Molecular Plant Pathology

O_LIHost specialization is a major driver of genetic structure in fungal plant pathogens, but it remains unclear whether specialization on different cereal hosts prevents sexual recombination when mating-type compatibility is retained. We addressed this question in stripe rust, caused by Puccinia striiformis, by crossing wheat-adapted P. striiformis f. sp. tritici and barley-adapted P. striiformis f. sp. hordei, two divergent host-adapted forms that share common barberry (Berberis vulgaris) as a sexual host. C_LIO_LIControlled reciprocal crosses on barberry produced 18 aeciospore-derived progeny, demonstrating that wheat- and barley-adapted Puccinia striiformis can undergo sexual recombination despite strong host specialization during asexual infection. Chromosome-scale parental assemblies placed the homeodomain (HD) mating-type locus, containing bW-HD1 and bE-HD2, on chromosome 2 and the pheromone receptor (PR) mating-type locus, containing STE3 and mfa genes, on chromosome 6. HD restriction genotyping showed biparental inheritance in all progeny, with each progeny carrying one HD haplotype from each parent. Together with conservation of PR-associated coding sequences and amplification of STE3-associated markers in progeny, these results are consistent with retention of tetrapolar mating across the two host-adapted lineages. C_LIO_LIHost interaction phenotypes were assessed across wheat and barley differentials, near-isogenic lines and wild relatives. The parental isolates retained contrasting wheat- and barley-restricted profiles, whereas progeny did not reproduce either parental virulence profile, but instead showed recombinant infection patterns, including compatibility with both wheat and barley genotypes. C_LIO_LIThese findings indicate that host specialization in Puccinia striiformis does not necessarily prevent sexual compatibility on a shared alternate host. Together with retention of tetrapolar mating, alternate-host sexual reproduction may provide a route for genetic exchange between host-specialized pathogen populations, enabling recombination to generate new combinations of host-interaction traits when divergent pathogen lineages mate on a shared alternate host. C_LI

Bacterial canker, caused the Pseudomonas syringae species complex, is a major constraint on sweet cherry production worldwide. However, the influence of agronomic practices on pathogen ecology, dispersal and evolution under field conditions remains poorly understood. Here, we combined a factorial-design field experiment with whole-genome sequencing to investigate the effects of polytunnel covering and nitrogen fertigation on phyllosphere populations and the dynamics of a key pathogen, P. syringae pathovar syringae 9644 (Pss9644) in young cherry trees. Epiphytic P. syringae populations initially resembled those in surrounding woodland environments. Over time, pathogenic phylogroup 2d lineages became dominant, particularly on uncovered trees. Diversity of P. syringae populations was higher in uncovered treatments. Polytunnel covering markedly altered community composition and limited rain-splash dispersal of Pss9644 from stem cankers to leaves, thereby interrupting a key stage of the disease cycle. By contrast, nitrogen fertigation had no detectable effect on phyllosphere community structure, but enhanced plant growth and reduced lesion expansion following inoculation. Whole-genome sequencing of re-isolated Pss9644 strains revealed limited short-term genomic diversification, with single-nucleotide polymorphisms detected in 22 re-isolates. In total, 36 mutations were identified across the chromosome although no mutation affected virulence or motility. Taken together, our results show that agronomic practices influence both pathogen ecology and disease outcomes through distinct mechanisms: polytunnel covering primarily limits pathogen dispersal and reshapes phyllosphere communities, while nitrogen fertigation enhances plant growth and reduces disease severity. These findings highlight the potential to integrate canopy management and nutrient strategies to mitigate bacterial canker risk in commercial cherry production.

Colletotrichum siamense is a predominant causal agent of anthracnose in rubber tree and numerous economically important crops, causing severe yield losses worldwide. Conidial germination represents a critical early step for successful infection, while the high-osmolarity glycerol (HOG) MAPK pathway and ergosterol biosynthesis individually govern fungal development, stress adaptation and fungicide responses. However, the molecular crosstalk between these two modules remains largely elusive in phytopathogenic fungi. Here, we identified CsErg5B, a sterol C-22 desaturase homolog, as a direct target of the HOG- regulated transcription factor CsAtf1 in C. siamense. CsErg5B was indispensable for ergosterol biosynthesis, conidial germination, appressorium formation, and full virulence. The {Delta}CsErg5B mutant showed increased conidiation but severely impaired germination, and exhibited elevated resistance to fludioxonil while hypersensitivity to azole fungicides. Epistasis analysis using the {Delta}CsErg5B/{Delta}CsCyp51G1 double mutant - where CsCyp51G1 serves as another downstream target of CsAtf1 - revealed that CsErg5B functions as the predominant downstream effector of CsAtf1 in modulating conidial development and fludioxonil sensitivity. Furthermore, overexpression of CsErg5B significantly rescued the defects in conidial germination and fludioxonil sensitivity in both {Delta}CsAtf1 and {Delta}CsPbs2 mutants. Taken together, our findings uncover a HOG MAPK - CsAtf1 - CsErg5B regulatory axis that connects HOG MAPK signaling to ergosterol homeostasis, thereby governing conidial germination and fungicide sensitivity in C. siamense. This study provides novel insights into the regulatory network underlying fungal development and fungicide response, and offers promising molecular targets for the integrated management of plant anthracnose.

