Ethylene: Traffic Controller on Hormonal Crossroads to Defense

Infection mechanism of Botryosphaeria dothidea and the disease resistance strategies of Chinese hickory (Carya cathayensis)

Botryosphaeria dothidea is the main fungal pathogen responsible for causing Chinese hickory (Carya cathayensis) dry rot disease, posing a serious threat to the Chinese hickory industry. Understanding the molecular basis of B. dothidea infection and the host's resistance mechanisms is crucial for controlling and managing the ecological impact of Chinese hickory dry rot disease. This study utilized ultrastructural observations to reveal the process of B. dothidea infection and colonization in Chinese hickory, and investigated the impact of B. dothidea infection on Chinese hickory biochemical indicators and plant hormone levels. Through high-throughput transcriptome sequencing, the gene expression profiles associated with different stages of B. dothidea infection in Chinese hickory and their corresponding defense responses were described. Additionally, a series of key genes closely related to non-structural carbohydrate metabolism, hormone metabolism, and plant-pathogen interactions during B. dothidea infection in Chinese hickory were identified, including genes encoding DUF, Myb_DNA-binding, and ABC transporter proteins. These findings provide important insights into elucidating the pathogenic mechanisms of B. dothidea and the resistance genes in Chinese hickory.

Crop antiviral defense: Past and future perspective

Viral pathogens not only threaten the health and life of humans and animals but also cause enormous crop yield losses and contribute to global food insecurity. To defend against viral pathogens, plants have evolved an intricate immune system to perceive and cope with such attacks. Although most of the fundamental studies were carried out in model plants, more recent research in crops has provided new insights into the antiviral strategies employed by crop plants. We summarize recent advances in understanding the biological roles of cellular receptors, RNA silencing, RNA decay, hormone signaling, autophagy, and ubiquitination in manipulating crop host-mediated antiviral responses. The potential functions of circular RNAs, the rhizosphere microbiome, and the foliar microbiome of crops in plant-virus interactions will be fascinating research directions in the future. These findings will be beneficial for the development of modern crop improvement strategies.

New Insights into the Connections between Flooding/Hypoxia Response and Plant Defenses against Pathogens

The impact of global climate change has highlighted the need for a better understanding of how plants respond to multiple simultaneous or sequential stresses, not only to gain fundamental knowledge of how plants integrate signals and mount a coordinated response to stresses but also for applications to improve crop resilience to environmental stresses. In recent years, there has been a stronger emphasis on understanding how plants integrate stresses and the molecular mechanisms underlying the crosstalk between the signaling pathways and transcriptional programs that underpin plant responses to multiple stresses. The combination of flooding (or resulting hypoxic stress) with pathogen infection is particularly relevant due to the frequent co-occurrence of both stresses in nature. This review focuses on (i) experimental approaches and challenges associated with the study of combined and sequential flooding/hypoxia and pathogen infection, (ii) how flooding (or resulting hypoxic stress) influences plant immunity and defense responses to pathogens, and (iii) how flooding contributes to shaping the soil microbiome and is linked to plants' ability to fight pathogen infection.

Influences of Ipomoea batatas Anti-Cancer Peptide on Tomato Defense Genes

AIMS

This study investigates the impact of IbACP (Ipomoea batatas anti-cancer peptide) on defense-related gene expression in tomato leaves, focusing on its role in plant defense mechanisms.

BACKGROUND

Previously, IbACP was isolated from sweet potato leaves, and it was identified as a peptide capable of inducing an alkalinization response in tomato suspension culture media. Additionally, IbACP was found to regulate the proliferation of human pancreatic adenocarcinoma cells.

OBJECTIVE

Elucidate IbACP's molecular influence on defense-related gene expression in tomato leaves using next-generation sequencing analysis.

METHODS

To assess the impact of IbACP on defense-related gene expression, transcriptome data were analyzed, encompassing various functional categories such as photosynthesis, metabolic processes, and plant defense. Semi-quantitative reverse-transcription polymerase chain reaction analysis was employed to verify transcription levels of defense-related genes in tomato leaves treated with IbACP for durations ranging from 0 h (control) to 24 h.

RESULTS

IbACP induced jasmonic acid-related genes (LoxD and AOS) at 2 h, with a significant up-regulation of salicylic acid-dependent gene NPR1 at 24 h. This suggested a temporal antagonistic effect between jasmonic acid and salicylic acid during the early hours of IbACP treatment. Downstream ethylene-responsive regulator genes (ACO1, ETR4, and ERF1) were consistently down-regulated by IbACP at all times. Additionally, IbACP significantly up-regulated the gene expressions of suberization-associated anionic peroxidases (TMP1 and TAP2) at all time points, indicating enhanced suberization of the plant cell wall to prevent pathogen invasion.

CONCLUSION

IbACP enhances the synthesis of defense hormones and up-regulates downstream defense genes, improving the plant's resistance to biotic stresses.

Deciphering the mechanisms, hormonal signaling, and potential applications of endophytic microbes to mediate stress tolerance in medicinal plants

The global healthcare market in the post-pandemic era emphasizes a constant pursuit of therapeutic, adaptogenic, and immune booster drugs. Medicinal plants are the only natural resource to meet this by supplying an array of bioactive secondary metabolites in an economic, greener and sustainable manner. Driven by the thrust in demand for natural immunity imparting nutraceutical and life-saving plant-derived drugs, the acreage for commercial cultivation of medicinal plants has dramatically increased in recent years. Limited resources of land and water, low productivity, poor soil fertility coupled with climate change, and biotic (bacteria, fungi, insects, viruses, nematodes) and abiotic (temperature, drought, salinity, waterlogging, and metal toxicity) stress necessitate medicinal plant productivity enhancement through sustainable strategies. Plants evolved intricate physiological (membrane integrity, organelle structural changes, osmotic adjustments, cell and tissue survival, reclamation, increased root-shoot ratio, antibiosis, hypersensitivity, etc.), biochemical (phytohormones synthesis, proline, protein levels, antioxidant enzymes accumulation, ion exclusion, generation of heat-shock proteins, synthesis of allelochemicals. etc.), and cellular (sensing of stress signals, signaling pathways, modulating expression of stress-responsive genes and proteins, etc.) mechanisms to combat stresses. Endophytes, colonizing in different plant tissues, synthesize novel bioactive compounds that medicinal plants can harness to mitigate environmental cues, thus making the agroecosystems self-sufficient toward green and sustainable approaches. Medicinal plants with a host set of metabolites and endophytes with another set of secondary metabolites interact in a highly complex manner involving adaptive mechanisms, including appropriate cellular responses triggered by stimuli received from the sensors situated on the cytoplasm and transmitting signals to the transcriptional machinery in the nucleus to withstand a stressful environment effectively. Signaling pathways serve as a crucial nexus for sensing stress and establishing plants' proper molecular and cellular responses. However, the underlying mechanisms and critical signaling pathways triggered by endophytic microbes are meager. This review comprehends the diversity of endophytes in medicinal plants and endophyte-mediated plant-microbe interactions for biotic and abiotic stress tolerance in medicinal plants by understanding complex adaptive physiological mechanisms and signaling cascades involving defined molecular and cellular responses. Leveraging this knowledge, researchers can design specific microbial formulations that optimize plant health, increase nutrient uptake, boost crop yields, and support a resilient, sustainable agricultural system.

QTL mapping and transcriptome analysis identify novel QTLs and candidate genes in Brassica villosa for quantitative resistance against Sclerotinia sclerotiorum

KEY MESSAGE

Novel QTLs and candidate genes for Sclerotinia-resistance were identified in B. villosa, a wild Brassica species, which represents a new genetic source for improving oilseed rape resistance to SSR. Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, is one of the most destructive diseases in oilseed rape growing regions. To date, there is no effective genetic resistance against S. sclerotiorum in the B. napus germplasm and knowledge of the molecular plant-fungal interaction is also limited. To identify new resistance resources, we screened a set of wild Brassica species and identified B. villosa (BRA1896) with a high level of Sclerotinia-resistance. Two segregating F2 populations for Sclerotinia-resistance, generated by interspecific crosses between the resistant B. villosa (BRA1896) and the wild susceptible B. oleracea (BRA1909) were assessed for Sclerotinia-resistance. Genetic mapping using a 15-k Illumina Infinium SNP-array resulted in a high-density genetic map containing 1,118 SNP markers and spanning a total genetic length of 792.2 cM. QTL analysis revealed seven QTLs explaining 3.8% to 16.5% of phenotypic variance. Intriguingly, RNAseq-based transcriptome analysis identified genes and pathways specific to B. villosa, of which a cluster of five genes encoding putative receptor-like kinases (RLKs) and two pathogenesis-related (PR) proteins are co-localized within a QTL on chromosome C07. Furthermore, transcriptomic analysis revealed enhanced ethylene (ET)-activated signaling in the resistant B. villosa, which is associated with a stronger plant immune response, depressed cell death, and enhanced phytoalexin biosynthesis compared to the susceptible B. oleracea. Our data demonstrates that B. villosa represents a novel and unique genetic source for improving oilseed rape resistance against SSR.

