Plant Pathology Research Articles

Banana Leaves Imagery Dataset

In this work, we present a dataset of banana leaf imagery, both with and without diseases. The dataset consists of 11,767 images, categorized as follows: 3,339 healthy images, 3,496 images of leaves affected by Black Sigatoka and 4,932 images of leaves affected by Fusarium Wilt Race 1. This data was collected to support machine learning diagnostics for disease detection. The data collection process involved farmers, researchers, agricultural experts and plant pathologists from the northern and southern highland regions of Tanzania. To ensure unbiased representation, farms were randomly selected from the Rungwe, Mbeya, Arumeru, and Arusha districts, based on the presence of banana crops and the targeted diseases. The dataset offers a comprehensive collection of images captured from November 2022 to January 2023, using a high-resolution smartphone camera across a wide geographical area. Researchers and developers can use this dataset to build machine learning solutions that automatically detect diseases in images, potentially enabling agricultural stakeholders, including farmers, to diagnose Fusarium Wilt Race 1 and Black Sigatoka early and take timely action.

Valsa canker of apple in China: can host nutrition tame a devastating disease?

China is the world's top apple producer, with 44% of the world's apple-producing area in 2022. However, apple production in China suffers from a devastating fungal disease known as apple Valsa canker (AVC). AVC causes severe tree damage and its control adds considerable labor and economic costs to growers. The traditional practice of surgically removing cankers does not prevent AVC recurrence. Eventually, AVC destroys tree vigor and leads to the abandonment of many orchards. Research on the etiology, pathogen infection biology and plant-pathogen interaction mechanisms of AVC has accelerated during the past two decades. Studies at Northwest A&F University have shown that potassium nutrient status significantly impacts AVC resistance and can be exploited to manage AVC. In this review, we summarize research advances on AVC and emphasize that sustainable AVC management should focus on disease prevention through improvement of tree health via both below-ground and above-ground measures. We discuss key factors related to tree health improvement and outline future basic and applied research needs relevant to sustainable AVC control.

Estimated yield reductions and economic losses on wheat caused by disease from 2018 through 2021

Wheat (Triticum aestivum L.) yield and economic losses caused by pathogens were estimated annually by plant pathologists from 29 U.S. states and Ontario, Canada from 2018 through 2021. During this four-year period, plant pathogens caused an estimated reduction of 560 million bushels with an estimated loss value of $2.9 billion USD. Annual losses ranged from 111 million bushels in 2018 to 188 million bushels in 2019. Based on the number of acres planted, the average per acre loss caused by plant pathogens was $18.10 USD across all years and states/province recording estimates. Fusarium head blight (caused by multiple species of Fusarium) was responsible for the greatest overall estimated reduction in yield, followed by stripe rust (caused by Puccinia striiformis) and leaf rust (caused by P. triticina). Although important disease management costs such as pesticide application were not considered, results show the importance of continued plant disease education and research. Quantifying estimated losses associated with plant pathogens impacting wheat remains an important endeavor. Estimates provided by this group of experts are expected to be used as a guide to influence funding for plant disease research by directing Extension and research through both applied and basic efforts. Moreover, the continued effort to quantify plant diseases and their influence on yield losses as well as the economics of managing plant diseases will help inform the industries that influence plant disease management as well as help shape and on-farm disease management efforts.

Limited hypersensitive response but enhanced lignin synthesis leads to Pseudomonas syringae pv. actinidiae tolerance in Actinidia eriantha

Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa), poses a significant threat to the kiwifruit industry. Certain kiwifruit species, such as Eri-1 (Actinidia eriantha), exhibit resistance to Psa, as indicated by the minimal symptoms observed on their shoots and canes. However, discrepancies between leaf disease symptoms and resistance levels have been noted, and the underlying mechanisms remain poorly understood. This study explored the distinctive responses of Psa-resistant Eri-1 leaves to Psa infection. Upon inoculation, Eri-1 leaves activated protein kinase genes associated with pattern-triggered immunity (PTI), induced stomatal closure, and subsequently triggered resistance genes involved in effector-triggered immunity (ETI). However, suppression of downstream hypersensitive response (HR) signaling pathways in both PTI and ETI was observed, limiting reactive oxygen species (ROS) production and programmed cell death (PCD), thus impairing pathogen elimination. Additionally, upon Psa inoculation, the Psa-resistant Eri-1 predominantly activated lignin biosynthesis genes, while the Psa-susceptible ‘Hongyang’ activated flavonol biosynthesis genes within the shared phenylpropanoid pathway. This differential response mechanism facilitates Psa containment in Eri-1 leaves by promoting lignin accumulation, ultimately leading to pathogen elimination. These findings deepen our understanding of plant-pathogen interactions, providing insights into Psa pathogenesis and kiwifruit resistance, and offering valuable guidance for early-stage prevention and control strategies to mitigate crop losses.

