responses of host plants, biotic factors, and their interaction to ionizing radiation exposure. Such systematic analysis contributes to improved risk assessment in radiologically contaminated areas.

Switching action modes of miR408-5p mediates auxin signaling in rice

MicroRNAs (miRNAs) play fundamental roles in many developmental and physiological processes in eukaryotes. MiRNAs in plants generally regulate their targets via either mRNA cleavage or translation repression; however, which approach plays a major role and whether these two function modes can shift remains elusive. Here, we identify a miRNA, miR408-5p that regulates AUXIN/INDOLE ACETIC ACID 30 (IAA30), a critical repressor in the auxin pathway via switching action modes in rice. We find that miR408-5p usually inhibits IAA30 protein translation, but in a high auxin environment, it promotes the decay of IAA30 mRNA when it is overproduced. We further demonstrate that IDEAL PLANT ARCHITECTURE1 (IPA1), an SPL transcription factor regulated by miR156, mediates leaf inclination through association with miR408-5p precursor promoter. We finally show that the miR156-IPA1-miR408-5p-IAA30 module could be controlled by miR393, which silences auxin receptors. Together, our results define an alternative auxin transduction signaling pathway in rice that involves the switching of function modes by miR408-5p, which contributes to a better understanding of the action machinery as well as the cooperative network of miRNAs in plants.

Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation

KEY MESSAGE

Barley AGO4 proteins complement expressional changes of epigenetically regulated genes in Arabidopsis ago4-3 mutant and show a distinct affinity for the 5' terminal nucleotide of small RNAs, demonstrating functional conservation and divergence. The function of Argonaute 4 (AGO4) in Arabidopsis thaliana has been extensively characterized; however, its role in monocots, which have large genomes abundantly supplemented with transposable elements (TEs), remains elusive. The study of barley AGO4 proteins can provide insights into the conserved aspects of RNA-directed DNA methylation (RdDM) and could also have further applications in the field of epigenetics or crop improvement. Bioinformatic analysis of RNA sequencing data identified two active AGO4 genes in barley, HvAGO4a and HvAGO4b. These genes function similar to AtAGO4 in an Arabidopsis heterologous complementation system, primarily binding to 24-nucleotide long small RNAs (sRNAs) and triggering methylation at specific target loci. Like AtAGO4, HvAGO4B exhibits a preference for binding sRNAs with 5' adenine residue, while also accepting 5' guanine, uracil, and cytosine residues. In contrast, HvAGO4A selectively binds only sRNAs with a 5' adenine residue. The diverse binding capacity of barley AGO4 proteins is reflected in TE-derived sRNAs and in their varying abundance. Both barley AGO4 proteins effectively restore the levels of extrachromosomal DNA and transcript abundancy of the heat-activated ONSEN retrotransposon to those observed in wild-type Arabidopsis plants. Our study provides insight into the distinct binding specificities and involvement in TE regulation of barley AGO4 proteins in Arabidopsis by heterologous complementation.

Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities

Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.

Identification of Tomato microRNAs in Late Response to Trichoderma atroviride

The tomato (Solanum lycopersicum) is an important crop worldwide and is considered a model plant to study stress responses. Small RNAs (sRNAs), 21-24 nucleotides in length, are recognized as a conserved mechanism for regulating gene expression in eukaryotes. Plant endogenous sRNAs, such as microRNA (miRNA), have been involved in disease resistance. High-throughput RNA sequencing was used to analyze the miRNA profile of the aerial part of 30-day-old tomato plants after the application of the fungus Trichoderma atroviride to the seeds at the transcriptional memory state. Compared to control plants, ten differentially expressed (DE) miRNAs were identified in those inoculated with Trichoderma, five upregulated and five downregulated, of which seven were known (miR166a, miR398-3p, miR408, miR5300, miR6024, miR6027-5p, and miR9471b-3p), and three were putatively novel (novel miR257, novel miR275, and novel miR1767). miRNA expression levels were assessed using real-time quantitative PCR analysis. A plant sRNA target analysis of the DE miRNAs predicted 945 potential target genes, most of them being downregulated (84%). The analysis of KEGG metabolic pathways showed that most of the targets harbored functions associated with plant-pathogen interaction, membrane trafficking, and protein kinases. Expression changes of tomato miRNAs caused by Trichoderma are linked to plant defense responses and appear to have long-lasting effects.

