miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses

Elucidating long non-coding RNA networks in tomato plants in response to Funneliformis mosseae colonization and cucumber mosaic virus infection

Tomato plants face biotic challenges like infections by cucumber mosaic virus (CMV), a member of the Cucumovirus genus in the Bromoviridae family, as well as beneficial interactions, such as colonization by the symbiotic fungus Funneliformis mosseae, which belongs to the Glomeraceae family. While this symbiosis boosts nutrient uptake and stress tolerance, viral infections can reduce yield and quality. Understanding how tomatoes manage these interactions is vital for enhancing crop productivity. To explore the molecular mechanisms behind these interactions, this study focuses on long non-coding RNAs (lncRNAs), which play crucial roles in gene regulation, stress response, and plant metabolic pathways. Tomato RNA-seq data were analyzed to identify lncRNAs and their interactions with microRNAs (miRNAs) through de novo assembly, mapping, expression analysis, and localization prediction. In this study, 3210 lncRNAs were identified from 12 SRA datasets of tomato plants, including control, CMV-infected, F. mosseae-colonized, and co-infected samples. Among these, 3194 were novel lncRNAs and 16 were conserved. Expression analysis revealed significant differential expression patterns across treatments. Pathway analysis indicated that these lncRNAs are involved in key metabolic processes, such as carbon metabolism, amino acid biosynthesis, and secondary metabolite production, suggesting their role in enhancing disease resistance. Furthermore, we predicted interactions between identified lncRNAs and miRNAs, including miR160a, miR166a/b, miR167a, miR171a/b/c, miR1917, miR1918, and miR395a/b, thereby highlighting potential regulatory networks that could modulate stress responses. The subcellular localization of identified lncRNAs revealed a predominance in the cytoplasm, implying their involvement in post-transcriptional regulation. This study accentuates the significance of lncRNAs in tomato plant defense mechanisms and provides a foundation for future research focused on enriching resistance to viral infections and boosting stress resilience.

Identification and characterization of Eco-miR 169-EcNF-YA13 gene regulatory network reveal their role in conferring tolerance to dehydration and salinity stress in finger millet

The finger millet (Eleusine coracana (L.) Gaertn) genome, comprised 166 conserved microRNAs (miRNAs) belonging to 39 families and three novel miRNAs. The miR169 is one of the most conserved miRNA families, while Eco_N1 is a species-specific miRNA prevalent in finger millet. Its members regulate the expression of genes encoding the Nuclear Factor-Y subunit A (NF-YA) via transcript cleavage. However, the role of miRNA genes in regulating the expression of NF-YA transcription factors in finger millet needs to be deciphered. The present study characterized 166 conserved and novel miRNAs (Eco_N1, Eco_N2 and Eco_N3). Further, secondary structures were predicted, and the potential miR genes targeting the NF-YA transcription factors regulating abiotic stress tolerance were analysed. Twenty-three Eco-miR169 members and one Eco_N1 miRNA targeting EcNF-YA13 were identified in the finger millet genome. The presence of relevant cis-elements such as ABRE (abscisic acid-responsive elements), DRE (dehydration-responsive element), and MYB (myeloblastosis) indicates that the target of Eco-miR169 might be involved in abiotic stress responses. The tissue-specific RNA-seq transcriptomic expression pattern of Eco-miR169 showed variable fold of expression in seedlings compared to the control. At the same time, the expression of EcNF-YA13 (target genes of Eco-miR169 members and Eco_N1) presented a downregulated trend under salinity and dehydration conditions compared to the control. Tissue-specific RNA-seq followed by expression analysis confirmed the antagonistic effect of Eco-miR genes on EcNF-YA13. In a nutshell, the results of this study could be utilized as a platform for further exploration and characterization of finger millet Eco-miR169-EcNF-YA13gene regulatory network.