Physiological and Transcriptomic Analyses Reveal the Mechanisms of Ilex chinensis Response to Different Types of Simulated Acid Rain

Acid rain has many negative effects on the ecological environment and poses serious abiotic stress onto plants, resulting in substantial ecological and economic impairments annually. Ilex chinensis, a well-known medicinal plant, is sensitive to acid rain, but its response mechanisms are unclear. In this study, we simulated sulfuric acid rain (SAR), mixed acid rain (MIX), and nitric acid rain (NAR) at different pH values to investigate their effects on growth condition, photosynthesis, antioxidants, and nitrogen metabolites. We also explored the metabolic pathways and key genes involved in the response of I. chinensis to acid rain through transcriptome analysis. Physiological analysis showed that I. chinensis suffered the most significant inhibition at pH 3.0, which is manifested in the decrease in height growth rate, specific leaf weight, photosynthetic pigments content, net photosynthetic rate, stomatal conductance, and transpiration rate; the increase in MDA content and SOD activity; and the reduction in glutamine synthetase activity, nitrogen content, and proline content. Transcriptome analysis isolated 314 and 21 shared differentially expressed genes (DEGs) from I. chinensis treated with acid rain at pH 3.0 for 5 d and 15 d, respectively. KEGG enrichment analysis found that different types of acid rain caused changes in multiple metabolic pathways of I. chinensis, and the shared DEGs in 5 d treatment were mainly enriched in ribosomes, oxidative phosphorylation, and glycolysis/glycolysis, etc. The shared DEGs in 115 d treatment were mainly enriched in sulfur metabolism, RNA polymerase, cysteine and methionine metabolism, etc. Further research on gene regulatory networks at the two time points showed that the key pathways of I. chinensis, in response to acid rain stress, include plant–pathogen interaction, MAPK signaling pathway-plant, protein processing in the endoplasmic reticulum, ubiquitin mediated proteolysis, etc., in which 6 hub genes were identified, including TRINITY_DN13584_c0_g1, TRINITY_DN164_c0_g4, TRINITY_DN654_c0_g1, TRINITY_DN13611_c1_g2, TRINITY_DN21290_c0_g2, TRINITY_DN44216_c0_g1. Our findings provide a basis for exploring the regulatory mechanisms of I. chinensis in response to acid rain at the physiological and molecular levels, and for identifying candidate genes with acid tolerance potential.

Annual Review of Phytopathology, Volume 62

There are 18 articles in the current issue. The Annual Review of Phytopathology, in publication since 1963, covers significant developments in the field of plant pathology, including plant disease diagnosis, pathogens, host-pathogen interactions, epidemiology and ecology, breeding for resistance and plant disease management, and includes a special section on the development of concepts

Elevated Atmospheric CO2 Concentrations Reduce Tomato Mosaic Virus Severity in Tomato Plants.