Rhizospheric miRNAs affect the plant microbiota

Small ribonucleic acids (RNAs) have been shown to play important roles in cross-kingdom communication, notably in plant-pathogen relationships. Plant micro RNAs (miRNAs)-one class of small RNAs-were even shown to regulate gene expression in the gut microbiota. Plant miRNAs could also affect the rhizosphere microbiota. Here we looked for plant miRNAs in the rhizosphere of model plants, and if these miRNAs could affect the rhizosphere microbiota. We first show that plant miRNAs were present in the rhizosphere of Arabidopsis thaliana and Brachypodium distachyon. These plant miRNAs were also found in or on bacteria extracted from the rhizosphere. We then looked at the effect these plants miRNAs could have on two typical rhizosphere bacteria, Variovorax paradoxus and Bacillus mycoides. The two bacteria took up a fluorescent synthetic miRNA but only V. paradoxus shifted its transcriptome when confronted to a mixture of six plant miRNAs. V. paradoxus also changed its transcriptome when it was grown in the rhizosphere of Arabidopsis that overexpressed a miRNA in its roots. As there were differences in the response of the two isolates used, we looked for shifts in the larger microbial community. We observed shifts in the rhizosphere bacterial communities of Arabidopsis mutants that were impaired in their small RNA pathways, or overexpressed specific miRNAs. We also found differences in the growth and community composition of a simplified soil microbial community when exposed in vitro to a mixture of plant miRNAs. Our results support the addition of miRNAs to the plant tools shaping rhizosphere microbial assembly.

Dicer-like 3a mediates intergenerational resistance against root-knot nematodes in rice via hormone responses

In a continuously changing and challenging environment, passing down the memory of encountered stress factors to offspring could provide an evolutionary advantage. In this study, we demonstrate the existence of "intergenerational acquired resistance" in the progeny of rice (Oryza sativa) plants attacked by the belowground parasitic nematode Meloidogyne graminicola. Transcriptome analyses revealed that genes involved in defense pathways are generally downregulated in progeny of nematode-infected plants under uninfected conditions but show a stronger induction upon nematode infection. This phenomenon was termed "spring loading" and depends on initial downregulation by the 24-nucleotide (nt) siRNA biogenesis gene dicer-like 3a (dcl3a) involved in the RNA-directed DNA methylation pathway. Knockdown of dcl3a led to increased nematode susceptibility and abolished intergenerational acquired resistance, as well as jasmonic acid/ethylene spring loading in the offspring of infected plants. The importance of ethylene signaling in intergenerational resistance was confirmed by experiments on a knockdown line of ethylene insensitive 2 (ein2b), which lacks intergenerational acquired resistance. Taken together, these data indicate a role for DCL3a in regulating plant defense pathways during both within-generation and intergenerational resistance against nematodes in rice.

Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles

Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.

miRNA mediated regulation of nitrogen response and nitrogen use efficiency of plants: the case of wheat

Nitrogen (N) is needed for plant growth and development and is the major limiting nutrient due to its higher demand in agricultural production globally. The use of N fertilizers has increased considerably in recent years to achieve higher cereal yields. High N inputs coupled with declining N use efficiency (NUE) result in the degradation of the environment. Plants have developed multidimensional strategies in response to changes in N availability in soil. These strategies include N stress-induced responses such as changes in gene expression patterns. Several N stress-induced genes and other regulatory factors, such as microRNAs (miRNAs), have been identified in different plant species, opening a new avenue of research in plant biology. This review presents a general overview of miRNA-mediated regulation of N response and NUE. Further, the in-silico target predictions and the predicted miRNA-gene network for nutrient metabolism/homeostasis in wheat provide novel insights. The information on N-regulated miRNAs and the differentially expressed target transcripts are necessary resources for genetic improvement of NUE by genome editing.