Aphanomyces euteiches, the causative agent of Aphanomyces root rot (ARR), is of major concern for pea and other legume crops globally. This oomycete pathogen causes substantial decreases in crop yields, is unaffected by most fungicides, and persists in the soil for many years via its resilient oospores. Given the significance of pea crops in sustainable agriculture, namely the ability to fix nitrogen and act as a sustainable protein source, solutions to ARR are of high importance. We used RNA-seq in a novel strain of Pseudomonas donghuensis to identify two biosynthetic gene clusters under GacA/S control that are involved in producing bioactive molecules capable of inhibiting A. euteiches. Based on similarity to other reported clusters in Pseudomonas, the first is predicted to encode for a pseudoiodinine compound, while the second is predicted to produce the siderophore 7-hydroxytropolone. Individual knockouts of each cluster showed loss of inhibitory action of P. donghuensis NRC29 against A, euteiches in vivo. This is the first report highlighting the potential of P. donghuensis and the products of the two identified biosynthetic pathways as biocontrol agents for A. euteiches. Further investigations into the efficacy of P. donghuensis NRC29 and its metabolites in inhibiting A. euteiches in field trials will be of high value in developing sustainable strategies for ARR mitigation. ImportanceModern fungicidal treatments for control of root rot in pulse crops are ineffective for control of A. euteiches, leaving limited strategies for management of A. euteiches infected fields. We describe a novel P. donghuensis strain with potential for biocontrol against this persistent pathogen. Given the economic value of peas and other pulses globally, further work into harnessing the bioactive metabolites produced by this strain into a practical in-field treatment will be valuable.

BackgroundPotato is an important crop worldwide, yet its production is severely threatened by Phytophthora infestans, the causal agent of late blight. Alternatives to the current control strategies are needed, as these rely heavily on environmentally harmful treatments. The recruitment of beneficial microbes by plants upon stress ("cry-for-help" mechanism) may represent an opportunity to find new biocontrol agents but this has not yet been reported for potato. The aim of this study was to analyse whether foliar late blight infection induces shifts in the phyllosphere, rhizosphere and soil bacterial communities associated with two potato cultivars of differing sensitivity to late blight. Moreover, we aimed at isolating members of the plant microbiota to test whether bacteria putatively recruited upon infection would be particularly active in protecting the plant against late blight. ResultsControlled foliar infection triggered substantial, cultivar-specific shifts in the rhizosphere communities across two successive generations. Despite the number of differentially abundant ASVs detected being ten times higher in the second generation than in the first one, the same taxonomic groups were concerned by the shifts: Burkholderiales, Flavobacteriales, and Bacillales. Furthermore, the communities linked to the susceptible cultivar consistently shifted more strongly than the communities linked to the resistant cultivar. The obtained ASV sequences were used to identify 163 corresponding isolates. The inhibition potential of these strains against P. infestans spores was assessed through biological assays, which revealed the biocontrol potential of strains otherwise not yet known to inhibit phytopathogenic organisms, such as Advenella, Nocardioides and Phyllobacterium strains. Although we found no correlation between the relative abundance shift of the ASVs upon infection and the activity of the corresponding strains, we observed that the overall activity of strains isolated from the resistant cultivar was higher than that of the strains isolated from the susceptible one. ConclusionTaken together, the higher activity of the strains isolated from the resistant cultivar, along with its comparatively modest microbiome shifts upon infection suggest that the investigated resistant cultivar might harbour specific microbiota enriched in strains with efficient protective abilities against their host plants pathogens, which possibly contribute to its higher resistance against P. infestans.

Plant pathogenic fungi secrete small proteins, termed effectors, to reprogram host metabolism and suppress immune responses during infection. Although transcriptional waves of effector expression have been described in several pathosystems, the cis-regulatory elements encoding infection-stage specificity remain largely unknown. Here, we investigate the temporal regulation of effector genes in the biotrophic smut fungus Ustilago maydis, a model organism for fungal plant pathogenesis. By integrating transcriptome reanalysis with comparative promoter motif enrichment across biotrophic fungi, we identify distinct promoter motifs associated with defined infection phases. In U. maydis, three candidate cis-regulatory elements correlate with early, proliferative, and late infection stages, respectively. Positional enrichment relative to transcription start sites supports their regulatory relevance. Functional promoter mutagenesis demonstrates that the early-phase motif GTGGG significantly contributes to effector gene expression in planta and is sufficient to drive stage-restricted gene expression in synthetic minimal promoters. Collectively, our findings demonstrate that temporal deployment of the effector repertoire is at least partially encoded at the promoter level. The identified cis-regulatory elements provide a framework for dissecting transcriptional control during biotrophic infection and offer tools for infection-stage-specific gene expression in synthetic biology applications.