Tomato mosaic disease, caused by tomato mosaic virus (ToMV), was studied under naturally elevated [CO2] concentrations to simulate the potential impacts of future climate scenarios on the ToMV-tomato pathosystem. Tomato plants infected with ToMV were cultivated under two distinct [CO2] environments: elevated [CO2] (naturally enriched to approximately 1000 μmol mol-1) and ambient [CO2] (ambient atmospheric [CO2] of 420 μmol mol-1). Key parameters, including phytopathological (disease index, ToMV gene expression), growth-related (plant height, leaf area), and physiological traits (chlorophyll content, flavonoid levels, nitrogen balance index), were monitored to assess the effects of elevated [CO2]. Elevated [CO2] significantly reduced the disease index from 2.4 under ambient [CO2] to 1.7 under elevated [CO2]. Additionally, viral RNA expression was notably lower in plants grown at elevated [CO2] compared to those under ambient [CO2]. While ToMV infection led to reductions in the chlorophyll content and nitrogen balance index and an increase in the flavonoid levels under ambient [CO2], these physiological effects were largely mitigated under elevated [CO2]. Infected plants grown at elevated [CO2] showed values for these parameters that approached those of healthy plants grown under ambient [CO2]. These findings demonstrate that elevated [CO2] helps to mitigate the effects of tomato mosaic disease and contribute to understanding how future climate scenarios may influence the tomato-ToMV interaction and other plant-pathogen interactions.

Challenges and update on fungal endophytes: classification, definition, diversity, ecology, evolution and functions

Abstract Fungal endophytes have generally been considered as hidden microorganisms that reside asymptomatically within plant tissues and have been exploited for their potential in medicine and plant pathology. They are ubiquitous and associated with nearly all plant species sampled. Even though the exact roles of endophytic fungi within a plant is yet to be established, many speculate that they play important roles in obtaining nutrients and thus improve plant growth, confer plant immunity and promote resistance against biotic and abiotic stresses. It has been postulated that endophytes can exhibit different lifestyles and can even switch lifestyle (i.e., from endophytic to pathogenic or saprobic depending upon plant growth stages). However, there is limited evidence as to whether this switch really happens in vivo. Along the same line, with increasing knowledge of endophytic diversity, defining endophytes has not been easy given their multifaceted functions. The present study provides an updated account with comprehensive knowledge on several aspects including problems with existing definitions, isolation and identification techniques, theoretical and experimental evidence of the role of endophytes, contribution to fungal diversity as well as agenda for future research avenues. For years there has been a number of controversies and debates surrounding as to what exactly is an endophyte. Most of the previous definitions were ephemeral in nature and rather vague and could not realistically define an endophyte. Taking into account numerous biological aspects, we propose herein that endophytes can be defined as “asymptomatic microbial partners that are intimately associated and co-inhabit within healthy internal plant tissues with the ability to confer benefits, co-evolve and alter their lifestyle depending upon plant life stages and adverse conditions”. We also discuss the evolution of endophytes based on fossil data and their co-evolution with their host partners. Studies on fungal endophytes have relied mostly on culture-dependent methods to enable their characterization. However, it is generally well known that these methods suffer drawbacks and there is a need to address the challenges associated with lack of sporulation to enable morphological characterization, slow growth on artificial media, as well as contamination issues. These issues are discussed and addressed in detail here. The molecular mechanisms underlying endophytic colonization, avoidance of plant defense mechanisms, lifestyle changes, as well as their genomics and transcriptomics, are also reviewed. We analyze the possibility of endophytes being host-specific or associated with certain hosts and finally provide an account of their economic importance. This outline of fungal endophytes will provide a more comprehensive understanding of endophytes and can serve for boost research into the exploration and their potential applications in the future.

Artificial Infection of Oats with Fusarium Species in Relation to (1-3)(1-4)-β-D-Glucan Content in the Grain

Oats are increasingly recognized for their nutritional and industrial significance. Among various bioactive compounds in the oat grain, (1-3)(1-4)-β-D-glucan is a key functional component providing industrial, nutritional, and health advantages. This study investigates the correlation between oat (Avena sativa L.) cultivars’ resistance to Fusarium artificial infection and the concentration of β-D-glucan in the grain. Five oat cultivars, including hulled and naked varieties, were artificially inoculated with Fusarium graminearum (FG) and Fusarium culmorum (FC) strains. β-D-glucan content and pathogenic DNA accumulation were analyzed pre- and post-infection. The results show that β-D-glucan content in uninfected grains ranges from 1.97% to 2.53%, with naked varieties generally containing higher levels (2.30%) in comparison with hulled varieties (2.08%). Fusarium infection reduced the concentration of β-D-glucan by 10.60% (FG) and 16.05% (FC). Naked varieties demonstrated greater resilience to infection-induced β-D-glucan loss. Pathogen DNA analysis confirmed higher virulence of FC compared to FG. Our findings suggest β-D-glucan’s dual role as a potential defense mechanism and a pathogen source, emphasizing its complexity in plant–pathogen interactions.

