The MicroRNA miR773 Is Involved in the Arabidopsis Immune Response to Fungal Pathogens

MicroRNA (miRNA) profiling of maize genotypes with differential response to Aspergillus flavus implies zma-miR156-squamosa promoter binding protein (SBP) and zma-miR398/zma-miR394-F -box combinations involved in resistance mechanisms

Maize (Zea mays), a major food crop worldwide, is susceptible to infection by the saprophytic fungus Aspergillus flavus that can produce the carcinogenic metabolite aflatoxin (AF) especially under climate change induced abiotic stressors that favor mold growth. Several studies have used "-omics" approaches to identify genetic elements with potential roles in AF resistance, but there is a lack of research identifying the involvement of small RNAs such as microRNAs (miRNAs) in maize-A. flavus interaction. In this study, we compared the miRNA profiles of three maize lines (resistant TZAR102, moderately resistant MI82, and susceptible Va35) at 8 h, 3 d, and 7 d after A. flavus infection to investigate possible regulatory antifungal role of miRNAs. A total of 316 miRNAs (275 known and 41 putative novel) belonging to 115 miRNA families were identified in response to the fungal infection across all three maize lines. Eighty-two unique miRNAs were significantly differentially expressed with 39 miRNAs exhibiting temporal differential regulation irrespective of the maize genotype, which targeted 544 genes (mRNAs) involved in diverse molecular functions. The two most notable biological processes involved in plant immunity, namely cellular responses to oxidative stress (GO:00345990) and reactive oxygen species (GO:0034614) were significantly enriched in the resistant line TZAR102. Coexpression network analysis identified 34 hubs of miRNA-mRNA pairs where nine hubs had a node in the module connected to their target gene with potentially important roles in resistance/susceptible response of maize to A. flavus. The miRNA hubs in resistance modules (TZAR102 and MI82) were mostly connected to transcription factors and protein kinases. Specifically, the module of miRNA zma-miR156b-nb - squamosa promoter binding protein (SBP), zma-miR398a-3p - SKIP5, and zma-miR394a-5p - F-box protein 6 combinations in the resistance-associated modules were considered important candidates for future functional studies.

Review: Plant microRNAs in pathogen defense: A panacea or a piece of the puzzle?

Plant microRNAs (miRNAs) control key agronomic traits that are associated with their conserved role(s) in development. However, despite a multitude of studies, the utility of miRNAs in plant-pathogen resistance remains less certain. Reviewing the literature identifies three general classes of miRNAs regarding plant pathogen defense. Firstly, a number of evolutionary dynamic 22 nucleotide miRNA families that repress large numbers of plant immunity genes, either directly, or through triggering the biogenesis of secondary siRNAs. However, understanding of their role in defense and of their manipulation to enhance pathogen resistance are still lacking. Secondly, highly conserved miRNAs that indirectly impact disease resistance through their targets that are primarily regulating development or hormone signaling. Any alteration of these miRNAs usually results in pleiotropic impacts, which may alter disease resistance in some plant species, and against some pathogens. Thirdly, are the comparatively diverse and evolutionary dynamic set of non-conserved miRNAs, some of which contribute to pathogen resistance, but whose narrow evolutionary presence will likely restrict their utility. Therefore, reflecting the diverse and evolving nature of plant-pathogen interactions, a complex interplay of plant miRNAs with pathogen responses exists. Any miRNA-based solution for pathogen resistance will likely be highly specific, rather than a general panacea.

Impact of biotic stresses on the Brassicaceae family and opportunities for crop improvement by exploiting genotyping traits

MAIN CONCLUSION

Utilizing RNAi, miRNA, siRNA, lncRNA and exploiting genotyping traits can help safeguard the food supply from illnesses and pest damage to Brassicas, as well as reduce yield losses caused by plant pathogens and insect pests. In the natural environment, plants face significant challenges in the form of biotic stress, due to various living organisms, leading to biological stress and a sharp decline in crop yields. To cope with these effects, plants have evolved specialized mechanisms to mitigate these challenges. Plant stress tolerance and resistance are influenced by genes associated with stress-responsive pathogens that interact with various stress-related signaling pathway components. Plants employ diverse strategies and mechanisms to combat biological stress, involving a complex network of transcription factors that interact with specific cis-elements to regulate gene expression. Understanding both plant developmental and pathogenic disease resistance mechanisms can allow us to develop stress-tolerant and -resistant crops. Brassica genus includes commercially important crops, e.g., broccoli, cabbage, cauliflower, kale, and rapeseed, cultivated worldwide, with several applications, e.g., oil production, consumption, condiments, fodder, as well as medicinal ones. Indeed, in 2020, global production of vegetable Brassica reached 96.4 million tones, a 10.6% rise from the previous decade. Taking into account their commercial importance, coupled to the impact that pathogens can have in Brassica productivity, yield losses up to 60%, this work complies the major diseases caused due to fungal, bacterial, viral, and insects in Brassica species. The review is structured into three parts. In the first part, an overview is provided of the various pathogens affecting Brassica species, including fungi, bacteria, viruses, and insects. The second part delves into the exploration of defense mechanisms that Brassica plants encounter against these pathogens including secondary metabolites, duplicated genes, RNA interference (RNAi), miRNA (micro-RNA), siRNA (small interfering RNA), and lncRNA (long non-coding RNA). The final part comprehensively outlines the current applications of CRISPR/Cas9 technology aimed at enhancing crop quality. Taken collectively, this review will contribute to our enhanced understanding of these mechanisms and their role in the development of resistance in Brassica plants, thus supporting strategies to protect this crucial crop.

