Overexpression of Pti4, Pti5, and Pti6 in tomato promote plant defense and fruit ripening

Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae

Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.

The StPti5 ethylene response factor acts as a susceptibility factor by negatively regulating the potato immune response to pathogens

Ethylene response factors (ERFs) have been associated with biotic stress in Arabidopsis, while their function in non-model plants is still poorly understood. Here we investigated the role of potato ERF StPti5 in plant immunity. We show that StPti5 acts as a susceptibility factor. It negatively regulates potato immunity against potato virus Y and Ralstonia solanacearum, pathogens with completely different modes of action, and thereby has a different role than its orthologue in tomato. Remarkably, StPti5 is destabilised in healthy plants via the autophagy pathway and accumulates exclusively in the nucleus upon infection. We demonstrate that StEIN3 and StEIL1 directly bind the StPti5 promoter and activate its expression, while synergistic activity of the ethylene and salicylic acid pathways is required for regulated StPti expression. To gain further insight into the mode of StPti5 action in attenuating potato defence responses, we investigated transcriptional changes in salicylic acid deficient potato lines with silenced StPti5 expression. We show that StPti5 regulates the expression of other ERFs and downregulates the ubiquitin-proteasome pathway as well as several proteases involved in directed proteolysis. This study adds a novel element to the complex puzzle of immune regulation, by deciphering a two-level regulation of ERF transcription factor activity in response to pathogens.

Ethylene-MPK8-ERF.C1-PR module confers resistance against Botrytis cinerea in tomato fruit without compromising ripening

The plant hormone ethylene plays a critical role in fruit defense against Botrytis cinerea attack, but the underlying mechanisms remain poorly understood. Here, we showed that ethylene response factor SlERF.C1 acts as a key regulator to trigger the ethylene-mediated defense against B. cinerea in tomato fruits without compromising ripening. Knockout of SlERF.C1 increased fruit susceptibility to B. cinerea with no effect on ripening process, while overexpression enhanced resistance. RNA-Seq, transactivation assays, EMSA and ChIP-qPCR results indicated that SlERF.C1 activated the transcription of PR genes by binding to their promoters. Moreover, SlERF.C1 interacted with the mitogen-activated protein kinase SlMPK8 which allowed SlMPK8 to phosphorylate SlERF.C1 at the Ser174 residue and increases its transcriptional activity. Knocking out of SlMPK8 increased fruit susceptibility to B. cinerea, whereas overexpression enhanced resistance without affecting ripening. Furthermore, genetic crosses between SlMPK8-KO and SlERF.C1-OE lines reduced the resistance to B. cinerea attack in SlERF.C1-OE fruits. In addition, B. cinerea infection induced ethylene production which in turn triggered SlMPK8 transcription and enhanced the phosphorylation of SlERF.C1. Overall, our findings reveal the regulatory mechanism of the 'Ethylene-MPK8-ERF.C1-PR' module in resistance against B. cinerea and provide new insight into the manipulation of gray mold disease in fruits.

Shoot transcriptome revealed widespread differential expression and potential molecular mechanisms of chickpea (Cicer arietinum L.) against Fusarium wilt

Introduction

The yield of chickpea is severely hampered by infection wilt caused by several races of Fusarium oxysporum f. sp. ciceris (Foc).

Methods

To understand the underlying molecular mechanisms of resistance against Foc4 Fusarium wilt, RNA sequencing-based shoot transcriptome data of two contrasting chickpea genotypes, namely KWR 108 (resistant) and GL 13001 (susceptible), were generated and analyzed.