Pioneering Plant Health: Biosensors for Early and Advanced Pathogen Detection

Plant diseases significantly threaten global food security, leading to 40% annual crop losses and an estimated $220 billion in financial damages. Traditional methods for detecting plant diseases such as symptomatology, microscopy, and molecular diagnostics such as polymerase chain reaction(PCR) and ,enzyme linked immuno sorbant assay (ELISA) are often time-consuming, labour-intensive, and difficult to scale. However, advanced technologies, particularly biosensors, have emerged as precise, efficient, and rapid tools for pathogen detection at the time of its initial appearance or even before it causes a significant damage to the crop as they combine biological recognition elements (such as DNA, antibodies, or enzymes) with transducers to produce measurable signals upon interaction with target analytes. This review categorizes biosensors based on their bio-recognition elements and transducer mechanisms, focusing on key types such as electrochemical, optical, piezoelectric, and nucleic acid-based sensors. It explores specific advancements like DNA-based biosensors for molecular-level detection and antibody-based sensors for antigen specificity. Additionally, emerging technologies such as electronic noses, which detect volatile organic compounds, and phage-based biosensors, known for their high sensitivity and specificity, highlight the extensive range of biosensing applications in plant pathology. Innovations in wireless sensing and real-time data capture promise to transform bio-sensing into a cornerstone of Integrated Disease Management (IDM) systems. These advancements can reduce agrochemical usage and improve crop sustainability. Hence, biosensors represent a pivotal technology for addressing the growing challenges of global agriculture.

AtTRM11 as a tRNA 2-methylguanosine methyltransferase modulates flowering and bacterial resistance via translational regulation.

AtTRM11 as a tRNA 2-methylguanosine methyltransferase modulates flowering and bacterial resistance via translational regulation.

Exploring multitasking proteins in Xanthomonas secretomes: Insights into mechanisms of plant-pathogen interactions

Exploring multitasking proteins in Xanthomonas secretomes: Insights into mechanisms of plant-pathogen interactions

Biosynthesis uses, and defensive mechanisms of kauralexins and zealexins against fungi that attack maize (Zea mays) crops- An Review

Fungal pathogens have a high effect on maize crops, where it leads to heavy loss of yield production globally. Secondary metabolites are biochemical compounds that play a crucial role in the stress and defense mechanism of plants. It controls several biotic and abiotic stresses and their related side effects. The fungi cause high-impact diseases to bio-organisms such as plants, animals, and humans. Evidently, throughout the world, a notable feed and used industrial product source is "Corn". Earlier studies have shown diverse approaches in plant defense mechanisms for plant growth and development. Here, we can see short-overview about the phytoalexin derivatives namely labdane-type diterpenoids kauralexins and acidic sesquiterpenoids zealexins biosynthesis, mode of action against fungal pathogens in maize crops. Additionally, past and current trend approach on plant-pathogen interactions used bioinformatics and metabolomic tools approach for disease resistance, database tools of plant metabolomics, and especially focused on resources database tools of plant-fungus interactions. Furthermore, this review is to pointout the “Phytoalexins” derivative bioactive diterpenoid compounds of kauralexins & zealexins antifungal defense mechanisms in maize (Z.mays) crops.

Can whole genome sequencing resolve taxonomic ambiguities in fungi? The case study of Colletotrichum associated with ferns.