Epigenetic weapons of plants against fungal pathogens

In the natural environment, plants face constant exposure to biotic stress caused by fungal attacks. The plant's response to various biotic stresses relies heavily on its ability to rapidly adjust the transcriptome. External signals are transmitted to the nucleus, leading to activation of transcription factors that subsequently enhance the expression of specific defense-related genes. Epigenetic mechanisms, including histone modifications and DNA methylation, which are closely linked to chromatin states, regulate gene expression associated with defense against biotic stress. Additionally, chromatin remodelers and non-coding RNA play a significant role in plant defense against stressors. These molecular modifications enable plants to exhibit enhanced resistance and productivity under diverse environmental conditions. Epigenetic mechanisms also contribute to stress-induced environmental epigenetic memory and priming in plants, enabling them to recall past molecular experiences and utilize this stored information for adaptation to new conditions. In the arms race between fungi and plants, a significant aspect is the cross-kingdom RNAi mechanism, whereby sRNAs can traverse organismal boundaries. Fungi utilize sRNA as an effector molecule to silence plant resistance genes, while plants transport sRNA, primarily through extracellular vesicles, to pathogens in order to suppress virulence-related genes. In this review, we summarize contemporary knowledge on epigenetic mechanisms of plant defense against attack by pathogenic fungi. The role of epigenetic mechanisms during plant-fungus symbiotic interactions is also considered.

Emerging roles of plant microRNAs during Colletotrichum spp. infection

MAIN CONCLUSION

This review provides valuable insights into plant molecular regulatory mechanisms during fungus attacks, highlighting potential miRNA candidates for future disease management. Plant defense responses to biotic stress involve intricate regulatory mechanisms, including post-transcriptional regulation of genes mediated by microRNAs (miRNAs). These small RNAs play a vital role in the plant's innate immune system, defending against viral, bacterial, and fungal attacks. Among the plant pathogenic fungi, Colletotrichum spp. are notorious for causing anthracnose, a devastating disease affecting economically important crops worldwide. Understanding the molecular machinery underlying the plant immune response to Colletotrichum spp. is crucial for developing tools to reduce production losses. In this comprehensive review, we examine the current understanding of miRNAs associated with plant defense against Colletotrichum spp. We summarize the modulation patterns of miRNAs and their respective target genes. Depending on the function of their targets, miRNAs can either contribute to host resistance or susceptibility. We explore the multifaceted roles of miRNAs during Colletotrichum infection, including their involvement in R-gene-dependent immune system responses, hormone-dependent defense mechanisms, secondary metabolic pathways, methylation regulation, and biosynthesis of other classes of small RNAs. Furthermore, we employ an integrative approach to correlate the identified miRNAs with various strategies and distinct phases of fungal infection. This study provides valuable insights into the current understanding of plant miRNAs and their regulatory mechanisms during fungus attacks.

DNABERT-based explainable lncRNA identification in plant genome assemblies

Long non-coding ribonucleic acids (lncRNAs) have been shown to play an important role in plant gene regulation, involving both epigenetic and transcript regulation. LncRNAs are transcripts longer than 200 nucleotides that are not translated into functional proteins but can be translated into small peptides. Machine learning models have predominantly used transcriptome data with manually defined features to detect lncRNAs, however, they often underrepresent the abundance of lncRNAs and can be biased in their detection. Here we present a study using Natural Language Processing (NLP) models to identify plant lncRNAs from genomic sequences rather than transcriptomic data. The NLP models were trained to predict lncRNAs for seven model and crop species (Zea mays, Arabidopsis thaliana, Brassica napus, Brassica oleracea, Brassica rapa, Glycine max and Oryza sativa) using publicly available genomic references. We demonstrated that lncRNAs can be accurately predicted from genomic sequences with the highest accuracy of 83.4% for Z. mays and the lowest accuracy of 57.9% for B. rapa, revealing that genome assembly quality might affect the accuracy of lncRNA identification. Furthermore, we demonstrated the potential of using NLP models for cross-species prediction with an average of 63.1% accuracy using target species not previously seen by the model. As more species are incorporated into the training datasets, we expect the accuracy to increase, becoming a more reliable tool for uncovering novel lncRNAs. Finally, we show that the models can be interpreted using explainable artificial intelligence to identify motifs important to lncRNA prediction and that these motifs frequently flanked the lncRNA sequence.

miRNAs for crop improvement

Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.