MiR164a-targeted NAM3 inhibits thermotolerance in tomato by regulating HSFA4b-mediated redox homeostasis

Extreme weather events, including high temperatures, frequently occur and adversely affect crop growth, posing substantial challenges to global agriculture. MicroRNAs (miRNAs) play integral roles in regulating plant growth and responses to various stresses. In this study, we reveal that microRNA164a (miR164a) in tomato (Solanum lycopersicum) is a pivotal element that exhibits a rapid positive response to heat stress (HS) among multiple miRNAs, while its target NO APICAL MERISTEM 3 (NAM3) shows an opposite complementary response. MiR164a/b-5p-deficient mutant and NAM3-overexpressing plants resulted in increased sensitivity to HS, whereas mutants with reduced NAM3 levels exhibited enhanced thermotolerance. Importantly, HS-induced reactive oxygen species (ROS) accumulation and antioxidant enzyme activities were positively regulated by miR164a and negatively by NAM3, respectively. Furthermore, we demonstrated that NAM3 transcriptionally activated the expression of HSFA4b, and silencing HSFA4b improved tomato thermotolerance. HSFA4b repressed the expression of the antioxidant gene APX1 and the heat shock protein (HSP) gene HSP90, disrupting redox homeostasis and exacerbating oxidative stress. Our findings unveil a pivotal regulatory pathway governed by the miR164a-NAM3 module that confers thermotolerance in tomato via its influence on ROS-related and HSP pathways. These findings provide valuable insights into the molecular mechanisms that underpin tomato thermotolerance, which are crucial for advancing sustainable agricultural practices, particularly in the face of the challenges presented by global climate change.

miR156 Is a Negative Regulator of Aluminum Response in Medicago sativa

Aluminum (Al) toxicity is a serious environmental constraint facing crop production in acidic soils, primarily due to the oxidative damage it causes to plant tissues. Alfalfa (Medicago sativa), a globally important forage crop, is highly susceptible to Al-induced stress, necessitating the development of Al-tolerant cultivars for sustainable forage production. In this study, we investigated the regulatory role of miR156 in Al stress response in alfalfa. Transcript analysis revealed significant downregulation of miR156 in alfalfa roots after 8 h of Al exposure, suggesting a negative role for miR156 in response to Al. To further investigate the role of miR156 in regulating agronomic traits and alfalfa's Al tolerance, we utilized the short tandem target mimic (STTM) method to silence miR156 in alfalfa (MsSTTM156), which led to an upregulation of SQUAMOSA PROMOTER BINDING-LIKE (SPL) target genes, albeit with variable miR156 dose-dependent effects across different transgenic genotypes. Morphological characterization of MsSTTM156 plants revealed significant negative changes in root architecture, root and shoot biomass, as well as flowering time. Under Al stress, overexpression of miR156 in alfalfa (MsmiR156OE) resulted in stunted growth and reduced biomass, whereas moderate MsmiR156 silencing enhanced root dry weight and increased stem basal diameter. In contrast, MsmiR156OE reduced plant height, stem basal diameter, shoot branching, and overall biomass under Al stress conditions. At the molecular level, silencing miR156 modulated the transcription of cell wall-related genes linked to Al tolerance, such as polygalacturonase 1(MsPG1) and polygalacturonase 4 (MsPG4). Furthermore, miR156 influenced the expression of indole-3-acetic acid (IAA) transport-related genes auxin transporter-like protein (MsAUX1) and auxin efflux carrier components 2 (MsPIN2), with MsSTTM156 and MsmiR156OE plants showing lower and higher transcript levels, respectively, upon Al exposure. These findings reveal the multi-layered role of miR156 in mediating Al tolerance, providing valuable insights into the genetic strategies that regulate response to Al stress in alfalfa.