The genus Colletotrichum comprises numerous fungal species with diverse ecological roles, including plant pathogenic, endophytic, and saprophytic lifestyles. Accurate species identification is crucial for understanding host-pathogen interactions, disease epidemiology, and fungal ecology. However, taxonomic classification within Colletotrichum remains challenging due to genetic complexity and phenotypic plasticity. Conventional approaches such as single-gene analyses and multilocus sequence typing (MLST) frequently fail to resolve closely related taxa, leading to misidentifications that hinder species delimitation and comparative evolutionary studies. Whole-genome sequencing (WGS) offers a promising alternative by providing genome-wide resolution for phylogenetic analysis. This study investigates Colletotrichum isolates associated with the fern Rumohra adiantiformis and evaluates the effectiveness of WGS in addressing taxonomic uncertainties. A total of 18 Colletotrichum isolates, including fern-associated strains, were analyzed. Genomic DNA was extracted and sequenced using the Illumina NovaSeq platform. High-quality genome assemblies were generated, and gene prediction was conducted using AUGUSTUS. Orthogroup assignment and phylogenomic analysis were performed based on single-copy orthologs, and phylogenetic trees were constructed using MLST and WGS-based approaches. Comparative analyses were carried out to assess the taxonomic resolution provided by WGS in relation to traditional methods. Genome-wide phylogenomic analysis revealed distinct evolutionary lineages among Colletotrichum isolates that MLST failed to resolve, highlighting host and geographic differentiation. High-quality genome assemblies were obtained, with 98.3% of genes assigned to orthogroups, indicating strong genomic conservation. Phylogenetic analyses confirmed a close relationship between Rumohra adiantiformis-associated isolates and Colletotrichum filicis, reinforcing the effectiveness of WGS in species identification. These findings demonstrate the superiority of WGS over MLST in resolving species boundaries and reconstructing evolutionary relationships. The enhanced resolution provided by genome-wide data enables more accurate taxonomic classification, reducing misidentifications and improving our understanding of fungal biodiversity. By refining Colletotrichum taxonomy, WGS facilitates ecological and pathogenic studies, offering a robust framework for future research in fungal systematics and plant pathology. As sequencing technologies continue to advance, WGS is expected to become a standard tool for fungal species delineation and evolutionary studies.

Transcriptomic analysis of two Chinese wheat landraces with contrasting Fusarium head blight resistance reveals miRNA-mediated defense mechanisms.

Fusarium head blight (FHB), caused primarily by Fusarium graminearum (Fg), poses a significant threat to wheat production. It is necessary to deeply understand the molecular mechanisms underlying FHB resistance in wheat breeding. In this study, the transcriptomic responses of two Chinese wheat landraces-Wuyangmai (WY, resistant) and Chinese Spring (CS, susceptible)-to F. graminearum infection were examined using RNA sequencing (RNA-seq). Differential expression of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) was analyzed at 3 and 5 days post-Fg inoculation (dpi). The results showed that WY exhibited a targeted miRNA response, primarily modulating defense-related pathways such as glutathione metabolism and phenylpropanoid biosynthesis, which are crucial for oxidative stress regulation and pathogen defense response. In contrast, CS displayed a broader transcriptional response, largely linked to general metabolic processes rather than immune activation. Notably, the up-regulation of genes involved in oxidative stress and immune defense in WY confirmed its enhanced resistance to FHB. The integrated analysis of miRNA-mRNA interactions highlighted miRNAs as central regulators of defense mechanisms in WY, particularly at later stages of infection. These miRNAs targeted genes involved in immune responses, while lncRNAs and circRNAs played a more limited role in the regulation of defense responses. The GO and KEGG pathway enrichment analyses further revealed that WY enriched for plant-pathogen interaction and secondary metabolite biosynthesis pathways, which are crucial for pathogen resistance. In contrast, CS prioritized metabolic homeostasis, suggesting a less effective defense strategy. Overall, this study underscores the critical role of miRNA-mediated regulation in FHB resistance in WY. These insights into miRNA-mediated regulatory mechanisms provide a molecular basis for breeding FHB-resistant wheat varieties and highlight miRNA-mRNA interactions as promising targets for enhancing disease resilience.

A novel method based on lesion expansion to assess plant disease severity.