Wheat Pore-Forming Toxin-Like Protein Confers Broad-Spectrum Resistance to Fungal Pathogens in Arabidopsis

Fusarium head blight (FHB), caused by the hemibiotrophic fungus Fusarium graminearum, is one of the major threats to global wheat productivity. A wheat pore-forming toxin-like (PFT) protein was previously reported to underlie Fhb1, the most widely used quantitative trait locus in FHB breeding programs worldwide. In the present work, wheat PFT was ectopically expressed in the model dicot plant Arabidopsis. Heterologous expression of wheat PFT in Arabidopsis provided a broad-spectrum quantitative resistance to fungal pathogens including F. graminearum, Colletotrichum higginsianum, Sclerotinia sclerotiorum, and Botrytis cinerea. However, there was no resistance to bacterial or oomycete pathogens Pseudomonas syringae and Phytophthora capsici, respectively in the transgenic Arabidopsis plants. To explore the reason for the resistance response to, exclusively, the fungal pathogens, purified PFT protein was hybridized to a glycan microarray having 300 different types of carbohydrate monomers and oligomers. It was found that PFT specifically hybridized with chitin monomer, N-acetyl glucosamine (GlcNAc), which is present in fungal cell walls but not in bacteria or oomycete species. This exclusive recognition of chitin may be responsible for the specificity of PFT-mediated resistance to fungal pathogens. Transfer of the atypical quantitative resistance of wheat PFT to a dicot system highlights its potential utility in designing broad-spectrum resistance in diverse host plants. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction

In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.

Cotton RSG2 Mediates Plant Resistance against Verticillium dahliae by miR482b Regulation

Cotton Verticillium wilt, mainly caused by Verticillium dahliae, has a serious impact on the yield and quality of cotton fiber. Many microRNAs (miRNAs) have been identified to participate in plant resistance to V. dahliae infection, but the exploration of miRNA's function mechanism in plant defense is needed. Here, we demonstrate that the ghr-miR482b-GhRSG2 module mediates cotton plant resistance to V. dahliae infection. Based on the mRNA degradation data and GUS fusion experiments, ghr-miR482b directedly bonds to GhRSG2 mRNA to lead to its degradation. The knockdown and overexpression of ghr-miR482b through virus-induced gene silencing strategies enhanced (decreased by 0.39-fold in disease index compared with the control) and weakened (increased by 0.46-fold) the plant resistance to V. dahliae, respectively. In addition, silencing GhRSG2 significantly increased (increased by 0.93-fold in disease index) the plant sensitivity to V. dahliae compared with the control plants treated with empty vector. The expression levels of two SA-related disease genes, GhPR1 and GhPR2, significantly decreased in GhRSG2-silenced plants by 0.71 and 0.67 times, respectively, and in ghr-miR482b-overexpressed (OX) plants by 0.59 and 0.75 times, respectively, compared with the control, whereas the expression levels of GhPR1 and GhPR2 were significantly increased by 1.21 and 2.59 times, respectively, in ghr-miR482b knockdown (KD) plants. In sum, the ghr-miR482b-GhRSG2 module participates in the regulation of plant defense against V. dahliae by inducing the expression of PR1 and PR2 genes.

Identification of miRNAs Involved in Maize-Induced Systemic Resistance Primed by Trichoderma harzianum T28 against Cochliobolus heterostrophus

microRNAs (miRNAs) are known to play important roles in the immune response to pathogen infection in different plants. Further, Trichoderma strains are able to activate plant defense responses against pathogen attacks. However, little is known about the involvement of miRNAs in the defense response primed by Trichoderma strains. To explore the miRNAs sensitive to priming by Trichoderma, we studied the small RNAs and transcriptome changes in maize leaves that were systemically induced by seed treatment with Trichoderma harzianum (strain T28) against Cochliobolus heterostrophus (C. heterostrophus) infection in leaves. Through analysis of the sequencing data, 38 differentially expressed miRNAs (DEMs) and 824 differentially expressed genes (DEGs) were identified. GO and KEGG analyses of DEGs demonstrated that genes involved in the plant hormone signal transduction pathway and oxidation-reduction process were significantly enriched. In addition, 15 miRNA-mRNA interaction pairs were identified through the combined analysis of DEMs and DEGs. These pairs were supposed to play roles in the maize resistance primed by T. harzianum T28 to C. heterostrophus, in which miR390, miR169j, miR408b, miR395a/p, and novel miRNA (miRn5231) were more involved in the induction of maize resistance. This study provided valuable information for understanding the regulatory role of miRNA in the T. harzianum primed defense response.