Australia is the largest producer of Pyrethrum (Tanacetum cinerariifolium) globally. Amongst the constraints on production are the fungal pathogens Didymella tanaceti and Stagonosporopsis tanaceti, which pose a significant threat to the industry, causing substantial yield losses. While the infection biology of S. tanaceti is well characterised, knowledge of D. tanaceti and its potential interaction with S. tanaceti on plants remains limited, hindering disease management. We developed fluorescently labelled strains of both pathogens via Agrobacterium tumefaciens-mediated transformation (ATMT). Binary vectors carrying the mNeonGreen or tdTomato fluorescent protein genes were introduced into D. tanaceti and S. tanaceti, respectively, and expression of the fluorescent proteins was confirmed by microscopy. Genome sequencing revealed single-copy T-DNA insertions in all transformants, with minor genomic rearrangements at insertion sites. Detached leaf assays demonstrated that transformed strains retained pathogenicity, producing disease symptoms indistinguishable from those of the wild type. These fluorescently labelled variants enabled detailed visualisation of D. tanaceti infection biology and its interactions with S. tanaceti, including co-infection dynamics. Co-infection assays using fluorescent strains further facilitated simultaneous visualisation and differentiation of both pathogens within host tissues. Importantly, these tools also allowed the first description of the early stages of infection by D. tanaceti in pyrethrum leaves. This study represents the first successful transformation of D. tanaceti and S. tanaceti, providing valuable resources to investigate their infection processes.

Colletotrichum sublineola (Cs) is a hemibiotrophic fungal pathogen that causes anthracnose in Sorghum bicolor, leading to significant yield losses. To enable infection, Cs secretes effectors - proteins, small RNAs, and metabolites - that damage the plant cell wall or enter the plant cell to suppress immune responses and manipulate host metabolism. Effectors can detoxify host antimicrobials, alter nutrient processing, and evade host immunity. Paradoxically, some effectors can also trigger pattern-triggered immunity (PTI), especially in biotrophic and necrotrophic fungi. More than half of fungal protein effectors lack conserved domains and functional network annotations. In this study, we identified prospective Cs effectors, separating those with non-conserved domains and classifying those with conserved domains by protein families. Comparative genomics is employed to predict effector functions and analyze their roles. Using their predicted locations and domains, we mapped the effectors into functional subsystems related to PTI. These include interactions in the apoplast, oxidative stress response, protein modification and degradation systems, and Cysteine-rich Fungus-specific Epidermal Growth Factor-like Module (CFEM) domain proteins involved in immune regulation. Our functional network analysis advances the understanding of Cs pathogenicity and offers insights into effector infection mechanisms.

Dutch elm disease (DED) has killed millions of field elms (Ulmus minor) in Britain and Europe since the 1970s, causing incalculable damage to landscapes and their associated biodiversity. While the species U. minor is highly susceptible to DED, some east Asian and Himalayan species of elm are resistant. These Asiatic species differ in their growth and form to U. minor and cannot fully substitute for it in the landscape. Several breeding programmes have attempted to generate trees that combine DED-resistance with the growth and form of U. minor via hybridisation and back-crossing. These have been partly successful, but further breeding is needed to fully realise these ambitions. Most recently in Britain, a complex resistant hybrid Wingham (FL493) was crossed with a surviving U. minor tree in Tonge Mill, Kent. Sixty progeny from this cross were tested for field resistance to DED and show segregation for this trait. Here, we analyse the genome of these progeny in order to: (1) construct a linkage map of the elm genome, and (2) identify regions of their genome derived from east Asian and Himalayan species that could be associated with DED-resistance. Such knowledge could accelerate future breeding programmes and enhance our understanding of the mechanistic basis of resistance.