Genome-wide association study reveals WRKY42 as a novel plant transcription factor that influences oviposition preference of Pieris butterflies

Insect herbivores are amongst the most destructive plant pests, damaging both naturally occurring and domesticated plants. As sessile organisms, plants make use of structural and chemical barriers to counteract herbivores. However, over 75% of herbivorous insect species are well adapted to their host's defenses and these specialists are generally difficult to ward off. By actively antagonizing the number of insect eggs deposited on plants, future damage by the herbivore's offspring can be limited. Therefore, it is important to understand which plant traits influence attractiveness for oviposition, especially for specialist insects that are well adapted to their host plants. In this study, we investigated the oviposition preference of Pieris butterflies (Lepidoptera: Pieridae) by offering them the choice between 350 different naturally occurring Arabidopsis accessions. Using a genome-wide association study of the oviposition data and subsequent fine mapping with full genome sequences of 164 accessions, we identified WRKY42 and AOC1 as candidate genes that are associated with the oviposition preference observed for Pieris butterflies. Host plant choice assays with Arabidopsis genotypes impaired in WRKY42 or AOC1 function confirmed a clear role for WRKY42 in oviposition preference of female Pieris butterflies, while for AOC1 the effect was mild. In contrast, WRKY42-impaired plants, which were preferred for oviposition by butterflies, negatively impacted offspring performance. These findings exemplify that plant genotype can have opposite effects on oviposition preference and caterpillar performance. This knowledge can be used for breeding trap crops or crops that are unattractive for oviposition by pest insects.

Phosphorylation status of Bβ subunit acts as a switch to regulate the function of phosphatase PP2A in ethylene-mediated root growth inhibition

The various combinations and regulations of different subunits of phosphatase PP2A holoenzymes underlie their functional complexity and importance. However, molecular mechanisms governing the assembly of PP2A complex in response to external or internal signals remain largely unknown, especially in Arabidopsis thaliana. We found that the phosphorylation status of Bβ of PP2A acts as a switch to regulate the activity of PP2A. In the absence of ethylene, phosphorylated Bβ leads to an inactivation of PP2A; the substrate EIR1 remains to be phosphorylated, preventing the EIR1-mediated auxin transport in epidermis, leading to normal root growth. Upon ethylene treatment, the dephosphorylated Bβ mediates the formation of the A2-C4-Bβ protein complex to activate PP2A, resulting in the dephosphorylation of EIR1 to promote auxin transport in epidermis of elongation zone, leading to root growth inhibition. Altogether, our research revealed a novel molecular mechanism by which the dephosphorylation of Bβ subunit switches on PP2A activity to dephosphorylate EIR1 to establish EIR1-mediated auxin transport in the epidermis in elongation zone for root growth inhibition in response to ethylene.

Comparative RNA-seq analysis reveals a critical role for ethylene in rose (Rosa hybrida) susceptible response to Podosphera pannosa

Rose is one of the most important ornamental flowers, accounting for approximately one-third of the world's cut flower market. Powdery mildew caused by Podosphera pannosa is a devastating fungal disease in rose, mainly infecting the young leaves and causing serious economic losses. Therefore, a study on the mechanism of the fungus infecting the rose leaves and the possibility to improve resistance hereby is interesting and meaningful. Accordingly, we conducted transcriptome sequencing of rose leaves infected by P. pannosa at different time points to reveal the molecular mechanism of resistance to powdery mildew. The high-quality reads were aligned to the reference genome of Rosa chinensis, yielding 51,230 transcripts. A total of 1,181 differentially expressed genes (DEGs) were identified in leaves during P. pannosa infection at 12, 24, and 48 hpi. The transcription factors of ERF, MYB, bHLH, WRKY, etc., family were identified among DEGs, and most of them were downregulated during P. pannosa infection. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the hormone signal transduction pathway, especially ethylene signal-related genes, was consistently showing a downregulated expression during powdery mildew infection. More importantly, exogenous 1-MCP (inhibitor of ethylene) treatment could improve the rose leaves' resistance to P. pannosa. In summary, our transcriptome of rose leaf infected by powdery mildew gives universal insights into the complex gene regulatory networks mediating the rose leaf response to P. pannosa, further demonstrating the positive role of 1-MCP in resistance to biotrophic pathogens.

Discovery of a novel nucleoside immune signaling molecule 2'-deoxyguanosine in microbes and plants

INTRODUCTION

Beneficial microorganisms play essential roles in plant growth and induced systemic resistance (ISR) by releasing signaling molecules. Our previous study obtained the crude extract from beneficial endophyte Paecilomyces variotii, termed ZNC (ZhiNengCong), which significantly enhanced plant resistance to pathogen even at 100 ng/ml. However, the immunoreactive components of ZNC remain unclear. Here, we further identified one of the immunoreactive components of ZNC is a nucleoside 2'-deoxyguanosine (2-dG).

OBJECTIVES

This paper intends to reveal the molecular mechanism of microbial-derived 2'-deoxyguanosine (2-dG) in activating plant immunity, and the role of plant-derived 2-dG in plant immunity.

METHODS

The components of ZNC were separated using a high-performance liquid chromatography (HPLC), and 2-dG is identified using a HPLC-mass spectrometry system (LC-MS). Transcriptome analysis and genetic experiments were used to reveal the immune signaling pathway dependent on 2-dG activation of plant immunity.

RESULTS

This study identified 2'-deoxyguanosine (2-dG) as one of the immunoreactive components from ZNC. And 2-dG significantly enhanced plant pathogen resistance even at 10 ng/ml (37.42 nM). Furthermore, 2-dG-induced resistance depends on NPR1, pattern-recognition receptors/coreceptors, ATP receptor P2K1 (DORN1), ethylene signaling but not salicylic acid accumulation. In addition, we identified Arabidopsis VENOSA4 (VEN4) was involved in 2-dG biosynthesis and could convert dGTP to 2-dG, and vne4 mutant plants were more susceptible to pathogens.

CONCLUSION

In summary, microbial-derived 2-dG may act as a novel immune signaling molecule involved in plant-microorganism interactions, and VEN4 is 2-dG biosynthesis gene and plays a key role in plant immunity.

Belowground and aboveground herbivory differentially affect the transcriptome in roots and shoots of maize

Plants recognize and respond to feeding by herbivorous insects by upregulating their local and systemic defenses. While defense induction by aboveground herbivores has been well studied, far less is known about local and systemic defense responses against attacks by belowground herbivores. Here, we investigated and compared the responses of the maize transcriptome to belowground and aboveground mechanical damage and infestation by two well-adapted herbivores: the soil-dwelling western corn rootworm Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) and the leaf-chewing fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae). In responses to both herbivores, maize plants were found to alter local transcription of genes involved in phytohormone signaling, primary and secondary metabolism. Induction by real herbivore damage was considerably stronger and modified the expression of more genes than mechanical damage. Feeding by the corn rootworm had a strong impact on the shoot transcriptome, including the activation of genes involved in defense and development. By contrast, feeding by the fall armyworm induced only few transcriptional changes in the roots. In conclusion, feeding by a leaf chewer and a root feeder differentially affects the local and systemic defense of maize plants. Besides revealing clear differences in how maize plants respond to feeding by these specialized herbivores, this study reveals several novel genes that may play key roles in plant-insect interactions and thus sets the stage for in depth research into the mechanism that can be exploited for improved crop protection.

Significance statement

Extensive transcriptomic analyses revealed a clear distinction between the gene expression profiles in maize plants upon shoot and root attack, locally as well as distantly from the attacked tissue. This provides detailed insights into the specificity of orchestrated plant defense responses, and the dataset offers a molecular resource for further genetic studies on maize resistance to herbivores and paves the way for novel strategies to enhance maize resistance to pests.

Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination

Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.

Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments

Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptations to aquatic environments by analyzing a data set that included 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptations, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as (Tofieldiaceae, Araceae) + core Alismatids. We also found phylogenetic conflict among the three main clades that was best explained by incomplete lineage sorting and introgression. Overall, we identified 18 putative WGD events across Alismatales. One of them occurred at the most recent common ancestor of core Alismatids, and three occurred at seagrass lineages. We also found that lineage and life-form were both important for different evolutionary patterns for the genes related to freshwater and marine adaptation. For example, several light- or ethylene-related genes were lost in the seagrass Zosteraceae, but are present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments and WGDs using phylogenomics.