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.

Identification of miRNAs Involving Potato-Phytophthora infestans Interaction

sRNAs (small RNAs) play an important role in regulation of plant immunity against a variety of pathogens. In this study, sRNA sequencing analysis was performed to identify miRNAs (microRNAs) during the interaction of potato and Phytophthora infestans. Totally, 171 potato miRNAs were identified, 43 of which were annotated in the miRNA database and 128 were assigned as novel miRNAs in this study. Those potato miRNAs may target 878 potato genes and half of them encode resistance proteins. Fifty-three potato miRNAs may target 194 P. infestans genes. Three potato miRNAs (novel 72, 133, and 140) were predicted to have targets only in the P. infestans genome. miRNAs transient expression and P. infestans inoculation assay showed that miR396, miR166, miR6149-5P, novel133, or novel140 promoted P. infestans colonization, while miR394 inhibited colonization on Nicotiana benthamiana leaves. An artificial miRNA target (amiRNA) degradation experiment demonstrated that miR394 could target both potato gene (PGSC0003DMG400034305) and P. infestans genes. miR396 targets the multicystatin gene (PGSC0003DMG400026899) and miR6149-5p could shear the galactose oxidase F-box protein gene CPR30 (PGSC0003DMG400021641). This study provides new information on the aspect of cross-kingdom immune regulation in potato-P. infestans interaction at the sRNAs regulation level.

The Arabidopsis thaliana-Fusarium oxysporum strain 5176 pathosystem: an overview

Fusarium oxysporum is a soil-borne fungal pathogen of several major food crops. Research on understanding the molecular details of fungal infection and the plant's defense mechanisms against this pathogen has long focused mainly on the tomato-infecting F. oxysporum strains and their specific host plant. However, in recent years, the Arabidopsis thaliana-Fusarium oxysporum strain 5176 (Fo5176) pathosystem has additionally been established to study this plant-pathogen interaction with all the molecular biology, genetic, and genomic tools available for the A. thaliana model system. Work on this system has since produced several new insights, especially with regards to the role of phytohormones involved in the plant's defense response, and the receptor proteins and peptide ligands involved in pathogen detection. Furthermore, work with the pathogenic strain Fo5176 and the related endophytic strain Fo47 has demonstrated the suitability of this system for comparative studies of the plant's specific responses to general microbe- or pathogen-associated molecular patterns. In this review, we highlight the advantages of this specific pathosystem, summarize the advances made in studying the molecular details of this plant-fungus interaction, and point out open questions that remain to be answered.

Distinguishing friends from foes: Can smRNAs modulate plant interactions with beneficial and pathogenic organisms?

In their agro-ecological habitats, plants are constantly challenged by fungal interactions that might be pathogenic or beneficial in nature, and thus, plants need to exhibit appropriate responses to discriminate between them. Such interactions involve sophisticated molecular mechanism of signal exchange, signal transduction and regulation of gene expression. Small RNAs (smRNAs), including the microRNAs (miRNAs), form an essential layer of regulation in plant developmental processes as well as in plant adaptation to environmental stresses, being key for the outcome during plant-microbial interactions. Further, smRNAs are mobile signals that can go across kingdoms from one interacting partner to the other and hence can be used as communication as well as regulatory tools not only by the host plant but also by the colonising fungus. Here, largely with a focus on plant-fungal interactions and miRNAs, we will discuss the role of smRNAs, and how they might help plants to discriminate between friends and foes.

Regulatory non-coding RNA: The core defense mechanism against plant pathogens

Plant pathogens damage crops and threaten global food security. Plants have evolved complex defense networks against pathogens, using crosstalk among various signaling pathways. Key regulators conferring plant immunity through signaling pathways include protein-coding genes and non-coding RNAs (ncRNAs). The discovery of ncRNAs in plant transcriptomes was first considered "transcriptional noise". Recent reviews have highlighted the importance of non-coding RNAs. However, understanding interactions among different types of noncoding RNAs requires additional research. This review attempts to consider how long-ncRNAs, small-ncRNAs and circular RNAs interact in response to pathogenic diseases within different plant species. Developments within genomics and bioinformatics could lead to the further discovery of plant ncRNAs, knowledge of their biological roles, as well as an understanding of their importance in exploiting the recent molecular-based technologies for crop protection.