Advances in understanding epigenetic regulation of plant trichome development: a comprehensive review

Plant growth and development are controlled by a complex gene regulatory network, which is currently a focal point of research. It has been established that epigenetic factors play a crucial role in plant growth. Trichomes, specialized appendages that arise from epidermal cells, are of great significance in plant growth and development. As a model system for studying plant development, trichomes possess both commercial and research value. Epigenetic regulation has only recently been implicated in the development of trichomes in a limited number of studies, and microRNA-mediated post-transcriptional regulation appears to dominate in this context. In light of this, we have conducted a review that explores the interplay between epigenetic regulations and the formation of plant trichomes, building upon existing knowledge of hormones and transcription factors in trichome development. Through this review, we aim to deepen our understanding of the regulatory mechanisms underlying trichome formation and shed light on future avenues of research in the field of epigenetics as it pertains to epidermal hair growth.

microRNA biogenesis and stabilization in plants

MicroRNAs (miRNAs) are short endogenous non-coding RNAs that regulate gene expression at the post-transcriptional level in a broad range of eukaryotic species. In animals, it is estimated that more than 60% of mammalian genes are targets of miRNAs, with miRNAs regulating cellular processes such as differentiation and proliferation. In plants, miRNAs regulate gene expression and play essential roles in diverse biological processes, including growth, development, and stress responses. Arabidopsis mutants with defective miRNA biogenesis are embryo lethal, and abnormal expression of miRNAs can cause severe developmental phenotypes. It is therefore crucial that the homeostasis of miRNAs is tightly regulated. In this review, we summarize the key mechanisms of plant miRNA biogenesis and stabilization. We provide an update on nuclear proteins with functions in miRNA biogenesis and proteins linking miRNA biogenesis to environmental triggers.

Role of mi RNA in Phytoremediation of Heavy Metals and Metal Induced Stress Alleviation

Anthropogenic activities have contributed hugely in enhancing various types of environmental toxicity. One of these is higher accumulation of toxic heavy metals in soil and plant tissues. Although many heavy metals act as essential component for the growth and development of plants when present in low concentrations but at higher concentrations it becomes cytotoxic. Several innate mechanisms have evolved in plants to cope with it. In recent years the mechanism of using miRNA to combat metal induced toxicity has come to fore front. The miRNA or the microRNA regulates different physiological processes and induces a negative control in expressing the complementary target genes. The cleavage formation by post-transcriptional method and the inhibition of targeted translational mRNA are the two main procedures by which plant miRNAs function. The heavy and enhanced metal accumulation in plants has increased the production of different kinds of free radicals like reactive nitrogen and oxygen which damage the plants oxidatively. Several plant miRNA are capable of targeting and reducing the expression of those genes which are responsible for higher metal accumulation and storage. This can reduce the metal load and hence its negative impact on plant can also be reduced. This review depicts the biogenesis, the mode of action of miRNA, and the control mechanisms of miRNA in metal induced stress response in plant. A detailed review on the role of plant miRNA in alleviation of metal induced stress is discussed in this present study.

Genome-wide identification of auxin-responsive microRNAs in the poplar stem

BACKGROUND

Wood (secondary xylem) of forests is a material of great economic importance. Wood development is strictly controlled by both the phytohormone auxin and microRNAs (miRNAs). Currently, the regulatory mechanisms underlying wood formation by auxin-associated miRNAs remain unclear.

OBJECTIVE

This report was designed to identify auxin-responsive miRNAs during wood formation.