Investigating Host and Parasitic Plant Interaction by Tissue-Specific Gene Analyses on Tomato and Cuscuta campestris Interface at Three Haustorial Developmental Stages

Parasitic weeds cause billions of dollars in agricultural losses each year worldwide. Cuscuta campestris (C. campestris), one of the most widespread and destructive parasitic plants in the United States, severely reduces yield in tomato plants. Reducing the spread of parasitic weeds requires understanding the interaction between parasites and hosts. Several studies have identified factors needed for parasitic plant germination and haustorium induction, and genes involved in host defense responses. However, knowledge of the mechanisms underlying the interactions between host and parasitic plants, specifically at the interface between the two organisms, is relatively limited. A detailed investigation of the crosstalk between the host and parasite at the tissue-specific level would enable development of effective parasite control strategies. To focus on the haustorial interface, we used laser-capture microdissection (LCM) with RNA-seq on early, intermediate and mature haustorial stages. In addition, the tomato host tissue that immediately surround the haustoria was collected to obtain tissue- resolution RNA-Seq profiles for C. campestris and tomato at the parasitism interface. After conducting RNA-Seq analysis and constructing gene coexpression networks (GCNs), we identified CcHB7, CcPMEI, and CcERF1 as putative key regulators involved in C. campestris haustorium organogenesis, and three potential regulators, SlPR1, SlCuRe1-like, and SlNLR, in tomatoes that are involved in perceiving signals from the parasite. We used host-induced gene silencing (HIGS) transgenic tomatoes to knock-down the candidate genes in C. campestris and produced CRISPR transgenic tomatoes to knock out candidate genes in tomatoes. The interactions of C. campestris with these transgenic lines were tested and compared with that in wild-type tomatoes. The results of this study reveal the tissue-resolution gene regulatory mechanisms at the parasitic plant-host interface and provide the potential of developing a parasite-resistant system in tomatoes.

The interplay of plant hormonal pathways and geminiviral proteins: partners in disease development

Viruses belonging to the family Geminiviridae infect plants and are responsible for a number of diseases of crops in the tropical and sub-tropical regions of the World. The innate immune response of the plant assists in its defense against such viral pathogens by the recognition of pathogen/microbe-associated molecular patterns through pattern-recognition receptors. Phytohormone signalling pathways play a vital role in plant defense responses against these devastating viruses. Geminiviruses, however, have developed counter-defense strategies that prevail over the above defense pathways. The proteins encoded by geminiviruses act as suppressors of plant immunity by interacting with the signalling components of several hormones. In this review we focus on the molecular interplay of phytohormone pathways and geminiviral infection and try to find interesting parallels with similar mechanisms known in other plant-infecting viruses and strengthen the argument that this interplay is necessary for disease development.

Integrated transcriptomic and metabolic analyses reveal that ethylene enhances peach susceptibility to Lasiodiplodia theobromae-induced gummosis

Gummosis, one of the most detrimental diseases to the peach industry worldwide, can be induced by Lasiodiplodia theobromae. Ethylene (ET) is known to trigger the production of gum exudates, but the mechanism underlying fungus-induced gummosis remains unclear. In this study, L. theobromae infection triggered the accumulation of ET and jasmonic acid (JA) but not salicylic acid (SA) in a susceptible peach variety. Gaseous ET and its biosynthetic precursor increased gum formation, whereas ET inhibitors repressed it. SA and methyl-jasmonate treatments did not influence gum formation. RNA-seq analysis indicated that L. theobromae infection and ET treatment induced a shared subset of 1808 differentially expressed genes, which were enriched in the category "starch and sucrose, UDP-sugars metabolism". Metabolic and transcriptional profiling identified a pronounced role of ET in promoting the transformation of primary sugars (sucrose, fructose, and glucose) into UDP-sugars, which are substrates of gum polysaccharide biosynthesis. Furthermore, ethylene insensitive3-like1 (EIL1), a key transcription factor in the ET pathway, could directly target the promoters of the UDP-sugar biosynthetic genes UXS1a, UXE, RGP and MPI and activate their transcription, as revealed by firefly luciferase and yeast one-hybrid assays. On the other hand, the supply of SA and inhibitors of ET and JA decreased the lesion size. ET treatment reduced JA levels and the transcription of the JA biosynthetic gene OPR but increased the SA content and the expression of its biosynthetic gene PAL. Overall, we suggest that endogenous and exogenous ET aggravate gummosis disease by transactivating UDP-sugar metabolic genes through EIL1 and modulating JA and SA biosynthesis in L. theobromae-infected peach shoots. Our findings shed light on the molecular mechanism by which ET regulates plant defense responses in peach during L. theobromae infection.

The transcription factor ORA59 exhibits dual DNA binding specificity that differentially regulates ethylene- and jasmonic acid-induced genes in plant immunity

Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens in a synergistic and interdependent manner, while JA and ET also have independent roles in certain processes, e.g. in responses to wounding and flooding, respectively. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, of which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. We previously demonstrated that Arabidopsis (Arabidopsis thaliana) GDSL LIPASE 1 (GLIP1) depends on ET for gene expression and pathogen resistance. Here, promoter analysis of GLIP1 revealed ERELEE4 as the critical cis-element for ET-responsive GLIP1 expression. In a yeast one-hybrid screening, ORA59 was isolated as a specific transcription factor that binds to the ERELEE4 element, in addition to the well-characterized GCC box. We found that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in gene promoters. Notably, ORA59 exhibited a differential preference for GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. JA and ET induced ORA59 phosphorylation, which was required for both activity and specificity of ORA59. Furthermore, RNA-seq and virus-induced gene silencing analyses led to the identification of ORA59 target genes of distinct functional categories in JA and ET pathways. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.

The Arabidopsis thaliana LysM-containing Receptor-Like Kinase 2 is required for elicitor-induced resistance to pathogens

In Arabidopsis thaliana, perception of chitin from fungal cell walls is mediated by three LysM-containing Receptor-Like Kinases (LYKs): CERK1, which is absolutely required for chitin perception, and LYK4 and LYK5, which act redundantly. The role in plant innate immunity of a fourth LYK protein, LYK2, is currently not known. Here we show that CERK1, LYK2 and LYK5 are dispensable for basal susceptibility to B. cinerea but are necessary for chitin-induced resistance to this pathogen. LYK2 is dispensable for chitin perception and early signalling events, though it contributes to callose deposition induced by this elicitor. Notably, LYK2 is also necessary for enhanced resistance to B. cinerea and Pseudomonas syringae induced by flagellin and for elicitor-induced priming of defence gene expression during fungal infection. Consistently, overexpression of LYK2 enhances resistance to B. cinerea and P. syringae and results in increased expression of defence-related genes during fungal infection. LYK2 appears to be required to establish a primed state in plants exposed to biotic elicitors, ensuring a robust resistance to subsequent pathogen infections.

Characterization of wall-associated kinase/wall-associated kinase-like (WAK/WAKL) family in rose (Rosa chinensis) reveals the role of RcWAK4 in Botrytis resistance

BACKGROUND

Wall-associated kinase (WAK)/WAK-like (WAKL) is one of the subfamily of receptor like kinases (RLK). Although previous studies reported that WAK/WAKL played an important role in plant cell elongation, response to biotic and abiotic stresses, there are no systematic studies on RcWAK/RcWAKL in rose.

RESULTS

In this study, we identified a total of 68 RcWAK/RcWAKL gene family members within rose (Rosa chinensis) genome. The RcWAKs contained the extracellular galacturonan-binding domain and calcium-binding epidermal growth factor (EGF)-like domain, as well as an intracellular kinase domains. The RcWAKLs are missing either calcium-binding EGF-like domain or the galacturonan-binding domain in their extracellular region. The phylogenetic analysis showed the RcWAK/RcWAKL gene family has been divided into five groups, and these RcWAK/RcWAKL genes were unevenly distributed on the 7 chromosomes of rose. 12 of RcWAK/RcWAKL genes were significantly up-regulated by Botrytis cinerea-inoculated rose petals, where RcWAK4 was the most strongly expressed. Virus induced gene silencing of RcWAK4 increased the rose petal sensitivity to B. cinerea. The results indicated RcWAK4 is involved in the resistance of rose petal against B. cinerea.

CONCLUSION

Our study provides useful information to further investigate the function of the RcWAK/RcWAKL gene family and breeding research for resistance to B. cinerea in rose.