DNA Methyltransferase 3 (MET3) is regulated by Polycomb group complex during Arabidopsis endosperm development

Complex epigenetic changes occur during plant reproduction. These regulations ensure the proper transmission of epigenetic information as well as allowing for zygotic totipotency. In Arabidopsis, the main DNA methyltransferase is called MET1 and is responsible for methylating cytosine in the CG context. The Arabidopsis genome encodes for three additional reproduction-specific homologs of MET1, namely MET2a, MET2b and MET3. In this paper, we show that the DNA methyltransferase MET3 is expressed in the seed endosperm and its expression is later restricted to the chalazal endosperm. MET3 is biallelically expressed in the endosperm but displays a paternal expression bias. We found that MET3 expression is regulated by the Polycomb complex proteins FIE and MSI1. Seed development is not impaired in met3 mutant, and we could not observe significant transcriptional changes in met3 mutant. MET3 might regulates gene expression in a Polycomb mutant background suggesting a further complexification of the interplay between H3K27me3 and DNA methylation in the seed endosperm. KEY MESSAGE: The DNA METHYLTRANSFERASE MET3 is controlled by Polycomb group complex during endosperm development.

Phosphate-induced resistance to pathogen infection in Arabidopsis

In nature, plants are concurrently exposed to a number of abiotic and biotic stresses. Our understanding of convergence points between responses to combined biotic/abiotic stress pathways remains, however, rudimentary. Here we show that MIR399 overexpression, loss-of-function of PHOSPHATE2 (PHO2), or treatment with high phosphate (Pi) levels is accompanied by an increase in Pi content and accumulation of reactive oxygen species (ROS) in Arabidopsis thaliana. High Pi plants (e.g., miR399 overexpressors, pho2 mutants, and plants grown under high Pi supply) exhibited resistance to infection by necrotrophic and hemibiotrophic fungal pathogens. In the absence of pathogen infection, the expression levels of genes in the salicylic acid (SA)- and jasmonic acid (JA)-dependent signaling pathways were higher in high Pi plants compared to wild-type plants grown under control conditions, which is consistent with increased levels of SA and JA in non-infected high Pi plants. During infection, an opposite regulation in the two branches of the JA pathway (ERF1/PDF1.2 and MYC2/VSP2) occurs in high Pi plants. Thus, while pathogen infection induces PDF1.2 expression in miR399 OE and pho2 plants, VSP2 expression is downregulated by pathogen infection in these plants. This study supports the notion that Pi accumulation promotes resistance to infection by fungal pathogens in Arabidopsis, while providing a basis to better understand interactions between Pi signaling and hormonal signaling pathways for modulation of plant immune responses.

Biogenesis and Mechanisms of miRNA-Mediated Gene Regulation

Endogenous RNAs that control post-transcriptional gene expression are microRNAs (miRNAs). These small regulatory molecules play a crucial role in certain biological processes and their expression is often strictly regulated. They are small 21-24 nucleotide molecules that act as major regulators of gene expression at the post-transcriptional level. One of the mechanisms by which miRNAs control the gene expression is to interact the interaction of the seeds with the 3'-end and more seldom the 5'-end of mRNA transcribed by the target genes. miRNAs have been identified as important cytoplasmic regulators of gene expression. miRNAs function as post-transcriptional regulators of their messenger RNA (mRNA) targets by mRNA degradation and/or translational repression. It is becoming evident, however, that miRNAs have nuclear functions as well. About the cell type, the physiological state of the body, and various external factors, the following explanation will summarize the complex multilevel regulation of miRNA expression. A better understanding of the molecular mechanisms controlling miRNA expression will provide clarification of the variations in the expression of protein-coding genes. This article is protected by copyright. All rights reserved.

Identification of miRNA-Target Gene Pairs Responsive to Fusarium Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles

Fusarium wilt (FW) of cucumber (Cucumis sativus L.) caused by Fusarium oxysporum f. sp. cucumerinum (Foc) is a destructive soil-borne disease that severely decreases cucumber yield and quality worldwide. MicroRNAs (miRNAs) are small non-coding RNAs (sRNAs) that are important for regulating host immunity because they affect target gene expression. However, the specific miRNAs and the miRNA/target gene crosstalk involved in cucumber resistance to FW remain unknown. In this study, we compared sRNA-seq and RNA-seq data for cucumber cultivar 'Rijiecheng', which is resistant to FW. The integrated analysis identified FW-responsive miRNAs and their target genes. On the basis of verified expression levels, we detected two highly expressed miRNAs with down-regulated expression in response to Foc. Moreover, an analysis of 21 target genes in cucumber inoculated with Foc indicated that JRL3 (Csa2G362470), which is targeted by miR319a, and BEE1 (Csa1G024150), DAHP1 (Csa2G369040), and PERK2 (Csa4G642480), which are targeted by miR6300, are expressed at high levels, but their expression is further up-regulated after Foc inoculation. These results imply that miR319a-JRL3, miR6300-BEE1, miR6300-DAHP1 and miR6300-PERK2 regulate cucumber defenses against FW, and provide the gene resources that may be useful for breeding programs focused on developing new cucumber varieties with enhanced resistance to FW.