Results and Discussion

The shoot transcriptome data showed 1,103 and 1,221 significant DEGs in chickpea genotypes KWR 108 and GL 13001, respectively. Among these, 495 and 608 genes were significantly down and up-regulated in genotypes KWR 108, and 427 and 794 genes were significantly down and up-regulated in genotype GL 13001. The gene ontology (GO) analysis of significant DEGs was performed and the GO of the top 50 DEGs in two contrasting chickpea genotypes showed the highest cellular components as membrane and nucleus, and molecular functions including nucleotide binding, metal ion binding, transferase, kinase, and oxidoreductase activity involved in biological processes such as phosphorylation, oxidation-reduction, cell redox homeostasis process, and DNA repair. Compared to the susceptible genotype which showed significant up-regulation of genes involved in processes like DNA repair, the significantly up-regulated DEGs of the resistant genotypes were involved in processes like energy metabolism and environmental adaptation, particularly host-pathogen interaction. This indicates an efficient utilization of environmental adaptation pathways, energy homeostasis, and stable DNA molecules as the strategy to cope with Fusarium wilt infection in chickpea. The findings of the study will be useful in targeting the genes in designing gene-based markers for association mapping with the traits of interest in chickpea under Fusarium wilt which could be efficiently utilized in marker-assisted breeding of chickpea, particularly against Foc4 Fusarium wilt.

APETALA2/ethylene-responsive factors in higher plant and their roles in regulation of plant stress response

Plants, anchored throughout their life cycles, face a unique set of challenges from fluctuating environments and pathogenic assaults. Central to their adaptative mechanisms are transcription factors (TFs), particularly the AP2/ERF superfamily-one of the most extensive TF families unique to plants. This family plays instrumental roles in orchestrating diverse biological processes ranging from growth and development to secondary metabolism, and notably, responses to both biotic and abiotic stresses. Distinguished by the presence of the signature AP2 domain or its responsiveness to ethylene signals, the AP2/ERF superfamily has become a nexus of research focus, with increasing literature elucidating its multifaceted roles. This review provides a synoptic overview of the latest research advancements on the AP2/ERF family, spanning its taxonomy, structural nuances, prevalence in higher plants, transcriptional and post-transcriptional dynamics, and the intricate interplay in DNA-binding and target gene regulation. Special attention is accorded to the ethylene response factor B3 subgroup protein Pti5 and its role in stress response, with speculative insights into its functionalities and interaction matrix in tomatoes. The overarching goal is to pave the way for harnessing these TFs in the realms of plant genetic enhancement and novel germplasm development.

Stenotrophomonas rhizophila Ep2.2 inhibits growth of Botrytis cinerea through the emission of volatile organic compounds, restricts leaf infection and primes defense genes

The bacterium Stenotrophomonas rhizophila is known to be beneficial for plants and has been frequently isolated from the rhizosphere of crops. In the present work, we isolated from the phyllosphere of an ornamental plant an epiphytic strain of S. rhizophila that we named Ep2.2 and investigated its possible application in crop protection. Compared to S. maltophilia LMG 958, a well-known plant beneficial species which behaves as opportunistic human pathogen, S. rhizophila Ep2.2 showed distinctive features, such as different motility, a generally reduced capacity to use carbon sources, a greater sensitivity to fusidic acid and potassium tellurite, and the inability to grow at the human body temperature. S. rhizophila Ep2.2 was able to inhibit in vitro growth of the plant pathogenic fungi Alternaria alternata and Botrytis cinerea through the emission of volatile compounds. Simultaneous PTR-MS and GC-MS analyses revealed the emission, by S. rhizophila Ep2.2, of volatile organic compounds (VOCs) with well-documented antifungal activity, such as furans, sulphur-containing compounds and terpenes. When sprayed on tomato leaves and plants, S. rhizophila Ep2.2 was able to restrict B. cinerea infection and to prime the expression of Pti5, GluA and PR1 plant defense genes.