Changes in physiology, gene expression and ethylene biosynthesis in MDMV-infected sweet corn primed by small RNA pre-treatment

The physiological condition of plants is significantly affected by viral infections. Viral proliferation occurs at the expense of the energy and protein stores in infected plant cells. At the same time, plants invest much of their remaining resources in the fight against infection, making them even less capable of normal growth processes. Thus, the slowdown in the development and growth processes of plants leads to a large-scale decrease in plant biomass and yields, which may be a perceptible problem even at the level of the national economy. One form of protection against viral infections is treatment with small interfering RNA (siRNA) molecules, which can directly reduce the amount of virus that multiplies in plant cells by enhancing the process of highly conserved RNA interference in plants. The present work demonstrated how pre-treatment with siRNA may provide protection against MDMV (Maize dwarf mosaic virus) infection in sweet corn (Zea mays cv. saccharata var. Honey Koern). In addition to monitoring the physiological condition of the maize plants, the accumulation of the virus in young leaves was examined, parallel, with changes in the plant RNA interference system and the ethylene (ET) biosynthetic pathway. The siRNA pre-treatment activated the plant antiviral defence system, thus significantly reducing viral RNA and coat protein levels in the youngest leaves of the plants. The lower initial amount of virus meant a weaker stress load, which allowed the plants to devote more energy to their growth and development. In contrast, small RNA pre-treatment did not initially have a significant effect on the ET biosynthetic pathway, but later a significant decrease was observed both in the level of transcription of genes responsible for ET production and, in the amount of ACC (1-aminocyclopropane-1-carboxylic acid) metabolite. The significantly better physiological condition, enhanced RNAi response and lower quantity of virus particles in siRNA pretreated plants, suggested that siRNA pre-treatment stimulated the antiviral defence mechanisms in MDMV infected plants. In addition, the consistently lower ACC content of the plants pre-treated with siRNA suggest that ET does not significantly contribute to the successful defence in this maize hybrid type against MDMV.

Activation of Local and Systemic Defence Responses by Flg22 Is Dependent on Daytime and Ethylene in Intact Tomato Plants

The first line of plant defence responses against pathogens can be induced by the bacterial flg22 and can be dependent on various external and internal factors. Here, we firstly studied the effects of daytime and ethylene (ET) using Never ripe (Nr) mutants in the local and systemic defence responses of intact tomato plants after flg22 treatments. Flg22 was applied in the afternoon and at night and rapid reactions were detected. The production of hydrogen peroxide and nitric oxide was induced by flg22 locally, while superoxide was induced systemically, in wild type plants in the light period, but all remained lower at night and in Nr leaves. Flg22 elevated, locally, the ET, jasmonic acid (JA) and salicylic acid (SA) levels in the light period; these levels did not change significantly at night. Expression of Pathogenesis-related 1 (PR1), Ethylene response factor 1 (ERF1) and Defensin (DEF) showed also daytime- and ET-dependent changes. Enhanced ERF1 and DEF expression and stomatal closure were also observable in systemic leaves of wild type plants in the light. These data demonstrate that early biotic signalling in flg22-treated leaves and distal ones is an ET-dependent process and it is also determined by the time of day and inhibited in the early night phase.

Temperature Differentially Influences the Capacity of Trichoderma Species to Induce Plant Defense Responses in Tomato Against Insect Pests

Species of the ecological opportunistic, avirulent fungus, Trichoderma are widely used in agriculture for their ability to protect crops from the attack of pathogenic fungi and for plant growth promotion activity. Recently, it has been shown that they may also have complementary properties that enhance plant defense barriers against insects. However, the use of these fungi is somewhat undermined by their variable level of biocontrol activity, which is influenced by environmental conditions. Understanding the source of this variability is essential for its profitable and wide use in plant protection. Here, we focus on the impact of temperature on Trichoderma afroharzianum T22, Trichoderma atroviride P1, and the defense response induced in tomato by insects. The in vitro development of these two strains was differentially influenced by temperature, and the observed pattern was consistent with temperature-dependent levels of resistance induced by them in tomato plants against the aphid, Macrosiphum euphorbiae, and the noctuid moth, Spodoptera littoralis. Tomato plants treated with T. afroharzianum T22 exhibited enhanced resistance toward both insect pests at 25°C, while T. atroviride P1 proved to be more effective at 20°C. The comparison of plant transcriptomic profiles generated by the two Trichoderma species allowed the identification of specific defense genes involved in the observed response, and a selected group was used to assess, by real-time quantitative reverse transcription PCR (qRT-PCR), the differential gene expression in Trichoderma-treated tomato plants subjected to the two temperature regimens that significantly affected fungal biological performance. These results will help pave the way toward a rational selection of the most suitable Trichoderma isolates for field applications, in order to best face the challenges imposed by local environmental conditions and by extreme climatic shifts due to global warming.

Sulfur Deprivation Modulates Salicylic Acid Responses via Nonexpressor of Pathogenesis-Related Gene 1 in Arabidopsis thaliana

Mineral nutrients are essential for plant growth and reproduction, yet only a few studies connect the nutritional status to plant innate immunity. The backbone of plant defense response is mainly controlled by two major hormones: salicylic acid (SA) and jasmonic acid (JA). This study investigated changes in the macronutrient concentration (deficiency/excess of nitrogen, phosphorus, potassium, magnesium, and sulfur) on the expression of PR1, a well-characterized marker in the SA-pathway, and PDF1.2 and LOX2 for the JA-pathway, analyzing plants carrying the promoter of each gene fused to GUS as a reporter. After histochemical GUS assays, we determined that PR1 gene was strongly activated in response to sulfur (S) deficiency. Using RT-PCR, we observed that the induction of PR1 depended on the function of Non-expressor of Pathogenesis-Related gene 1 (NPR1) and SA accumulation, as PR1 was not expressed in npr1-1 mutant and NahG plants under S-deprived conditions. Plants treated with different S-concentrations showed that total S-deprivation was required to induce SA-mediated defense responses. Additionally, bioassays revealed that S-deprived plants, induced resistance to the hemibiotrophic pathogen Pseudomonas syringae pv. DC3000 and increase susceptibility to the necrotrophic Botrytis cinerea. In conclusion, we observed a relationship between S and SA/JA-dependent defense mechanisms in Arabidopsis.

Integrating Transcriptome and Coexpression Network Analyses to Characterize Salicylic Acid- and Jasmonic Acid-Related Genes in Tolerant Poplars Infected with Rust

Melampsora larici-populina causes serious poplar foliar diseases called rust worldwide. Salicylic acid (SA) and jasmonic acid (JA) are important phytohormones that are related to plant defence responses. To investigate the transcriptome profiles of SA- and JA-related genes involved in poplar rust interaction, two tolerant poplars and one intolerant poplar were selected for this study. Weighted gene coexpression network analysis (WGCNA) was applied to characterize the changes in the transcriptome profiles and contents of SA and JA after infection with the virulent E4 race of M. larici-populina. In response to infection with the E4 race of M. larici-populina, tolerant symptoms were correlated with the expression of genes related to SA and JA biosynthesis, the levels of SA and JA, and the expression of defence-related genes downstream of SA and JA. Tolerant poplars could promptly regulate the occurrence of defence responses by activating or inhibiting SA or JA pathways in a timely manner, including regulating the expression of genes related to programmed cell death, such as Kunitz-type trypsin inhibitor (KTI), to limit the growth of E4 and protect themselves. WGCNA suggested that KTI might be regulated by a Cytochrome P450 family (CYP) gene. Some CYPs should play an important role in both JA- and SA-related pathways. In contrast, in intolerant poplar, the inhibition of SA-related defence signalling through increasing JA levels in the early stage led to continued inhibition of a large number of plant–pathogen interaction-related and signalling-related genes, including NBS-LRRs, EDS1, NDR1, WRKYs, and PRs. Therefore, timely activation or inhibition of the SA or JA pathways is the key difference between tolerant and intolerant poplars.

Virus-induced phytohormone dynamics and their effects on plant-insect interactions

Attacks on plants by both viruses and their vectors is common in nature. Yet the dynamics of the plant-virus-vector tripartite system, in particular the effects of viral infection on plant-insect interactions, have only begun to emerge in the last decade. Viruses can modulate the interactions between insect vectors and plants via the jasmonate, salicylic acid and ethylene phytohormone pathways, resulting in changes in fitness and viral transmission capacity of their insect vectors. Virus infection of plants may also modulate other phytohormones, such as auxin, gibberellins, cytokinins, brassinosteroids and abscisic acid, with yet undefined consequences on plant-insect interactions. Moreover, virus infection in plants may incur changes to other plant traits, such as nutrition and secondary metabolites, that potentially contribute to virus-associated, phytohormone-mediated manipulation of plant-insect interactions. In this article, we review the research progress, discuss issues related to the complexity and variability of the viral modulation of plant interactions with insect vectors, and suggest future directions of research in this field.