Tomato miR398 knockout disrupts ROS dynamics during stress conferring heat tolerance but hypersusceptibility to necrotroph infection

An imbalance between ROS production and scavenging during stress results in oxidative bursts, which causes cellular damage. miR398 is a regulator of ROS scavenging since it targets crucial Cu/Zn superoxide dismutases (CSDs). Established functional studies aligned miR398 with plants' heat and heavy metal stress fitness. However, a knowledge gap in the dynamics of miR398-CSD interaction for redox regulation during pathogenic development impeded their use in crop improvement programmes. We use tomato, Solanum lycopersicum, plants, and necrotrophic and biotrophic pathogens to show that a complex transcriptional and post-transcriptional regulatory circuit maintains SlmiR398 and its target SlCSD genes' level. The interaction is indispensable for ROS regulation in either the pathogenic outcome, thermal stress, or a combination of both stresses, as observed in the cultivation field. The SlmiR398 knockout plants display feeble O2∙- accumulation but enhanced levels of H2O2, several defense-related genes, metabolites, and vital HSFs and HSPs, which were heightened upon stress. Depletion of SlmiR398, although it renders thermotolerance and resilience to biotrophic pathogens likely due to the augmented hypersensitive response, facilitates necrotrophy. Thus, SlmiR398-mediated ROS regulation seemingly works at the interface of abiotic and biotic stress response for a sustainable reaction of tomato plants.

SVALKA: A Long Noncoding Cis-Natural Antisense RNA That Plays a Role in the Regulation of the Cold Response of Arabidopsis thaliana

RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through which SVALKA fine tunes the transcriptional response to cold temperatures. SVALKA regulates the expression of the CBF1 (C-Repeat Dehydration Binding Factor 1) transcription factor through a collisional transcription mechanism and a dsRNA and DICER mediated mechanism. SVALKA also interacts with Polycomb Repressor Complex 2 to regulate the histone methylation of CBF3. Both CBF1 and CBF3 are key components of the COLD REGULATED (COR) regulon that direct the plant's response to cold temperature over time, as well as plant drought adaptation, pathogen responses, and growth regulation. The different isoforms of SVALKA and its potential to form dynamic RNA conformations are important features in regulating a complex gene network in concert with several other noncoding RNA. This review will summarize the three mechanisms through which SVALKA participates in gene regulation, describe the ways that dynamic RNA structures support the function of regulatory noncoding RNA, and explore the potential for improving agricultural genetic engineering with a better understanding of the roles of noncoding RNA.

Advances in understanding plant-pathogen interactions: insights from tomato as a model system

The impact of plant diseases coupled with climate change on agriculture worldwide cannot be overemphasized from negative effects on crop yield as well as economy to food insecurity. The model plants are essential for understanding the intricacies of plant-pathogen interactions. One of such plants is the tomato (Solanum lycopersicum L.). Researchers hope to increase tomato productivity and boost its resilience to pathogen attacks by utilizing OMICS and biotechnological methods. With an emphasis on tomato viral infections, this review summarizes significant discoveries and developments from earlier research. The analysis elucidates ongoing efforts to advance plant pathology by exploring the implications for sustainability and tomato production.

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.

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.

Tomato plant response to heat stress: a focus on candidate genes for yield-related traits

Climate change and global warming represent the main threats for many agricultural crops. Tomato is one of the most extensively grown and consumed horticultural products and can survive in a wide range of climatic conditions. However, high temperatures negatively affect both vegetative growth and reproductive processes, resulting in losses of yield and fruit quality traits. Researchers have employed different parameters to evaluate the heat stress tolerance, including evaluation of leaf- (stomatal conductance, net photosynthetic rate, Fv/Fm), flower- (inflorescence number, flower number, stigma exertion), pollen-related traits (pollen germination and viability, pollen tube growth) and fruit yield per plant. Moreover, several authors have gone even further, trying to understand the plants molecular response mechanisms to this stress. The present review focused on the tomato molecular response to heat stress during the reproductive stage, since the increase of temperatures above the optimum usually occurs late in the growing tomato season. Reproductive-related traits directly affects the final yield and are regulated by several genes such as transcriptional factors, heat shock proteins, genes related to flower, flowering, pollen and fruit set, and epigenetic mechanisms involving DNA methylation, histone modification, chromatin remodelling and non-coding RNAs. We provided a detailed list of these genes and their function under high temperature conditions in defining the final yield with the aim to summarize the recent findings and pose the attention on candidate genes that could prompt on the selection and constitution of new thermotolerant tomato plant genotypes able to face this abiotic challenge.