METHODS

Morphological observation of wood development in the poplar stems was performed under the treatment of different concentrations (0 mg/L, CK; 5 mg/L, Low; 10 mg/L, High) of indol-3-butyric acid (IBA). Using a small RNA sequencing strategy, the effect of IBA treatment on miRNAs expression was genome-widely analyzed.

RESULTS

In this study, we found that wood development of poplar was promoted by low concentration of IBA treatment but inhibited by high concentration of IBA treatment. Stringent bioinformatic analysis led to identification of 118 known and 134 novel miRNAs candidates. Sixty-nine unique developmental-related miRNAs, corresponding to 269 target genes, exhibited specific expression patterns in response to auxin, as was consistent with the influence of auxin application on wood formation. Three novel miRNAs had the most number (≥ 9) of target genes, belonging to SPL, GRF and ARF gene families. The evolutionary relationships and tissue expression patterns of 41 SPL, GRF and ARF genes in poplar were thus analyzed. Of them, four representative members and corresponding miRNAs were confirmed using RT-qPCR.

CONCLUSIONS

Our results may be helpful for a better understanding of auxin-induced regulation of wood formation in tree species.

Beyond transcription: compelling open questions in plant RNA biology

The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.

Complexity and regulation of age-dependent alternative splicing in Brachypodium distachyon

Alternative splicing (AS) is a gene regulatory mechanism that generates multiple transcripts of the same gene precursor by the spliceosome complex, promoting messenger RNA complexity and proteome diversity. Although AS is extensively studied in response to environmental stresses, whether it mediates age-dependent development and how it is adjusted by growth transitions are largely unknown. Here, we comprehensively explored the AS landscape at different development stages in the grass model plant Brachypodium (Brachypodium distachyon). We identified abundant coding genes and non-coding transcripts subject to dynamic AS regulation during juvenile, adult, and reproductive transitions. Moreover, we revealed that SC35-LIKE SPLICING FACTOR 33 (SCL33), a serine/arginine-rich splicing factor in spliceosomes, plays a redundant and antagonistic role with its putative paralog, SCL33L, in regulating intron assembly across distinct developmental stages. In addition, we determined global AS variations in microRNA156 (miR156)-overproducing plants, in which growth transitions are delayed, and found that SPLs were regulated by miR156 in intron retention alteration in addition to mRNA clearance and translation inhibition manners. Finally, we demonstrated a complex regulatory process of age-dependent AS events in B. distachyon that were coincidently or separately regulated by miR156 and SCL33/SCL33L. These results illustrate a substantial -machinery of AS that mediates phase transitions in plants.

An OsPRMT5-OsAGO2/miR1875-OsHXK1 module regulates rice immunity to blast disease

Rice ARGONAUTE2 (OsAGO2) is a core component of the rice RNA-induced silencing complex (RISC), which is repressed by Magnaporthe oryzae (M. oryzae) infection. Whether and how OsAGO2-mediated gene silencing plays a role in rice blast resistance and which sRNAs participate in this process are unknown. Our results indicate that OsAGO2 is a key immune player that manipulates rice defense responses against blast disease. OsAGO2 associates with the 24-nt miR1875 and binds to the promoter region of HEXOKINASE1 (OsHXK1), which causes DNA methylation and leads to gene silencing. Our multiple genetic evidence showed that, without M. oryzae infection, OsAGO2/miR1875 RISC promoted OsHXK1 promoter DNA methylation and OsHXK1 silencing; after M. oryzae infection, the reduced OsAGO2/miR1875 led to a relatively activated OsHXK1 expression. OsHXK1 acts as a positive regulator of blast disease resistance that OsHXK1-OE rice exhibited enhanced resistance, whereas Cas9-Oshxk1 rice showed reduced resistance against M. oryzae infection. OsHXK1 may function through its sugar sensor activity as glucose induced defense-related gene expression and reactive oxygen species (ROS) accumulation in Nipponbare and OsHXK1-OE but not in Cas9-Oshxk1 rice. OsAGO2 itself is delicately regulated by OsPRMT5, which senses M. oryzae infection and attenuates OsAGO2-mediated gene silencing through OsAGO2 arginine methylation. Our study reveals an OsPRMT5-OsAGO2/miR1875-OsHXK1 regulatory module that fine tunes the rice defense response to blast disease.