Unraveling the Molecular Mechanisms of Tomatoes' Defense against Botrytis cinerea: Insights from Transcriptome Analysis of Micro-Tom and Regular Tomato Varieties

Botrytis cinerea is a devastating fungal pathogen that causes severe economic losses in global tomato cultivation. Understanding the molecular mechanisms driving tomatoes' response to this pathogen is crucial for developing effective strategies to counter it. Although the Micro-Tom (MT) cultivar has been used as a model, its stage-specific response to B. cinerea remains poorly understood. In this study, we examined the response of the MT and Ailsa Craig (AC) cultivars to B. cinerea at different time points (12-48 h post-infection (hpi)). Our results indicated that MT exhibited a stronger resistant phenotype at 18-24 hpi but became more susceptible to B. cinerea later (26-48 hpi) compared to AC. Transcriptome analysis revealed differential gene expression between MT at 24 hpi and AC at 22 hpi, with MT showing a greater number of differentially expressed genes (DEGs). Pathway and functional annotation analysis revealed significant differential gene expression in processes related to metabolism, biological regulation, detoxification, photosynthesis, and carbon metabolism, as well as some immune system-related genes. MT demonstrated an increased reliance on Ca2+ pathway-related proteins, such as CNGCs, CDPKs, and CaMCMLs, to resist B. cinerea invasion. B. cinerea infection induced the activation of PTI, ETI, and SA signaling pathways, involving the modulation of various genes such as FLS2, BAK1, CERK1, RPM, SGT1, and EDS1. Furthermore, transcription factors such as WRKY, MYB, NAC, and AUX/IAA families played crucial regulatory roles in tomatoes' defense against B. cinerea. These findings provide valuable insights into the molecular mechanisms underlying tomatoes' defense against B. cinerea and offer potential strategies to enhance plant resistance.

Transcriptional regulatory mechanism of a variant transcription factor CsWRKY23 in citrus fruit resistance to Penicillium digitatum

As the most productive fruit in the world, there is a lack of research on disease resistance mechanisms in citrus. WRKY transcription factors are mediators of disease resistance in plants. In this research, CsWRKY23, which could respond to exogenous salicylic acid (SA) was identified. As a variant WRKY, the transient overexpression of CsWRKY23 in citrus peel enhanced the resistance to Penicillium digitatum. The potential targets of CsWRKY23 were identified by using DNA affinity purification sequencing (DAP-seq). In combination with RNA sequencing (RNA-seq) data, 48 direct target genes of CsWRKY23 were identified. In addition, five genes for EMSA and dual-luciferase report system analysis were selected and the results showed that CsWRKY23 activate CsAAE12, CsRbohD, CsSARD1, CsWRKY22 and CsIQM6 expressions. Further analysis revealed that CsWRKY23 contributed to SA synthesis pathway, reactive oxygen species (ROS) accumulation, and cell wall strengthening. This study presented a possible regulatory network for disease resistance involving the CsWRKY23.

Engineering plant immune circuit: walking to the bright future with a novel toolbox

Plant pathogens destroy crops and cause severe yield losses, leading to an insufficient food supply to sustain the human population. Apart from relying on natural plant immune systems to combat biological agents or waiting for the appropriate evolutionary steps to occur over time, researchers are currently seeking new breakthrough methods to boost disease resistance in plants through genetic engineering. Here, we summarize the past two decades of research in disease resistance engineering against an assortment of pathogens through modifying the plant immune components (internal and external) with several biotechnological techniques. We also discuss potential strategies and provide perspectives on engineering plant immune systems for enhanced pathogen resistance and plant fitness.

A tomato HD-zip I transcription factor, VAHOX1, acts as a negative regulator of fruit ripening