Signaling in the Tomato Immunity against Fusarium oxysporum

New strategies of control need to be developed with the aim of economic and environmental sustainability in plant and crop protection. Metabolomics is an excellent platform for both understanding the complex plant-pathogen interactions and unraveling new chemical control strategies. GC-MS-based metabolomics, along with a phytohormone analysis of a compatible and incompatible interaction between tomato plants and Fusarium oxysporum f. sp. lycopersici, revealed the specific volatile chemical composition and the plant signals associated with them. The susceptible tomato plants were characterized by the over-emission of methyl- and ethyl-salicylate as well as some fatty acid derivatives, along with an activation of salicylic acid and abscisic acid signaling. In contrast, terpenoids, benzenoids, and 2-ethylhexanoic acid were differentially emitted by plants undergoing an incompatible interaction, together with the activation of the jasmonic acid (JA) pathway. In accordance with this response, a higher expression of several genes participating in the biosynthesis of these volatiles, such as MTS1, TomloxC,TomloxD, and AOS, as well as JAZ7, a JA marker gene, was found to be induced by the fungus in these resistant plants. The characterized metabolome of the immune tomato plants could lead to the development of new resistance inducers against Fusarium wilt treatment.

Linking Plant Secondary Metabolites and Plant Microbiomes: A Review

Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, and mediating organismal interactions. Similarly, plant microbiomes participate in many of the above-mentioned processes directly or indirectly by regulating plant metabolism. Studies have shown that plants can influence their microbiome by secreting various metabolites and, in turn, the microbiome may also impact the metabolome of the host plant. However, not much is known about the communications between the interacting partners to impact their phenotypic changes. In this article, we review the patterns and potential underlying mechanisms of interactions between PSMs and plant microbiomes. We describe the recent developments in analytical approaches and methods in this field. The applications of these new methods and approaches have increased our understanding of the relationships between PSMs and plant microbiomes. Though the current studies have primarily focused on model organisms, the methods and results obtained so far should help future studies of agriculturally important plants and facilitate the development of methods to manipulate PSMs-microbiome interactions with predictive outcomes for sustainable crop productions.

VAPYRIN attenuates defence by repressing PR gene induction and localized lignin accumulation during arbuscular mycorrhizal symbiosis of Petunia hybrida

The intimate association of host and fungus in arbuscular mycorrhizal (AM) symbiosis can potentially trigger induction of host defence mechanisms against the fungus, implying that successful symbiosis requires suppression of defence. We addressed this phenomenon by using AM-defective vapyrin (vpy) mutants in Petunia hybrida, including a new allele (vpy-3) with a transposon insertion close to the ATG start codon. We explore whether abortion of fungal infection in vpy mutants is associated with the induction of defence markers, such as cell wall alterations, accumulation of reactive oxygen species (ROS), defence hormones and induction of pathogenesis-related (PR) genes. We show that vpy mutants exhibit a strong resistance against intracellular colonization, which is associated with the generation of cell wall appositions (papillae) with lignin impregnation at fungal entry sites, while no accumulation of defence hormones, ROS or callose was observed. Systematic analysis of PR gene expression revealed that several PR genes are induced in mycorrhizal roots of the wild-type, and even more in vpy plants. Some PR genes are induced exclusively in vpy mutants. Our results suggest that VPY is involved in avoiding or suppressing the induction of a cellular defence syndrome that involves localized lignin deposition and PR gene induction.

ADAP is a possible negative regulator of glucosinolate biosynthesis in Arabidopsis thaliana based on clustering and gene expression analyses

Glucosinolates (GSLs) are plant secondary metabolites consisting of sulfur and nitrogen, commonly found in Brassicaceae crops, such as Arabidopsis thaliana. These compounds are known for their roles in plant defense mechanisms against pests and pathogens. 'Guilt-by-association' (GBA) approach predicts genes encoding proteins with similar function tend to share gene expression pattern generated from high throughput sequencing data. Recent studies have successfully identified GSL genes using GBA approach, followed by targeted verification of gene expression and metabolite data. Therefore, a GSL co-expression network was constructed using known GSL genes obtained from our in-house database, SuCComBase. DPClusO was used to identify subnetworks of the GSL co-expression network followed by Fisher's exact test leading to the discovery of a potential gene that encodes the ARIA-interacting double AP2-domain protein (ADAP) transcription factor (TF). Further functional analysis was performed using an effective gene silencing system known as CRES-T. By applying CRES-T, ADAP TF gene was fused to a plant-specific EAR-motif repressor domain (SRDX), which suppresses the expression of ADAP target genes. In this study, ADAP was proposed as a negative regulator in aliphatic GSL biosynthesis due to the over-expression of downstream aliphatic GSL genes (UGT74C1 and IPMI1) in ADAP-SRDX line. The significant over-expression of ADAP gene in the ADAP-SRDX line also suggests the behavior of the TF that negatively affects the expression of UGT74C1 and IPMI1 via a feedback mechanism in A. thaliana.

Interior design: how plant pathogens optimize their living conditions

Pathogens use effectors to suppress host defence mechanisms, promote the derivation of nutrients, and facilitate infection within the host plant. Much is now known about effectors that target biotic pathways, particularly those that interfere with plant innate immunity. By contrast, an understanding of how effectors manipulate nonimmunity pathways is only beginning to emerge. Here, we focus on exciting new insights into effectors that target abiotic stress adaptation pathways, tampering with key functions within the plant to promote colonization. We critically assess the role of various signalling agents in linking different pathways upon perturbation by pathogen effectors. Additionally, this review provides a summary of currently known bacterial, fungal, and oomycete pathogen effectors that induce biotic and abiotic stress responses in the plant, as a first step towards establishing a comprehensive picture for linking effector targets to pathogenic lifestyles.

Genome-wide identification and expression profiling of chitinase genes in tea (Camellia sinensis (L.) O. Kuntze) under biotic stress conditions

Chitinases are a diverse group of enzymes having the ability to degrade chitin. Chitin is the second most abundant polysaccharide on earth, predominantly found in insect exoskeletons and fungal cell walls. In this study, we performed a genome-wide search for chitinase genes and identified a total of 49 chitinases in tea. These genes were categorized into 5 classes, where an expansion of class V chitinases has been observed in comparison to other plant species. Extensive loss of introns in 46% of the GH18 chitinases indicates that an evolutionary pressure is acting upon these genes to lose introns for rapid gene expression. The promoter upstream regions in 65% of the predicted chitinases contain methyl-jasmonate, salicylic acid and defense responsive cis-acting elements, which may further illustrate the possible role of chitinases in tea plant's defense against various pests and pathogens. Differential expression analysis revealed that transcripts of two GH19 chitinases TEA028279 and TEA019397 got upregulated during three different fungal infections in tea. While GH19 chitinase TEA031377 showed an increase in transcript abundance in the two insect infested tea tissues. Semi-quantitative RT-PCR analysis revealed that five GH19 chitinases viz. TEA018892, TEA031484, TEA28279, TEA033470 and TEA031277 showed significant increase in expression in the tea plants challenged with a biotrophic pathogen Exobasidium vexans. The study endeavours in highlighting biotic stress responsive defensive role of chitinase genes in tea.

Ethylene-Cytokinin Interaction Determines Early Defense Response of Wheat against Stagonospora nodorum Berk

Ethylene, salicylic acid (SA), and jasmonic acid are the key phytohormones involved in plant immunity, and other plant hormones have been demonstrated to interact with them. The classic phytohormone cytokinins are important participants of plant defense signaling. Crosstalk between ethylene and cytokinins has not been sufficiently studied as an aspect of plant immunity and is addressed in the present research. We compared expression of the genes responsible for hormonal metabolism and signaling in wheat cultivars differing in resistance to Stagonospora nodorum in response to their infection with fungal isolates, whose virulence depends on the presence of the necrotrophic effector SnTox3. Furthermore, we studied the action of the exogenous cytokinins, ethephon (2-chloroethylphosphonic acid, ethylene-releasing agent) and 1-methylcyclopropene (1-MCP, inhibitor of ethylene action) on infected plants. Wheat susceptibility was shown to develop due to suppression of reactive oxygen species production and decreased content of active cytokinins brought about by SnTox3-mediated activation of the ethylene signaling pathway. SnTox3 decreased cytokinin content most quickly by its activated glucosylation in an ethylene-dependent manner and, furthermore, by oxidative degradation and inhibition of biosynthesis in ethylene-dependent and ethylene-independent manners. Exogenous zeatin application enhanced wheat resistance against S. nodorum through inhibition of the ethylene signaling pathway and upregulation of SA-dependent genes. Thus, ethylene inhibited triggering of SA-dependent resistance mechanism, at least in part, by suppression of the cytokinin signaling pathway.