High-temperature stress in crops: male sterility, yield loss and potential remedy approaches

Global food security is one of the utmost essential challenges in the 21st century in providing enough food for the growing population while coping with the already stressed environment. High temperature (HT) is one of the main factors affecting plant growth, development and reproduction and causes male sterility in plants. In male reproductive tissues, metabolic changes induced by HT involve carbohydrates, lipids, hormones, epigenetics and reactive oxygen species, leading to male sterility and ultimately reducing yield. Understanding the mechanism and genes involved in these pathways during the HT stress response will provide a new path to improve crops by using molecular breeding and biotechnological approaches. Moreover, this review provides insight into male sterility and integrates this with suggested strategies to enhance crop tolerance under HT stress conditions at the reproductive stage.

Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution

Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.

Identification of Small RNAs Associated with Salt Stress in Chrysanthemums through High-Throughput Sequencing and Bioinformatics Analysis

The Chrysanthemum variety “Niu 9717” exhibits excellent characteristics as an ornamental plant and has good salt resistance. In this study, this plant was treated with 200 mM NaCl for 12 h followed by high-throughput sequencing of miRNA and degradome. Subsequently, the regulatory patterns of potential miRNAs and their target genes were searched to elucidate how Chrysanthemum miRNAs respond to salt. From the root and leaf samples, we identified a total of 201 known miRNAs belonging to 40 families; furthermore, we identified 79 new miRNAs, of which 18 were significantly differentially expressed (p < 0.05). The expressed miRNAs, which targeted a total of 144 mRNAs in the leaf and 215 mRNAs in the root, formed 144 and 226 miRNA–target pairs in roots and leaves, respectively. Combined with the miRNA expression profile, degradome and transcriptome data were then analyzed to understand the possible effects of the miRNA target genes and their pathways on salt stress. The identified genes were mostly located in pathways related to hormone signaling during plant growth and development. Overall, these findings suggest that conserved and novel miRNAs may improve salt tolerance through the regulation of hormone signal synthesis or expression of genes involved in hormone synthesis.

Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant

Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.

Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp

In the growth and development of plants, some non-coding small RNAs (sRNAs) not only mediate RNA interference at the post-transcriptional level, but also play an important regulatory role in chromatin modification at the transcriptional level. In these processes, the protein factors Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) play very important roles in the synthesis of sRNAs respectively. Though they have been identified in many plants, the information about these gene families in strawberry was poorly understood. In this study, using a genome-wide analysis and a phylogenetic approach, 13 AGO, six DCL, and nine RDR genes were identified in diploid strawberry Fragaria vesca. We also identified 33 AGO, 18 DCL, and 28 RDR genes in octoploid strawberry Fragaria × ananassa, studied the expression patterns of these genes in various tissues and developmental stages of strawberry, and researched the response of these genes to some hormones, finding that almost all genes respond to the five hormone stresses. This study is the first report of a genome-wide analysis of AGO, DCL, and RDR gene families in Fragaria spp., in which we provide basic genomic information and expression patterns for these genes. Additionally, this study provides a basis for further research on the functions of these genes and some evidence for the evolution between diploid and octoploid strawberries.

Plant gene silencing signals move from the phloem to influence gene expression in shoot apical meristems

BACKGROUND

Small RNAs (sRNA) are potent regulators of gene expression that can diffuse short distances between cells and move long distances through plant vasculature. However, the degree to which sRNA silencing signals can move from the phloem to the shoot apical meristem (SAM) remains unclear.