Homeodomain-leucine zipper (HD-Zip) transcription factors are only present in higher plants and are involved in plant development and stress responses. However, our understanding of their participation in the fruit ripening of economical plants, such as tomato (Solanum lycopersicum), remains largely unclear. Here, we report that VAHOX1, a member of the tomato HD-Zip I subfamily, was expressed in all tissues, was highly expressed in breaker+4 fruits, and could be induced by ethylene. RNAi repression of VAHOX1 (VAHOX1-RNAi) resulted in accelerated fruit ripening, enhanced sensitivity to ethylene, and increased total carotenoid content and ethylene production. Conversely, VAHOX1 overexpression (VAHOX1-OE) in tomato had the opposite effect. RNA-Seq results showed that altering VAHOX1 expression affected the transcript accumulation of a series of genes involved in ethylene biosynthesis and signal transduction and cell wall modification. Additionally, a dual-luciferase reporter assay, histochemical analysis of GUS activity and a yeast one-hybrid (Y1H) assay revealed that VAHOX1 could activate the expression of AP2a. Our findings may expand our knowledge about the physiological functions of HD-Zip transcription factors in tomato and highlight the diversities of transcriptional regulation during the fruit ripening process.

Construction of a high-density genetic map and localization of grazing-tolerant QTLs in Medicago falcata L

BACKGROUND

Using genomic DNA from 79 F1 plants resulted from a crossing between parents with strong and weak grazing tolerance in Medicago falcata L., we generated an EcoRI restriction site-associated DNA (RAD) sequencing library. After sequencing and assembly, a high-density genetic map with high-quality SNP markers was constructed, with a total length of 1312.238 cM and an average density of 0.844 SNP/cM.

METHODS

The phenotypic traits of 79 F1 families were observed and the QTLS of 6 traits were analyzed by interval mapping.

RESULTS

Sixty three QTLs were identified for seven traits with LOD values from 3 to 6 and the contribution rates from 15% to 30%. Among the 63 QTLs, 17 were for natural shoot height, 12 for rhizome Length, 10 for Shoot canopy diameter, 9 for Basal plant diameter, 6 for stem number, 5 for absolute shoot height, and 4 for rhizome width. These QTLs were concentrated on LG2, LG4, LG5, LG7, and LG8. LG6 had only 6 QTLs. According to the results of QTL mapping, comparison of reference genomes, and functional annotation, 10 candidate genes that may be related to grazing tolerance were screened. qRT-PCR analysis showed that two candidate genes (LOC11412291 and LOC11440209) may be the key genes related to grazing tolerance of M. falcata.

CONCLUSION

The identified trait-associated QTLs and candidate genes in this study will provide a solid foundation for future molecular breeding for enhanced grazing-tolerance in M. falcata.

Antioxidant activation, cell wall reinforcement, and reactive oxygen species regulation promote resistance to waterlogging stress in hot pepper (Capsicum annuum L.)

BACKGROUND

Hot pepper (Capsicum annuum L.) is one of the world's oldest domesticated crops. It has poor waterlogging tolerance, and flooding frequently results in plant death and yield reduction. Therefore, understanding the molecular mechanisms associated with pepper waterlogging tolerance is essential to grow new varieties with stronger tolerance.

RESULTS

In this study, we discovered that after 5 days of flooding, the growth rate of waterlogging-tolerant pepper cultivars did not reduce to a large extent. Physiological data revealed that chlorophyll concentration was not significantly affected by flooding; however, stomatal conductance was altered considerably 0-5 days after flooding, and the net photosynthesis rate changed substantially 5-10 days after flooding. In addition, the root activity of waterlogging-tolerant varieties was substantially higher after flooding for 10 days than that of the control. This implies that the effect of flooding is associated with changes in the root environment, which ultimately affects photosynthesis. We evaluated changes in gene expression levels between two pepper types at the same time point and the same pepper variety at different time points after flooding stress treatment and performed a screening for multiple potential genes. These differentially expressed genes (DEGs) were further analyzed for functional enrichment, and the results revealed that antioxidase genes, cell wall synthesis pathway genes, and calcium ion regulation pathway genes might be associated with waterlogging tolerance. Other genes identified in peppers with waterlogging tolerance included those associated with lignin synthesis regulation, reactive oxygen species (ROS) regulation pathways, and others associated with stress resistance. Considerable changes in the expression levels of these genes were recorded 5 days after waterlogging, which was consistent with a considerable increase in oxidase content that was also noted on the fifth day after flooding. The quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) findings revealed that among the 20 selected DEGs, including genes such as mitogen-activated protein kinase 3 (MPK3) and calcium-binding protein 4 (CML4), approximately 80% of the gene expression patterns were consistent with our RNA-seq dataset.