Botrytis cinerea induces local hypoxia in Arabidopsis leaves

Low oxygen availability often is associated with soil waterlogging or submergence, but may occur also as hypoxic niches in otherwise aerobic tissues. Experimental evidence assigns a role in Botrytis cinerea resistance to a group of oxygen-unstable Ethylene Response Factors (ERF-VII). Given that infection by B. cinerea often occurs in aerobic organs such as leaves, where ERF-VII stability should be compromised, we explored the possibility of local leaf hypoxia at the site of infection. We analyzed the expression of hypoxia-responsive genes in infected leaves. Confocal microscopy was utilized to verify the localization of the ERF-VII protein RAP2.12. Oxygen concentration was measured to evaluate the availability of oxygen (O₂ ). We discovered that infection by B. cinerea induces increased respiration, leading to a drastic drop in the O₂ concentration in an otherwise fully aerobic leaf. The establishment of a local hypoxic area results in stabilization and nuclear relocalization of RAP2.12. The possible roles of defence elicitors, ABA and ethylene were evaluated. Local hypoxia at the site of B. cinerea infection allows the stabilization of ERF-VII proteins. Hypoxia at the site of pathogen infection generates a nearly O₂ -free environment that may affect the stability of other N-degron-regulated proteins as well as the metabolism of elicitors.

Molecular and Cellular Mechanisms Involved in Host-Specific Resistance to Cyst Nematodes in Crops

Cyst nematodes are able to infect a wide range of crop species and are regarded as a major threat in crop production. In response to invasion of cyst nematodes, plants activate their innate immune system to defend themselves by conferring basal and host-specific defense responses depending on the plant genotype. Basal defense is dependent on the detection of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs), while host-specific defense mainly relies on the activation of canonical and non-canonical resistance (R) genes or quantitative trait loci (QTL). Currently, application of R genes and QTLs in crop species is a major approach to control cyst nematode in crop cultivation. However, emerging virulent cyst nematode field populations are threatening crop production due to host genetic selection by the application of a limited set of resistance genes in current crop cultivars. To counteract this problem, increased knowledge about the mechanisms involved in host-specific resistance mediated by R genes and QTLs to cyst nematodes is indispensable to improve their efficient and sustainable use in field crops. Despite the identification of an increasing number of resistance traits to cyst nematodes in various crops, the underlying genes and defense mechanisms are often unknown. In the last decade, indebt studies on the functioning of a number of cyst nematode R genes and QTLs have revealed novel insights in how plants respond to cyst nematode infection by the activation of host-specific defense responses. This review presents current knowledge of molecular and cellular mechanisms involved in the recognition of cyst nematodes, the activation of defense signaling and resistance response types mediated by R genes or QTLs. Finally, future directions for research are proposed to develop management strategies to better control cyst nematodes in crop cultivation.

Auxin response factors (ARFs) differentially regulate rice antiviral immune response against rice dwarf virus

There are 25 auxin response factors (ARFs) in the rice genome, which play critical roles in regulating myriad aspects of plant development, but their role (s) in host antiviral immune defense and the underneath mechanism remain largely unknown. By using the rice-rice dwarf virus (RDV) model system, here we report that auxin signaling enhances rice defense against RDV infection. In turn, RDV infection triggers increased auxin biosynthesis and accumulation in rice, and that treatment with exogenous auxin reduces OsIAA10 protein level, thereby unleashing a group of OsIAA10-interacting OsARFs to mediate downstream antiviral responses. Strikingly, our genetic data showed that loss-of-function mutants of osarf12 or osarf16 exhibit reduced resistance whereas osarf11 mutants display enhanced resistance to RDV. In turn, OsARF12 activates the down-stream OsWRKY13 expression through direct binding to its promoter, loss-of-function mutants of oswrky13 exhibit reduced resistance. These results demonstrated that OsARF 11, 12 and 16 differentially regulate rice antiviral defense. Together with our previous discovery that the viral P2 protein stabilizes OsIAA10 protein via thwarting its interaction with OsTIR1 to enhance viral infection and pathogenesis, our results reveal a novel auxin-IAA10-ARFs-mediated signaling mechanism employed by rice and RDV for defense and counter defense responses.

The phytohormone auxin is often critical for plant growth and orchestrates many developmental processes. Here we find that rice accumulates more auxin upon RDV infection and treatment with exogenous auxin enhances rice tolerance to RDV infection. Auxin treatment reduces the protein level of OsIAA10, thus releasing a group of OsIAA10-interacting OsARFs to mediate downstream antiviral responses. Among the 25 ARFs in the rice genome, their functions on regulation of rice antiviral defense are diversified. Our findings elucidate a novel auxin-OsIAA10-ARFs-mediated signaling mechanism employed by rice and RDV for defense and counter defense responses. These findings significantly deepen our understanding of virus-host interactions and provide novel targets for molecular breeding (or engineering) rice cultivars resistant to RDV.

Quantitative Hormone Signaling Output Analyses of Arabidopsis thaliana Interactions With Virulent and Avirulent Hyaloperonospora arabidopsidis Isolates at Single-Cell Resolution

The phytohormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) are central regulators of biotic and abiotic stress responses in Arabidopsis thaliana. Here, we generated modular fluorescent protein-based reporter lines termed COLORFUL-PR1pro, -VSP2pro, and -PDF1.2apro. These feature hormone-controlled nucleus-targeted transcriptional output sensors and the simultaneous constitutive expression of spectrally separated nuclear reference and plasma membrane-localized reporters. This set-up allowed the study of cell-type specific hormone activities, cellular viability and microbial invasion. Moreover, we developed a software-supported high-throughput confocal microscopy imaging protocol for output quantification to resolve the spatio-temporal dynamics of respective hormonal signaling activities at single-cell resolution. Proof-of-principle analyses in A. thaliana leaves revealed distinguished hormone sensitivities in mesophyll, epidermal pavement and stomatal guard cells, suggesting cell type-specific regulatory protein activities. In plant-microbe interaction studies, we found that virulent and avirulent Hyaloperonospora arabidopsidis (Hpa) isolates exhibit different invasion dynamics and induce spatio-temporally distinct hormonal activity signatures. On the cellular level, these hormone-controlled reporter signatures demarcate the nascent sites of Hpa entry and progression, and highlight initiation, transduction and local containment of immune signals.

Dissecting the Role of Promoters of Pathogen-sensitive Genes in Plant Defense

Plants inherently show resistance to pathogen attack but are susceptible to multiple bacteria, viruses, fungi, and phytoplasmas. Diseases as a result of such infection leads to the deterioration of crop yield. Several pathogen-sensitive gene activities, promoters of such genes, associated transcription factors, and promoter elements responsible for crosstalk between the defense signaling pathways are involved in plant resistance towards a pathogen. Still, only a handful of genes and their promoters related to plant resistance have been identified to date. Such pathogen-sensitive promoters are accountable for elevating the transcriptional activity of certain genes in response to infection. Also, a suitable promoter is a key to devising successful crop improvement strategies as it ensures the optimum expression of the required transgene. The study of the promoters also helps in mining more details about the transcription factors controlling their activities and helps to unveil the involvement of new genes in the pathogen response. Therefore, the only way out to formulate new solutions is by analyzing the molecular aspects of these promoters in detail. In this review, we provided an overview of the promoter motifs and cis-regulatory elements having specific roles in pathogen attack response. To elaborate on the importance and get a vivid picture of the pathogen-sensitive promoter sequences, the key motifs and promoter elements were analyzed with the help of PlantCare and interpreted with available literature. This review intends to provide useful information for reconstructing the gene networks underlying the resistance of plants against pathogens.

Developmentally regulated activation of defense allows for rapid inhibition of infection in age-related resistance to Phytophthora capsici in cucumber fruit

Background

Age-related resistance (ARR) is a developmentally regulated phenomenon conferring resistance to pathogens or pests. Although ARR has been observed in several host-pathogen systems, the underlying mechanisms are largely uncharacterized. In cucumber, rapidly growing fruit are highly susceptible to Phytophthora capsici but become resistant as they complete exponential growth. We previously demonstrated that ARR is associated with the fruit peel and identified gene expression and metabolomic changes potentially functioning as preformed defenses.

Results

Here, we compare the response to infection in fruit at resistant and susceptible ages using microscopy, quantitative bioassays, and weighted gene co-expression analyses. We observed strong transcriptional changes unique to resistant aged fruit 2–4 h post inoculation (hpi). Microscopy and bioassays confirmed this early response, with evidence of pathogen death and infection failure as early as 4 hpi and cessation of pathogen growth by 8–10 hpi. Expression analyses identified candidate genes involved in conferring the rapid response including those encoding transcription factors, hormone signaling pathways, and defenses such as reactive oxygen species metabolism and phenylpropanoid biosynthesis.

Conclusion

The early pathogen death and rapid defense response in resistant-aged fruit provide insight into potential mechanisms for ARR, implicating both pre-formed biochemical defenses and developmentally regulated capacity for pathogen recognition as key factors shaping age-related resistance.