A novel Transposable element-derived microRNA participates in plant immunity to rice blast disease

MicroRNAs (miRNAs) are small non-coding RNAs that direct post-transcriptional gene silencing in plant development and stress responses through cleavage or translational repression of target mRNAs. Here, we report the identification and functional characterization of a new member of the miR812 family in rice (named as miR812w) involved in disease resistance. miR812w is present in cultivated Oryza species, both japonica and indica subspecies, and wild rice species within the Oryza genus, but not in dicotyledonous species. miR812w is a 24nt-long that requires DCL3 for its biogenesis and is loaded into AGO4 proteins. Whereas overexpression of miR812w increased resistance to infection by the rice blast fungus Magnaporthe oryzae, CRISPR/Cas9-mediated MIR812w editing enhances disease susceptibility, supporting that miR812w plays a role in blast resistance. We show that miR812w derives from the Stowaway type of rice MITEs (Miniature Inverted-Repeat Transposable Elements). Moreover, miR812w directs DNA methylation in trans at target genes that have integrated a Stowaway MITE copy into their 3' or 5' untranslated region (ACO3, CIPK10, LRR genes), as well as in cis at the MIR812w locus. The target genes of miR812 were found to be hypo-methylated around the miR812 recognition site, their expression being up-regulated in transgene-free CRISPR/Cas9-edited miR812 plants. These findings further support that, in addition to post-transcriptional regulation of gene expression, miRNAs can exert their regulatory function at the transcriptional level. This relationship between miR812w and Stowaway MITEs integrated into multiple coding genes might eventually create a network for miR812w-mediated regulation of gene expression with implications in rice immunity.

Physcomitrium patens Infection by Colletotrichum gloeosporioides: Understanding the Fungal-Bryophyte Interaction by Microscopy, Phenomics and RNA Sequencing

Anthracnose caused by the hemibiotroph fungus Colletotrichum gloeosporioides is a devastating plant disease with an extensive impact on plant productivity. The process of colonization and disease progression of C. gloeosporioides has been studied in a number of angiosperm crops. To better understand the evolution of the plant response to pathogens, the study of this complex interaction has been extended to bryophytes. The model moss Physcomitrium patens Hedw. B&S (former Physcomitrella patens) is sensitive to known bacterial and fungal phytopathogens, including C. gloeosporioides, which cause infection and cell death. P. patens responses to these microorganisms resemble that of the angiosperms. However, the molecular events during the interaction of P. patens and C. gloeosporioides have not been explored. In this work, we present a comprehensive approach using microscopy, phenomics and RNA-seq analysis to explore the defense response of P. patens to C. gloeosporioides. Microscopy analysis showed that appressoria are already formed at 24 h after inoculation (hai) and tissue colonization and cell death occur at 24 hai and is massive at 48 hai. Consequently, the phenomics analysis showed progressing browning of moss tissues and impaired photosynthesis from 24 to 48 hai. The transcriptomic analysis revealed that more than 1200 P. patens genes were differentially expressed in response to Colletotrichum infection. The analysis of differentially expressed gene function showed that the C. gloeosporioides infection led to a transcription reprogramming in P. patens that upregulated the genes related to pathogen recognition, secondary metabolism, cell wall reinforcement and regulation of gene expression. In accordance with the observed phenomics results, some photosynthesis and chloroplast-related genes were repressed, indicating that, under attack, P. patens changes its transcription from primary metabolism to defend itself from the pathogen.

Regulatory non-coding RNAs: a new frontier in regulation of plant biology

Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.

Role of non-coding RNAs in plant immunity

Crops are exposed to attacks by various pathogens that cause substantial yield losses and severely threaten food security. To cope with pathogenic infection, crops have elaborated strategies to enhance resistance against pathogens. In addition to the role of protein-coding genes as key regulators in plant immunity, accumulating evidence has demonstrated the importance of non-coding RNAs (ncRNAs) in the plant immune response. Here, we summarize the roles and molecular mechanisms of endogenous ncRNAs, especially microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), in plant immunity. We discuss the coordination between miRNAs and small interfering RNAs (siRNAs), between lncRNAs and miRNAs or siRNAs, and between circRNAs and miRNAs in the regulation of plant immune responses. We also address the role of cross-kingdom mobile small RNAs in plant-pathogen interactions. These insights improve our understanding of the mechanisms by which ncRNAs regulate plant immunity and can promote the development of better approaches for breeding disease-resistant crops.