CONCLUSIONS

The findings of this study suggest that ROS modulation, increased antioxidase activity, lignin formation, and the expression of stress resistance genes help peppers with waterlogging tolerance resist flooding stress in the early stages. These findings provide a basis for further investigation of the molecular mechanisms responsible for waterlogging tolerance in pepper and may be a critical reference for the breeding of hot pepper.

Gene expression and phytohormone levels in the asymptomatic and symptomatic phases of infection in potato tubers inoculated with Dickeya solani

Dickeya solani is a soft rot bacterium with high virulence. In potato, D. solani, like the other potato-infecting soft rot bacteria, causes rotting and wilting of the stems and rotting of tubers in the field and in storage. Latent, asymptomatic infections of potato tubers are common in harvested tubers, and if the storage conditions are not optimal, the latent infection turns into active rotting. We characterized potato gene expression in artificially inoculated tubers in nonsymptomatic, early infections 1 and 24 hours post-inoculation (hpi) and compared the results to the response in symptomatic tuber tissue 1 week (168 hpi) later with RNA-Seq. In the beginning of the infection, potato tubers expressed genes involved in the detection of the bacterium through pathogen-associated molecular patterns (PAMPs), which induced genes involved in PAMPs-triggered immunity, resistance, production of pathogenesis-related proteins, ROS, secondary metabolites and salicylic acid (SA) and jasmonic acid (JA) biosynthesis and signaling genes. In the symptomatic tuber tissue one week later, the PAMPs-triggered gene expression was downregulated, whereas primary metabolism was affected, most likely leading to free sugars fueling plant defense but possibly also aiding the growth of the pathogen. In the symptomatic tubers, pectic enzymes and cell wall-based defenses were activated. Measurement of hormone production revealed increased SA concentration and almost no JA in the asymptomatic tubers at the beginning of the infection and high level of JA and reduced SA in the symptomatic tubers one week later. These findings suggest that potato tubers rely on different defense strategies in the different phases of D. solani infection even when the infection takes place in fully susceptible plants incubated in conditions leading to rotting. These results support the idea that D. solani is a biotroph rather than a true necrotroph.

FytoSol, a Promising Plant Defense Elicitor, Controls Early Blight (Alternaria solani) Disease in the Tomato by Inducing Host Resistance-Associated Gene Expression

Early blight (EB), caused by the necrotrophic pathogen Alternaria solani, is one of the most common and destructive diseases in the tomato (Solanum lycopersicum L.). The use of fungicides is a prominent tactic used to control EB; however, their undesirable effects on the environment and human health, as well as involvement in the development of resistant strains, have driven researchers to search for new alternatives. Plant defense elicitors are exogenous defense-triggering molecules that induce a plant’s defense system associated with extensive transcriptional- and metabolic reprogramming of the genome and do not cause direct toxicity to phytopathogens. Moreover, 2,6-dichloroisonicotinic acid (INA) was an early-identified and strong plant defense elicitor to various phytopathogens. Recently, the combination of chitosan oligomers and pectin-derived oligogalacturonides that can mimic the induction of plants by a pathogen or damaged-derived molecules (PAMP and DAMP) were characterized as defense elicitors, named FytoSol. In this study, the preventive roles of these two defense elicitors—FytoSol and INA—against EB disease and its molecular basis, were explored. According to the results, FytoSol significantly reduced disease severity by an average of 30% for almost one month with an AUDPC value of 399 compared to the control, which had an AUDPC value of 546. On the contrary, INA did not provide any protection against EB. Gene expression analyses of these two distinct plant defense elicitors indicated that the expression patterns of several SA-, JA-, or ET-pathway-related genes (Pti4, TPK1b, Pto kinase, TomloxD, PRB1-2, SABP2, WRKY33b, WRKY70, PR-5, and PR3) were induced by defense elicitors differently. FytoSol extensively upregulated gene expressions of PR3, downregulated the SA-related defense pathway, and provided remarkable protection against the necrotrophic pathogen Alternaria solani. On the contrary, INA mostly induced genes related to biotrophic and/or hemibiotrophic pathogen protection. Our results indicate that FytoSol is a promising plant defense elicitor against EB and the modes of action of the elicitors are important to characterize their effects against pathogens. Further research may extend the use of defense elicitors as alternatives to pesticides in agriculture.