Functional analysis of RXLR effectors from the New Zealand kauri dieback pathogen Phytophthora agathidicida

New Zealand kauri is an ancient, iconic, gymnosperm tree species that is under threat from a lethal dieback disease caused by the oomycete Phytophthora agathidicida. To gain insight into this pathogen, we determined whether proteinaceous effectors of P. agathidicida interact with the immune system of a model angiosperm, Nicotiana, as previously shown for Phytophthora pathogens of angiosperms. From the P. agathidicida genome, we defined and analysed a set of RXLR effectors, a class of proteins that typically have important roles in suppressing or activating the plant immune system. RXLRs were screened for their ability to activate or suppress the Nicotiana plant immune system using Agrobacterium tumefaciens transient transformation assays. Nine P. agathidicida RXLRs triggered cell death or suppressed plant immunity in Nicotiana, of which three were expressed in kauri. For the most highly expressed, P. agathidicida (Pa) RXLR24, candidate cognate immune receptors associated with cell death were identified in Nicotiana benthamiana using RNA silencing-based approaches. Our results show that RXLRs of a pathogen of gymnosperms can interact with the immune system of an angiosperm species. This study provides an important foundation for studying the molecular basis of plant-pathogen interactions in gymnosperm forest trees, including kauri.

Proteomic and Transcriptomic Analyses Indicate Metabolic Changes and Reduced Defense Responses in Mycorrhizal Roots of Oeceoclades maculata (Orchidaceae) Collected in Nature

Orchids form endomycorrhizal associations with fungi mainly belonging to basidiomycetes. The molecular events taking place in orchid mycorrhiza are poorly understood, although the cellular changes necessary to accommodate the fungus and to control nutrient exchanges imply a modulation of gene expression. Here, we used proteomics and transcriptomics to identify changes in the steady-state levels of proteins and transcripts in the roots of the green terrestrial orchid Oeceoclades maculata. When mycorrhizal and non-mycorrhizal roots from the same individuals were compared, 94 proteins showed differential accumulation using the label-free protein quantitation approach, 86 using isobaric tagging and 60 using 2D-differential electrophoresis. After de novo assembly of transcriptomic data, 11,179 plant transcripts were found to be differentially expressed, and 2175 were successfully annotated. The annotated plant transcripts allowed the identification of up- and down-regulated metabolic pathways. Overall, proteomics and transcriptomics revealed, in mycorrhizal roots, increased levels of transcription factors and nutrient transporters, as well as ethylene-related proteins. The expression pattern of proteins and transcripts involved in plant defense responses suggested that plant defense was reduced in O. maculata mycorrhizal roots sampled in nature. These results expand our current knowledge towards a better understanding of the orchid mycorrhizal symbiosis in adult plants under natural conditions.

Potential Role of Photosynthesis in the Regulation of Reactive Oxygen Species and Defence Responses to Blumeria graminis f. sp. tritici in Wheat

Photosynthesis is not only a primary generator of reactive oxygen species (ROS) but also a component of plant defence. To determine the relationships among photosynthesis, ROS, and defence responses to powdery mildew in wheat, we compared the responses of the Pm40-expressing wheat line L658 and its susceptible sister line L958 at 0, 6, 12, 24, 48, and 72 h post-inoculation (hpi) with powdery mildew via analyses of transcriptomes, cytology, antioxidant activities, photosynthesis, and chlorophyll fluorescence parameters. The results showed that H₂O₂ accumulation in L658 was significantly greater than that in L958 at 6 and 48 hpi, and the enzymes activity and transcripts expression of peroxidase and catalase were suppressed in L658 compared with L958. In addition, the inhibition of photosynthesis in L658 paralleled the global downregulation of photosynthesis-related genes. Furthermore, the expression of the salicylic acid-related genes non-expressor of pathogenesis related genes 1 (NPR1), pathogenesis-related 1 (PR1), and pathogenesis-related 5 (PR5) was upregulated, while the expression of jasmonic acid- and ethylene-related genes was inhibited in L658 compared with L958. In conclusion, the downregulation of photosynthesis-related genes likely led to a decline in photosynthesis, which may be combined with the inhibition of peroxidase (POD) and catalase (CAT) to generate two stages of H₂O₂ accumulation. The high level of H₂O_2, salicylic acid and PR1 and PR5 in L658 possible initiated the hypersensitive response.

A gain of function mutation in SlNRC4a enhances basal immunity resulting in broad-spectrum disease resistance

Plants rely on innate immunity to perceive and ward off microbes and pests, and are able to overcome the majority of invading microorganisms. Even so, specialized pathogens overcome plant defenses, posing a persistent threat to crop and food security worldwide, raising the need for agricultural products with broad, efficient resistance. Here we report a specific mutation in a tomato (S. lycopersicum) helper nucleotide-binding domain leucine-rich repeat H-NLR, SlNRC4a, which results in gain of function constitutive basal defense activation, in absence of PRR activation. Knockout of the entire NRC4 clade in tomato was reported to compromise Rpi-blb2 mediated immunity. The SlNRC4a mutant reported here possesses enhanced immunity and disease resistance to a broad-spectrum of pathogenic fungi, bacteria and pests, while lacking auto-activated HR or negative effects on plant growth and crop yield, providing promising prospects for agricultural adaptation in the war against plant pathogens that decrease productivity.

Lorena Pizarro, Meirav Leibman-Markus et al. explore the genetic mechanisms for plant innate immunity. They functionally characterize a gain of function mutation in SlNRC4a in tomato. They characterize the structure of the mutant protein and functionally demonstrate that it confers broad-spectrum resistance without triggering a hypersensitive response or negatively impacting plant growth and crop yield.

Infection of Medicago truncatula by the Root-Knot Nematode Meloidogyne javanica Does Not Require Early Nodulation Genes

Because of the developmental similarities between root nodules induced by symbiotic rhizobia and root galls formed by parasitic nematodes, we investigated the involvement of nodulation genes in the infection of Medicago truncatula by the root knot nematode (RKN), Meloidogyne javanica. We found that gall formation, including giant cell formation, pericycle and cortical cell division, as well as egg laying, occurred successfully in the non-nodulating mutants nfp1 (nod factor perception1), nin1 (nodule inception1) and nsp2 (nodulation signaling pathway2) and the cytokinin perception mutant cre1 (cytokinin receptor1). Gall and egg formation were significantly reduced in the ethylene insensitive, hypernodulating mutant skl (sickle), and to a lesser extent, in the low nodulation, abscisic acid insensitive mutant latd/nip (lateral root-organ defective/numerous infections and polyphenolics). Despite its supernodulation phenotype, the sunn4 (super numeric nodules4) mutant, which has lost the ability to autoregulate nodule numbers, did not form excessive numbers of galls. Co-inoculation of roots with nematodes and rhizobia significantly reduced nodule numbers compared to rhizobia-only inoculated roots, but only in the hypernodulation mutant skl. Thus, this effect is likely to be influenced by ethylene signaling, but is not likely explained by resource competition between galls and nodules. Co-inoculation with rhizobia also reduced gall numbers compared to nematode-only infected roots, but only in the wild type. Therefore, the protective effect of rhizobia on nematode infection does not clearly depend on nodule number or on Nod factor signaling. Our study demonstrates that early nodulation genes that are essential for successful nodule development are not necessary for nematode-induced gall formation, that gall formation is not under autoregulation of nodulation control, and that ethylene signaling plays a positive role in successful RKN parasitism in M. truncatula.

A temporal gene expression map of Chrysanthemum leaves infected with Alternaria alternata reveals different stages of defense mechanisms

Chrysanthemum (Chrysanthemum morifolium) black spot disease (CBS) poses a major threat to Chrysanthemum cultivation owing to suitable climate conditions and current lack of resistant cultivars for greenhouse cultivation. In this study, we identified a number of genes that respond to Alternaria alternata infection in resistant and susceptible Chrysanthemum cultivars. Based on RNA sequencing technology and a weighted gene coexpression network analysis (WGCNA), we constructed a model to elucidate the response of Chrysanthemum leaves to A. alternata infection at different stages and compared the mapped response of the resistant cultivar 'Jinba' to that of the susceptible cultivar 'Zaoyihong'. In the early stage of infection, when lesions had not yet formed, abscisic acid (ABA), salicylic acid (SA) and EDS1-mediated resistance played important roles in the Chrysanthemum defense system. With the formation of necrotic lesions, ethylene (ET) metabolism and the Ca2+ signal transduction pathway strongly responded to A. alternata infection. During the late stage, when necrotic lesions continued to expand, members of the multidrug and toxic compound extrusion (MATE) gene family were highly expressed, and their products may be involved in defense against A. alternata invasion by exporting toxins produced by the pathogen, which plays important roles in the pathogenicity of A. alternata. Furthermore, the function of hub genes was verified by qPCR and transgenic assays. The identification of hub genes at different stages, the comparison of hub genes between the two cultivars and the highly expressed genes in the resistant cultivar 'Jinba' provide a theoretical basis for breeding cultivars resistant to CBS.