Long non-coding RNA-mediated epigenetic response for abiotic stress tolerance in plants

Plants perceive environmental fluctuations as stress and confront several stresses throughout their life cycle individually or in combination. Plants have evolved their sensing and signaling mechanisms to perceive and respond to a variety of stresses. Epigenetic regulation plays a critical role in the regulation of genes, spatiotemporal expression of genes under stress conditions and imparts a stress memory to encounter future stress responses. It is quintessential to integrate our understanding of genetics and epigenetics to maintain plant fitness, achieve desired genetic gains with no trade-offs, and durable long-term stress tolerance. The long non-coding RNA >200 nts having no coding potential (or very low) play several roles in epigenetic memory, contributing to the regulation of gene expression and the maintenance of cellular identity which include chromatin remodeling, imprinting (dosage compensation), stable silencing, facilitating nuclear organization, regulation of enhancer-promoter interactions, response to environmental signals and epigenetic switching. The lncRNAs are involved in a myriad of stress responses by activation or repression of target genes and hence are potential candidates for deploying in climate-resilient breeding programs. This review puts forward the significant roles of long non-coding RNA as an epigenetic response during abiotic stresses in plants and the prospects of deploying lncRNAs for designing climate-resilient plants.

Emphasizing the Role of Long Non-Coding RNAs (lncRNA), Circular RNA (circRNA), and Micropeptides (miPs) in Plant Biotic Stress Tolerance

Biotic stress tolerance in plants is complex as it relies solely on specific innate immune responses from different plant species combating diverse pathogens. Each component of the plant immune system is crucial to comprehend the molecular basis underlying sustainable resistance response. Among many other regulatory components, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have recently emerged as novel regulatory control switches in plant development and stress biology. Besides, miPs, the small peptides (100-150 amino acids long) encoded by some of the non-coding portions of the genome also turned out to be paramount regulators of plant stress. Although some studies have been performed in deciphering the role of miPs in abiotic stress tolerance, their function in regulating biotic stress tolerance is still largely elusive. Hence, the present review focuses on the roles of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in combating biotic stress in plants. The probable role of miPs in plant-microbe interaction is also comprehensively highlighted. This review enhances our current understanding of plant lncRNAs, circRNAs, and miPs in biotic stress tolerance and raises intriguing questions worth following up.

Overexpression of Sly-miR398b Compromises Disease Resistance against Botrytis cinerea through Regulating ROS Homeostasis and JA-Related Defense Genes in Tomato

MicroRNAs (miRNAs) have been shown to be critical components in plant immunity. MicroRNA398 (miR398) is a highly conserved miRNA in all land plants and plays crucial roles in diverse biotic stress responses. However, the role of miR398 has not yet been characterized in tomato resistance against Botrytis cinerea. In this report, the transcript levels of sly-miR398b were strongly decreased in B. cinerea-infected leaves and the overexpression of sly-miR398b resulted in enhanced susceptibility. The attenuated expression of cytosol Cu/Zn-SOD (CSD1), chloroplast Cu/Zn-SOD (CSD2), and guaiacol peroxidase (GPOD), as well as the decreased activities of superoxide dismutase (SOD) and GPOD, collectively led to increased hydrogen peroxide (H₂O₂) accumulation in sly-miR398b overexpressing plants. Furthermore, sly-miR398b was induced by methyl jasmonate (MeJA) treatment. The overexpression of sly-miR398b suppressed the expression of TomLoxD, LapA, and PR-STH2 in response to B. cinerea and MeJA treatment. Our data demonstrate that sly-miR398b overexpression negatively regulates the resistance to B. cinerea in tomato by inducing the accumulation of reactive oxygen species (ROS) and downregulating the expression of MeJA-responsive defense genes.