MicroRNA775 regulates intrinsic leaf size and reduces cell wall pectin levels by targeting a galactosyltransferase gene in Arabidopsis

Plants possess unique primary cell walls made of complex polysaccharides that play critical roles in determining intrinsic cell and organ size. How genes responsible for synthesizing and modifying the polysaccharides in the cell wall are regulated by microRNAs (miRNAs) to control plant size remains largely unexplored. Here we identified 23 putative cell wall-related miRNAs, termed as CW-miRNAs, in Arabidopsis thaliana and characterized miR775 as an example. We showed that miR775 post-transcriptionally silences GALT9, which encodes an endomembrane-located galactosyltransferase belonging to the glycosyltransferase 31 family. Over-expression of miR775 and deletion of GALT9 led to significantly enlarged leaf-related organs, primarily due to increased cell size. Monosaccharide quantification, confocal Raman imaging, and immunolabeling combined with atomic force microscopy revealed that the MIR775A-GALT9 circuit modulates pectin levels and the elastic modulus of the cell wall. We also showed that MIR775A is directly repressed by the transcription factor ELONGATED HYPOCOTYL5 (HY5). Genetic analysis confirmed that HY5 is a negative regulator of leaf size that acts through the HY5-MIR775A-GALT9 repression cascade to control pectin levels. These findings demonstrate that miR775-regulated cell wall remodeling is an integral determinant of intrinsic leaf size in A. thaliana. Studying other CW-miRNAs would provide more insights into cell wall biology.

Regulation of pri-MIRNA processing: mechanistic insights into the miRNA homeostasis in plant

miRNAs in plant plays crucial role in controlling proper growth, development and fitness by modulating the expression of their target genes. Therefore to modulate the expression of any stress/development related gene specifically, it is better to modulate expression of the miRNA that can target that gene. To modulate the expression level of miRNA, it is prerequisite to uncover the underlying molecular mechanism of its biogenesis. The biogenesis pathway consists of two major steps, transcription of MIR gene to pri-MIRNA and processing of pri-MIRNA into mature miRNA via sequential cleavage steps. Both of these pathways are tightly controlled by several different factors involving structural and functional molecules. This review is mainly focused on different aspects of pri-MIRNA processing mechanism to emphasize on the fact that to modulate the level of a miRNA in the cell only over-expression or knock-down of that MIR gene is not always sufficient rather it is also crucial to take processing regulation into consideration. The data collected from the recent and relevant literatures depicts that processing regulation is controlled by several aspects like structure and size of the pri-MIRNA, presence of introns in MIR gene and their location, interaction of processing factors with the core components of processing machinery etc. These detailed information can be utilized to figure out the particular point which can be utilized to modulate the expression of the miRNA which would ultimately be beneficial for the scientist and researcher working in this field to generate protocol for engineering plant with improved yield and stress tolerance.

MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops

Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.

A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease

MicroRNAs regulate plant responses to fungal infections and immunity. In this study, miRNAs were identified in six rice cultivars during a Rhizoctonia solani Kühn AG1-IA infection using a deep sequencing approach. Known and novel miRNAs were analyzed in these rice cultivars, and a set of fungal infection/immunity-associated miRNAs and target genes were quantified by reverse transcription (RT)-qPCR in six rice cultivars. Additionally, the relative expression of these miRNAs was analyzed in different time points of the infection, wild species of rice, and in response to different strains of R. solani. Osa-miR1320-5p showed preferential expression during the fungal infection in all the six rice genotypes, while Osa-miR156d, Osa-miR159b, Osa-miR820c, and Osa-miR1876 were differentially regulated in susceptible and resistant genotypes. A greater degree of downregulation of miRNAs was observed during the initial time points of infection (24-72 h), suggesting a maximum molecular activity of rice-R. solani interaction and resistance response of the host during the early phase of infection. After R. solani infection, the expression of Osa-miR820c and Osa-miR156d was downregulated in Oryza rufipogon, O. alta, O. latifolia, and O. minuta, while Osa-miR397b was downregulated in all the wild rice species except O. officinalis. This study provided comprehensive information on the repertoire of miRNAs expressed in six sheath blight disease-susceptible and resistant indica and aus rice cultivars.

MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot

Fusarium ear rot (FER) caused by Fusarium verticillioides is one of the most common diseases affecting maize production worldwide. FER results in severe yield losses and grain contamination with health-threatening mycotoxins. Although most studies to date have focused on comprehensive analysis of gene regulation in maize during defense responses against F. verticillioides infection, less is known about the role of microRNAs (miRNAs) in this process. We used deep sequencing to compare small RNA libraries from the maize kernels of susceptible (N6) or resistant (BT-1) inbred lines from uninfected plants and upon F. verticillioides infection. We found that pathogen exposure was accompanied by dynamic alterations in expression levels of multiple miRNAs, including new members of previously annotated miRNA families. A combination of transcriptomic, degradomic, and bioinformatics analyses revealed that F. verticillioides-responsive miRNAs and their potential target genes displayed opposite expression patterns in the susceptible and resistant genotypes. Functional category analysis uncovered preferential enrichment of the pathogen-responsive miRNAs and their targets in the phenylpropanoid metabolic processes, plant-pathogen interactions, and plant phytohormone signal transduction pathways. Furthermore, transgenic maize plants overexpressing miR408b exhibited reduced resistance to F. verticillioides infection in a susceptible maize line. These findings provide new insights into the regulatory roles of miRNAs in maize immunity against FER and new resources for breeding disease resistance into maize.

Osa-miR167d facilitates infection of Magnaporthe oryzae in rice

MicroRNAs (miRNAs) play important roles in rice response to Magnaporthe oryzae, the causative agent of rice blast disease. Studying the roles of rice miRNAs is of great significance for the disease control. Osa-miR167d belongs to a conserved miRNA family targeting auxin responsive factor (ARF) genes that act in developmental and stress-induced responses. Here, we show that Osa-miR167d plays a negative role in rice immunity against M. oryzae by suppressing its target gene. The expression of Osa-miR167d was significantly suppressed in a resistant accession at and after 24 h post inoculation (hpi), however, its expression was significantly increased at 24 hpi in the susceptible accession upon M. oryzae infection. Transgenic rice lines over-expressing Osa-miR167d were highly susceptible to multiple blast fungal strains. By contrast, transgenic lines expressing a target mimicry to block Osa-miR167d enhanced resistance to rice blast disease. In addition, knocking out the target gene ARF12 led to hyper-susceptibility to multiple blast fungal strains. Taken together, our results indicate that Osa-miR167d negatively regulate rice immunity to facilitate the infection of M. oryzae by downregulating ARF12. Thus, Osa-miR167d-ARF12 regulatory module could be valuable in improvement of blast-disease resistance.

Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses

This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.

Lineage-Specific Evolved MicroRNAs Regulating NB-LRR Defense Genes in Triticeae

Disease resistance genes encoding proteins with nucleotide binding sites and Leucine-Rich Repeat (NB-LRR) domains include many members involved in the effector-triggered immunity pathway in plants. The transcript levels of these defense genes are negatively regulated by diverse microRNAs (miRNAs) in angiosperms and gymnosperms. In wheat, using small RNA expression datasets and degradome datasets, we identified five miRNA families targeting NB-LRR defense genes in monocots, some of which arose in the Triticeae species era. These miRNAs regulate different types of NB-LRR genes, most of them with coil-coiled domains, and trigger the generation of secondary small interfering RNAs (siRNA) as a phased pattern in the target site regions. In addition to acting in response to biotic stresses, they are also responsive to abiotic stresses such as heat, drought, salt, and light stress. Their copy number and expression variation in Triticeae suggest a rapid birth and death frequency. Altogether, non-conserved miRNAs as conserved transcriptional regulators in gymnosperms and angiosperms regulating the disease resistance genes displayed quick plasticity including the variations of sequences, gene copy number, functions, and expression level, which accompanied with NB-LRR genes may be tune-regulated to plants in natural environments with various biotic and abiotic stresses.

Evolution of Disease Defense Genes and Their Regulators in Plants

Biotic stresses do damage to the growth and development of plants, and yield losses for some crops. Confronted with microbial infections, plants have evolved multiple defense mechanisms, which play important roles in the never-ending molecular arms race of plant–pathogen interactions. The complicated defense systems include pathogen-associated molecular patterns (PAMP) triggered immunity (PTI), effector triggered immunity (ETI), and the exosome-mediated cross-kingdom RNA interference (CKRI) system. Furthermore, plants have evolved a classical regulation system mediated by miRNAs to regulate these defense genes. Most of the genes/small RNAs or their regulators that involve in the defense pathways can have very rapid evolutionary rates in the longitudinal and horizontal co-evolution with pathogens. According to these internal defense mechanisms, some strategies such as molecular switch for the disease resistance genes, host-induced gene silencing (HIGS), and the new generation of RNA-based fungicides, have been developed to control multiple plant diseases. These broadly applicable new strategies by transgene or spraying ds/sRNA may lead to reduced application of pesticides and improved crop yield.

Plant Responses to Pathogen Attack: Small RNAs in Focus

Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.