The TuMYB46L-TuACO3 module regulates ethylene biosynthesis in einkorn wheat defense to powdery mildew

Powdery mildew disease, elicited by the obligate fungal pathogen Blumeria graminis f.sp. tritici (Bgt), causes widespread yield losses in global wheat crop. However, the molecular mechanisms governing wheat defense to Bgt are still not well understood. Here we found that TuACO3, encoding the 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase functioning in ethylene (ET) biosynthesis, was induced by Bgt infection of the einkorn wheat Triticum urartu, which was accompanied by increased ET content. Silencing TuACO3 decreased ET production and compromised wheat defense to Bgt, whereas both processes were enhanced in the transgenic wheat overexpressing TuACO3. TuMYB46L, phylogenetically related to Arabidopsis MYB transcription factor AtMYB46, was found to bind to the TuACO3 promoter region in yeast-one-hybrid and EMSA experiments. TuMYB46L expression decreased rapidly following Bgt infection. Silencing TuMYB46L promoted ET content and Bgt defense, but the reverse was observed when TuMYB46L was overexpressed. Hence, decreased expression of TuMYB46L permits elevated function of TuACO3 in ET biosynthesis in Bgt-infected wheat. The TuMYB46L-TuACO3 module regulates ET biosynthesis to promote einkorn wheat defense against Bgt. Furthermore, we found four chitinase genes acting downstream of the TuMYB46L-TuACO3 module. Collectively, our data shed a new light on the molecular mechanisms underlying wheat defense to Bgt.

Reynoutria sachalinensis extract elicits SA-dependent defense responses in courgette genotypes against powdery mildew caused by Podosphaera xanthii

Powdery mildew (PM) caused by Podosphaera xanthii is one of the most important courgette diseases with high yield losses and is currently controlled by fungicides and sulphur applications in conventional and organic production. Plant derived elicitors/inducers of resistance are natural compounds that induce resistance to pathogen attack and promote a faster and/or more robust activation of plant defense responses. Giant knotweed (Reynoutria sachalinensis, RS) extract is a known elicitor of plant defenses but its mode of action remains elusive. The aim of this study was to investigate the mechanisms of foliar RS applications and how these affect PM severity and crop performance when used alone or in combination with genetic resistance. RS foliar treatments significantly reduced conidial germination and PM severity on both an intermediate resistance (IR) and a susceptible (S) genotype. RS application triggered plant defense responses, which induced the formation of callose papillae, hydrogen peroxide accumulation and the Salicylic acid (SA) - dependent pathway. Increased SA production was detected along with increased p-coumaric and caffeic acid concentrations. These findings clearly indicate that RS elicits plant defenses notably as a consequence of SA pathway induction.

Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants

BACKGROUND

Stress-induced hormones are essential for plants to modulate their microbiota and dynamically adjust to the environment. Despite the emphasis of the role of the phytohormone ethylene in the plant physiological response to heterospecific neighbour detection, less is known about how this activated signal mediates focal plant rhizosphere microbiota to enhance plant fitness. Here, using 3 years of peanut (Arachis hypogaea L.), a legume, and cyanide-containing cassava (Manihot esculenta Crantz) intercropping and peanut monocropping field, pot and hydroponic experiments in addition to exogenous ethylene application and soil incubation experiments, we found that ethylene, a cyanide-derived signal, is associated with the chemical identification of neighbouring cassava and the microbial re-assemblage in the peanut rhizosphere.

RESULTS

Ethylene production in peanut roots can be triggered by cyanide production of neighbouring cassava plants. This gaseous signal alters the microbial composition and re-assembles the microbial co-occurrence network of peanut by shifting the abundance of an actinobacterial species, Catenulispora sp., which becomes a keystone in the intercropped peanut rhizosphere. The re-assembled rhizosphere microbiota provide more available nutrients to peanut roots and support seed production.

CONCLUSIONS

Our findings suggest that root ethylene acts as a signal with a dual role. It plays a role in perceiving biochemical cues from interspecific neighbours, and also has a regulatory function in mediating the rhizosphere microbial assembly, thereby enhancing focal plant fitness by improving seed production. This discovery provides a promising direction to develop novel intercropping strategies for targeted manipulations of the rhizosphere microbiome through phytohormone signals. Video abstract.

The Ecology of Salicylic Acid Signaling: Primary, Secondary and Tertiary Effects with Applications in Agriculture

The salicylic acid pathway is one of the primary plant defense pathways, is ubiquitous in vascular plants, and plays a role in rapid adaptions to dynamic abiotic and biotic stress. Its prominence and ubiquity make it uniquely suited for understanding how biochemistry within plants can mediate ecological consequences. Induction of the salicylic acid pathway has primary effects on the plant in which it is induced resulting in genetic, metabolomic, and physiologic changes as the plant adapts to challenges. These primary effects can in turn have secondary consequences for herbivores and pathogens attacking the plant. These secondary effects can both directly influence plant attackers and mediate indirect interactions between herbivores and pathogens. Additionally, stimulation of salicylic acid related defenses can affect natural enemies, predators and parasitoids, which can recruit to plant signals with consequences for herbivore populations and plant herbivory aboveground and belowground. These primary, secondary, and tertiary ecological consequences of salicylic acid signaling hold great promise for application in agricultural systems in developing sustainable high-yielding management practices that adapt to changing abiotic and biotic environments.

Molecular and genetic analysis of defensive responses of Brassica juncea - B. fruticulosa introgression lines to Sclerotinia infection

Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a major disease of crop brassicas, with inadequate variation for resistance in primary gene pools. We utilized a wild Brassicaceae species with excellent resistance against stem rot to develop a set of B. juncea - B. fruticulosa introgression lines (ILs). These were assessed for resistance using a highly reproducible stem inoculation technique against a virulent pathogen isolate. Over 40% of ILs showed higher levels of resistance. IL-43, IL-175, IL-215, IL-223 and IL-277 were most resistant ILs over three crop seasons. Sequence reads (21x) from the three most diverse ILs were then used to create B. juncea pseudomolecules, by replacing SNPs of reference B. juncea with those of re-sequenced ILs. Genotyping by sequencing (GBS) was also carried out for 88 ILs. Resultant sequence tags were then mapped on to the B. juncea pseudomolecules, and SNP genotypes prepared for each IL. Genome wide association studies helped to map resistance responses to stem rot. A total of 13 significant loci were identified on seven B. juncea chromosomes (A01, A03, A04, A05, A08, A09 and B05). Annotation of the genomic region around identified SNPs allowed identification of 20 candidate genes belonging to major disease resistance protein families, including TIR-NBS-LRR class, Chitinase, Malectin/receptor-like protein kinase, defensin-like (DEFL), desulfoglucosinolate sulfotransferase protein and lipoxygenase. A majority of the significant SNPs could be validated using whole genome sequences (21x) from five advanced generation lines being bred for Sclerotinia resistance as compared to three susceptible B. juncea germplasm lines. Our findings not only provide critical new understanding of the defensive pathway of B. fruticulosa resistance, but will also enable development of marker candidates for assisted transfer of introgressed resistant loci in to agronomically superior cultivars of crop Brassica.

Bark tissue transcriptome analyses of inverted Populus yunnanensis cuttings reveal the crucial role of plant hormones in response to inversion

Inverted cuttings of Populus yunnanensis exhibit an interesting growth response to inversion. This response is characterized by enlargement of the stem above the shoot site, while the upright stem shows obvious outward growth below the shoot site. In this study, we examined transcriptome changes in bark tissue at four positions on upright and inverted cuttings of P. yunnanensis: position B, the upper portion of the stem; position C, the lower portion of the stem; position D, the bottom of new growth; and position E, the top of new growth. The results revealed major transcriptomic changes in the stem, especially at position B, but little alteration was observed in the bark tissue of the new shoot. The differentially expressed genes (DEGs) were mainly assigned to four pathways: plant hormone signal transduction, plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway-plant, and adenosine triphosphate-binding cassette (ABC) transporters. Most of these DEGs were involved in at least two pathways. The levels of many hormones, such as auxin (IAA), cytokinin (CTK), gibberellins (GAs), ethylene (ET), and brassinosteroids (BRs), underwent large changes in the inverted cuttings. A coexpression network showed that the top 20 hub unigenes at position B in the upright and inverted cutting groups were associated mainly with the BR and ET signaling pathways, respectively. Furthermore, brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) in the BR pathway and both ethylene response (ETR) and constitutive triple response 1 (CTR1) in the ET pathway were important hubs that interfaced with multiple pathways.