Severity is a key indicator utilized in plant disease monitoring and pathogen-plant interaction phenotyping. A plant disease severity assessment method based on lesion expansion was proposed in this study to more accurately and quickly assess the severity of plant diseases for which the lesion area ratio of an investigated plant unit at each severity class in the corresponding severity grading standard is not the actual ratio of the lesion area to the area of the whole investigated plant unit. By taking wheat stripe rust caused by Puccinia striiformis f. sp. tritici as an example, after image segmentation operations of single diseased wheat leaves with wheat stripe rust, lesion expansion processing was carried out using nine method combinations of three proposed lesion expansion methods and three proposed lesion expansion coefficient determination methods, and then the severity assessments of single diseased wheat leaves were conducted. The results showed that the accuracy of severity assessments of single diseased wheat leaves in each severity class was in the range of 78.00% to 100.00%. No matter which method was used to determine the lesion expansion coefficient/coefficients, the performance of the severity assessments of the single diseased leaves achieved after lesion expansion using lesion expansion method 3 (the lesion expansion method based on an image scaling algorithm) outperformed that achieved after lesion expansion using the other two lesion expansion methods. The performance of the method combination of lesion expansion method 3 and lesion expansion coefficient determination method 1 with a lesion expansion coefficient of 2.74, achieving an accuracy of 96.16% for severity assessments of all the single diseased wheat leaves, was the optimal method among the nine method combinations. The results demonstrated that satisfactory severity assessment results could be achieved using the proposed method based on lesion expansion. The results indicated that the lesion-expansion-based plant disease severity assessment method is feasible, and can be used to solve the severity assessment problem described above. This study provided a new idea and method for accurate severity assessment of plant diseases and provided support for the automatic and intelligent assessment of plant disease severity.

Physiological responses and transcriptional regulation of Prunus mume 'Meiren' under drought stress

Prunus mume is an ecologically and economically valuable plant with both medicinal and edible values. However, drought severely limits the promotion and cultivation of P. mume in the arid and semi-arid areas in northern China. In this study, we treated P. mume 'Meiren' with natural drought and then assessed photosynthetic and physiological indexes such as osmoregulatory substances, photosynthetic parameters, and antioxidant enzyme activities. Furthermore, we employed transcriptome sequencing to explore the internal regulatory mechanism of P. mume under drought stress. As the drought stress aggravated, the levels of chlorophyll a (Chla), chlorophyll b (Chlb), chlorophyll (a+b)[Chl(a+b)], and soluble protein (SP) in P. mume first elevated and then declined. The net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), maximum photochemical efficiency (Fv/Fm), effective photochemical quantum yield [Y(Ⅱ)], photochemical quenching (qP), and relative electron transport rate (ETR) all kept decreasing, while the levels of malondialdehyde, superoxide dismutase (SOD), peroxidase (POD), and osmoregulatory substances rose. Transcriptome sequencing revealed a total of 24 853 high-quality genes. Gene ontology (GO) enrichment showed that differentially expressed genes (DEGs) were the most under severe drought. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that the DEGs during the four drought periods were mainly involved in the biosynthesis of secondary metabolites, plant-pathogen interaction, plant hormone signal transduction, starch and sucrose metabolism, and mitogen-activated protein kinase signaling pathways. Furthermore, we identified 16 key genes associated with the drought tolerance of P. mume 'Meiren'. This study discovered that P. mume might up-regulate or down-regulate the expression of drought tolerance-related genes such as SUS, P5CS, LEA, SOD, POD, SOD1, TPPD, and TPPA via transcription factors like MYB, ERF, bHLH, NAC, and WRKY to promote the accumulation of osmoregulatory substances like sucrose and enhance the activities of antioxidant enzymes such as SOD and POD, thus reducing the harm of reactive oxygen species and protecting the structure and function of the membrane system under drought stress. The findings provide theoretical references for further exploration of candidate genes of P. mume in response to drought stress and breeding of drought-tolerant varieties.

Thaumatin-like Gene TLP1b Confers to Seed Oil Content and Resistance to Sclerotinia sclerotiorum in Arabidopsis.