RESULTS

Two independent transgenic approaches were used to examine whether phloem sRNA silencing can reach different domains of the SAM and silence SAM-expressed genes. First, the phloem companion-cell specific SUCROSE-PROTON SYMPORTER2 (SUC2) promoter was used to drive expression of an inverted repeat to target the FD gene, an exclusively SAM-localized floral regulator. Second, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) transgene in SAM stem cells. Both phloem silencing signals phenocopied the loss of function of their targets and altered target gene expression suggesting that a phloem-to-SAM silencing communication axis exists, connecting distal regions of the plant to SAM stem cells.

CONCLUSIONS

Demonstration of phloem-to-SAM silencing reveals a regulatory link between somatic sRNA expressed in distal regions of the plant and the growing shoot. Since the SAM stem cells ultimately produce the gametes, we discuss the intriguing possibility that phloem-to-SAM sRNA trafficking could allow transient somatic sRNA expression to manifest stable, transgenerational epigenetic changes.

The pattern of DNA methylation alteration, and its association with the expression changes of non-coding RNAs and mRNAs in Moso bamboo under abiotic stress

Epigenetic changes play an important role in plant growth and development and in stress response. However, DNA methylation pattern and its relationship with the expression changes of non-coding RNAs and mRNAs of Moso bamboo in response to abiotic stress is still largely unknown. In this work, we used whole-genome bisulfite sequencing in combination with whole-transcriptome sequencing to analyze the DNA methylation and transcription patterns of mRNAs and non-coding RNAs in Moso bamboo under abiotic stresses such as cold, heat, ultraviolet (UV) and salinity. We found that CHH methylation in the promoter region was positively correlated with gene expression, while CHG and CHH methylations in the gene body regions were negatively associated with gene expression. Moreover, CG and CHG methylations in the promoter regions were negatively correlated with the transcript abundance of long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs). Similarly, the methylation levels of three contexts in the genic regions were negatively correlated with the transcript abundance of lncRNAs and miRNAs but positively correlated with that of circRNAs. In addition, we suggested that the reduction of 21-nt and 24-nt small interfering RNA (siRNA) expression tended to increase methylation levels in the genic regions. We found that stress-responsive genes such as CRPK1, HSFB2A and CIPK were differentially methylated and expressed. Our results also proposed that DNA methylation may regulate the expression of the transcription factors (TFs) and plant hormone signalling genes such as IAA9, MYC2 and ERF110 in response to abiotic stress. This study firstly reports the abiotic stress-responsive DNA methylation pattern and its involvement of expression of coding RNAs and non-coding RNAs in Moso bamboo. The results expand the knowledge of epigenetic mechanisms in Moso bamboo under abiotic stress and support in-depth deciphering of the function of specific non-coding RNAs in future studies.

Evolution of lmiRNAs and their targets from MITEs for rice adaptation

Twenty-four nucleotide long microRNAs (lmiRNAs) direct DNA methylation at target genes and regulate their transcription. The evolutionary origin of lmiRNAs and the range of lmiRNA-mediated regulation remain obscure. Here, we reannotated lmiRNAs and their targets in rice by applying stringent criteria. We found that the majority of lmiRNAs are derived from Miniature Inverted-repeat Transposable Elements (MITEs) and most sites targeted by MITE-derived lmiRNAs reside within MITEs, suggesting co-evolution of lmiRNAs and their targets through MITE amplification. lmiRNAs undergo dynamically changes under stress conditions and the genes targeted by lmiRNAs show an enrichment for stress-responsive genes, suggesting that lmiRNAs are widely involved in plant responses to stresses. We constructed the evolutionary histories of lmiRNAs and their targets. Nearly half of lmiRNAs emerged before or when the AA genome was diverged, while the emergence of lmiRNA targets coincided with or followed the emergence of lmiRNAs. Furthermore, we found that the sequences of a lmiRNA target site underwent variations, coincident with the divergence of rice accessions and the distribution of rice accessions in different geographical locations and climatic conditions. Our findings highlight MITEs as an important origin of lmiRNAs and suggest that the evolution of lmiRNA-target regulatory modules may contribute to rice adaptation to environmental changes.