Exogenous melatonin improves the resistance to cucumber bacterial angular leaf spot caused by Pseudomonas syringae pv. Lachrymans

Pseudomonas syringae pv. Lachrymans (Psl) is a bacterial pathogen that causes cucumber bacterial angular leaf spot (BALS). It is known that melatonin (MT), as a pleiotropic signal molecule, can improve plant stress tolerance, but less information is available about the function of MT on plant resistance to bacteria disease. Here, we investigated the effect of MT on cucumber BALS. Our results show that MT inhibited the bacteria Psl growth significantly in vitro and attenuated cucumber BALS remarkably in vivo. The concentration of bacteria in leaves treated with 0.1 mM MT was approximately 10,000 times reduced at 5 days-post-inoculation (dpi), compared to the control without MT. Transcriptomic analysis showed that 225 differentially expressed genes (DEGs) were induced in leaves after just MT treatment for 3 h. The functions of these DEGs were mainly associated with hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling pathway, and photosynthesis, suggesting that MT could regulate plant growth and induce plant immunity. Moreover, 665 DEGs were induced when leaves were treated with exogenous MT in combination with the bacteria inoculation for 12 h. The functions of these DEGs were much related to plant-pathogen interaction, hormone signal transduction, and amino acids biosynthesis pathways. Many MT-induced DEGs were involved in some distinct signal transduction pathways, such as calmodulin (CaM), polyamines (PAs), nitric oxide (NO), and salicylic acid (SA). The physiological analysis shows that exogenous MT spray reduced the stomatal aperture and enhanced the activities of antioxidant and defense enzymes, which were in consistent with the results of the transcriptome analysis. In addition, MT may function in regulating the metabolic balance between plant growth and defense. In conclusion, our results demonstrate that MT could alleviate the cucumber BALS via inhibiting propagation and invasion of Psl, activating plant signaling, enhancing antioxidative and defense systems, inducing stress-related genes expression, and regulating the plant growth-defense balance.

Pto Interaction Proteins: Critical Regulators in Plant Development and Stress Response

Pto interaction (Pti) proteins are a group of proteins that can be phosphorylated by serine/threonine protein kinase Pto, which have diverse functions in plant development and stress response. In this study, we analyzed the phylogenetic relationship, gene structure, and conserved motifs of Pti1s and predicted the potential cis-elements in the promoters of Pti1 genes using bioinformatics methods. Importantly, we systematically summarized the diverse functions of Pti1s in tomato, rice, Arabidopsis, potato, apple, and cucumber. The potential cis-elements in promoters of Pti1s decide their functional diversity in response to various biotic and abiotic stresses. The protein kinase Pti1 was phosphorylated by Pto and then modulated the downstream signaling pathways for PTI and ETI in the disease insistence process. In addition, some transcription factors have been defined as Ptis (e.g., Pti4, Pti5, and Pti6) originally, which actually were ethylene-response factors (ERFs). Pti4, Pti5, and Pti6 were modulated by salicylic acid (SA), jasmonate (JA), and ethylene signaling pathways and regulated diverse defense-related gene expression to cope with Pst infection and insect wounding.