The synergistic optimization of yield and abiotic/biotic resistance is of great significance in plant breeding. However, the genomic mechanisms underlying the selection for environmental adaptation and yield-related traits remain poorly understood. In this study, we identified a thaumatin-like protein (TLP), AtTLP1b, which was shown to pleiotropically regulate seed oil content and resistance to Sclerotinia sclerotiorum by gene knockout and overexpressing experiments in Arabidopsis. The oil composition oleic acid (C18:1), linoleic acid (C18:2), linolenic acid (C18:3) and eicosenoic acid (C20:1) were altered significantly in overexpressing and knockout lines. RNA-seq analysis revealed that overexpression of AtTLP1b significantly downregulated the expression levels of genes involved in wax, suberin synthesis, oxylipin metabolism and plant-pathogen interaction. Furthermore, more than half of the genes involved in the circadian rhythm-plant pathway were differentially expressed in the overexpressing lines. We propose that AtTLP1b primarily inhibits fatty acid synthesis and plant immune responses via the circadian rhythm-plant pathway. Our findings suggest that AtTLP1b plays a vital role in simultaneous improvement of seed oil content and resistance to S. sclerotiorum and provides a valuable resource for molecular breeding.

Molecular Mechanisms of Gene Expression Regulation in Response to Heat Stress in Hemerocallis fulva.

Hemerocallis fulva is one of the three major flowers in the world; its flower type and color are very rich, with high ornamental value and economic value. Heat stress severely limits the cultivation and geographical distribution of H. fulva. Genetic resources and their underlying molecular mechanisms constitute the cornerstone of contemporary breeding technologies. However, research on the response of H. fulva to heat stress remains relatively scant. In this study, we used the heat-resistant 'Dan Yang' variety and heat-sensitive 'Nuo Mi Lu' variety with phenotypic expression as experimental materials to determine the changes in substance and gene expression levels, and used bioinformatics technology to study the molecular mechanisms and gene resource mining of H. fulva in response to heat stress. We identified several thousand differentially expressed genes (DEGs) in different comparison groups. At the same time, 1850 shared DEGs were identified in two H. fulva genotypes responding to heat stress. The dynamic cutting algorithm was used to cluster the genes, and 23 gene co-expression modules were obtained. The MEorangered, MElightpink, and MEmagenta modules were significantly correlated with physiological and biochemical traits. We identified ten key genes closely related to the response of H. fulva to heat stress, including plant-pathogen interactions, plant hormone signal transduction, oxidative transduction phosphorylation, and the plant hormone signal transduction pathway. This study not only analyzes the molecular mechanism of H. fulva response to heat stress, but also provides genetic resources for breeding H. fulva heat tolerance.

Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome

Endophytic Pseudomonas species from agricultural crops have been extensively studied for their plant-growth-promoting (PGP) potential, but little is known about their PGP potential when isolated from perennial trees. This study investigated the plant-growth-promoting (PGP) potential of an endophyte, Pseudomonas oryzihabitans GDW1, isolated from a healthy pine tree by taking tomato as a host plant. We employed multiomics approaches (transcriptome and bacteriome analyses) to elucidate the underlying PGP mechanisms of GDW1. The results of greenhouse experiments revealed that the application of GDW1 significantly improved tomato plant growth, increasing shoot length, root length, fresh weight, and biomass accumulation by up to 44%, 38%, 54%, and 59%, respectively, compared with control. Transcriptomic analysis revealed 1158 differentially expressed genes significantly enriched in the plant hormone signaling (auxin, gibberellin, and cytokinin) and stress response (plant–pathogen interaction, MAPK signaling pathway-plant, and phenylpropanoid biosynthesis) pathways. Protein–protein interaction network analysis revealed nine hub genes (MAPK10, ARF19-1, SlCKX1, GA2ox2, PAL5, SlWRKY37, GH3.6, XTH3, and NML1) related to stress tolerance, hormone control, and plant defense. Analysis of the tomato root bacteriome through 16S rRNA gene amplicon sequencing revealed that GDW1 inoculation dramatically altered the root bacterial community structure, enhancing the diversity and abundance of beneficial taxa (Proteobacteria and Bacteroidota). Co-occurrence network analysis showed a complex bacterial network in treated plants, suggesting increasingly intricate microbial relationships and improved nutrient absorption. Additionally, FAPROTAX and PICRUSt2 functional prediction analyses suggested the role of GDW1 in nitrogen cycling, organic matter degradation, plant growth promotion, and stress resistance. In conclusion, this study provides novel insights into the symbiotic relationship between P. oryzihabitans GDW1 and tomato plants, highlighting its potential as a biofertilizer for sustainable agriculture and a means of reducing the reliance on agrochemicals.