What Do We Know about Barley miRNAs?

Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.

Tomato MicroRNAs and Their Functions

MicroRNAs (miRNAs) define an essential class of non-coding small RNAs that function as posttranscriptional modulators of gene expression. They are coded by MIR genes, several hundreds of which exist in the genomes of Arabidopsis and rice model plants. The functional analysis of Arabidopsis and rice miRNAs indicate that their miRNAs regulate a wide range of processes including development, reproduction, metabolism, and stress. Tomato serves as a major model crop for the study of fleshy fruit development and ripening but until recently, information on the identity of its MIR genes and their coded miRNAs was limited and occasionally contradictory. As a result, the majority of tomato miRNAs remained uncharacterized. Recently, a comprehensive annotation of tomato MIR genes has been carried out by several labs and us. In this review, we curate and organize the resulting partially overlapping MIR annotations into an exhaustive and non-redundant atlas of tomato MIR genes. There are 538 candidate and validated MIR genes in the atlas, of which, 169, 18, and 351 code for highly conserved, Solanaceae-specific, and tomato-specific miRNAs, respectively. Furthermore, a critical review of functional studies on tomato miRNAs is presented, highlighting validated and possible functions, creating a useful resource for future tomato miRNA research.

Versatile Roles of Microbes and Small RNAs in Rice and Planthopper Interactions

Planthopper infestation in rice causes direct and indirect damage through feeding and viral transmission. Host microbes and small RNAs (sRNAs) play essential roles in regulating biological processes, such as metabolism, development, immunity, and stress responses in eukaryotic organisms, including plants and insects. Recently, advanced metagenomic approaches have facilitated investigations on microbial diversity and its function in insects and plants, highlighting the significance of microbiota in sustaining host life and regulating their interactions with the environment. Recent research has also suggested significant roles for sRNA-regulated genes during rice-planthopper interactions. The response and behavior of the rice plant to planthopper feeding are determined by changes in the host transcriptome, which might be regulated by sRNAs. In addition, the roles of microbial symbionts and sRNAs in the host response to viral infection are complex and involve defense-related changes in the host transcriptomic profile. This review reviews the structure and potential functions of microbes and sRNAs in rice and the associated planthopper species. In addition, the involvement of the microbiota and sRNAs in the rice-planthopper-virus interactions during planthopper infestation and viral infection are discussed.

An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism

The present review highlights the regulatory roles of microRNAs in plant secondary metabolism and focuses on different bioengineering strategies to modulate secondary metabolite content in plants. MicroRNAs (miRNAs) are the class of small endogenous, essential, non-coding RNAs that riboregulate the gene expression involved in various biological processes in most eukaryotes. MiRNAs has emerged as important regulators in plants that function by silencing target genes through cleavage or translational inhibition. These miRNAs plays an important role in a wide range of plant biological and metabolic processes, including plant development and various environmental response controls. Several important plant secondary metabolites like alkaloids, terpenoids, and phenolics are well studied for their function in plant defense against different types of pests and herbivores. Due to the presence of a wide range of biological and pharmaceutical properties of plant secondary metabolites, it is important to study the regulation of their biosynthetic pathways. The contribution of miRNAs in regulating plant secondary metabolism is not well explored. Recent advancements in molecular techniques have improved our knowledge in understanding the molecular function of genes, proteins, enzymes, and small RNAs involved in different steps of secondary metabolic pathways. In the present review, we have discussed the recent progress made on miRNA biogenesis, its regulation, and highlighted the current research developed in the field of identification, analysis, and characterizations of various miRNAs that regulate plant secondary metabolism. We have also discussed how different bioengineering strategies such as artificial miRNA (amiRNA), endogenous target mimicry, and CRISPR/Cas9 could be utilized to enhance the secondary metabolite production in plants.