Biological control using beneficial bacteria is a promising strategy for managing pea Ascochyta blight (AB), yet the underlying mechanisms remain poorly understood. In this study, we identified ten bacterial strains from four genera, including Bacillus, Paenibacillus, Peribacillus, and Pseudomonas, that significantly reduced the severity of AB caused by Didymella pinodes under greenhouse conditions. Most strains inhibited D. pinodes in vitro, suggesting antibiosis as a primary mode of action. To further elucidate the biocontrol mechanisms, we used Pseudomonas protegens Pf-5, which produces eight known antimicrobial compounds, as a model. While wild-type Pf-5 strongly inhibited D. pinodes in cultures and controlled AB in planta, a derivative ({Delta}8-fold mutant) lacking all eight compounds showed significantly compromised biocontrol efficacy. Individual complementation of biosynthetic genes for rhizoxin, 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin, or hydrogen cyanide partially restored inhibitory activity, confirming their roles in inhibition of D. pinodes. Notably, restoring rhizoxin and DAPG biosynthesis recovered the disease control capability of the {Delta}8-fold mutant in greenhouse trials. These results demonstrate that rhizoxin and DAPG are key metabolites driving the biocontrol activity of P. protegens against D. pinodes. SIGNIFICANCEAn advanced understanding of how beneficial bacteria control plant diseases can help us better use these microorganisms in agriculture. In this study, beneficial bacteria isolated from pea roots and soils effectively mitigated damages of pea Ascochyta blight caused by the fungal pathogen Didymella pinodes. Most of the identified beneficial bacteria inhibited the fungal pathogen in cultures, indicating antimicrobial compounds were likely produced by the bacteria to control the disease. Using the soil beneficial bacterium Pseudomonas protegens Pf-5 as a model, we demonstrated that four bacteria-derived antimicrobial compounds, rhizoxin and 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin, and hydrogen cyanide play important roles in inhibiting D. pinodes growth. This study also showed that rhizoxin and DAPG produced by Pf-5 contribute to the suppression of AB development. These findings provided new insights into the molecular basis of beneficial bacteria-mediated disease suppression of pea Ascochyta blight.

BackgroundThe cotton bollworm Helicoverpa armigera is a major global pest controlled by genetically engineered crops expressing Bacillus thuringiensis (Bt) toxins, including Vip3Aa. While Vip3Aa is widely deployed, the genetic basis of resistance remains poorly understood. Previous work identified disruption of a thyroglobulin-like gene (HaVipR1) as one mechanism of resistance, suggesting additional loci may be involved. ResultsUsing linkage analysis, transcriptomics, long-read sequencing, and CRISPR-Cas9 gene editing, we identify a second thyroglobulin-like gene, HaVipR2, as a novel mediator of Vip3Aa resistance. Resistance in a field-derived H. armigera line was shown to be monogenic, recessive, and autosomal, mapping to chromosome 29. Long-read sequencing revealed a [~]16 kb transposable element insertion disrupting HaVipR2, which was undetectable using standard short-read approaches. CRISPR-Cas9 knockout of HaVipR2 conferred >900-fold resistance, confirming its causal role. Comparative analyses show that HaVipR1 and HaVipR2 share conserved domain architecture, indicating that thyroglobulin-domain proteins represent a recurrent target of resistance evolution. ConclusionsOur findings establish thyroglobulin-domain proteins as a new class of Bt resistance genes in Lepidoptera and demonstrate that transposable element insertions can drive adaptive resistance while evading detection by conventional methods. These results highlight the importance of long-read sequencing and accurate genome annotation for resistance monitoring and provide new insights into the molecular basis and evolution of Vip3Aa resistance.

Botrytis cinerea is a necrotrophic fungal pathogen that infects thousands of plant species. During infection, these diverse plant hosts produce different specialized metabolites that can inhibit pathogen growth and shape pathogen fitness. However, the genetic architecture of pathogen resistance toward individual host defense metabolites remains poorly understood. To address this question, we exposed 83 B. cinerea isolates to the metabolite linalool and quantified metabolic and structural responses. Exposure revealed extensive phenotypic diversity across isolates. Genome-wide association identified 101 genes of interest associated with membrane transport and stress response regulation. Genetic associations were stronger for morphological traits than for metabolic traits, suggesting that hyphal architecture may have a complex genetic architecture contributing to linalool resistance. Together, these results establish natural variation in linalool response and provide candidate loci for understanding how generalist pathogens respond to host-derived chemical defenses. Article SummaryTo understand how a generalist pathogen responds to host defenses, we asked how Botrytis cinerea responds to linalool, a widespread monoterpene involved in plant defense. We exposed 83 B. cinerea isolates to 1000 {micro}M of linalool for 72 hours and quantified metabolic traits (growth curves and growth dynamics over time) and morphological traits (hyphal network features). Using GWA, we linked phenotypic variation to genetic variants. Results indicate substantial natural variation in linalool resistance and distinct genetic architectures across trait classes: metabolic responses are driven by a relatively small number of loci with larger effects, whereas structural/morphological responses appear more polygenic.

Cyclic diguanosine monophosphate (c-di-GMP) is a ubiquitous bacterial second messenger that regulates diverse cellular processes, including colony morphology, motility, biofilm formation, and virulence. It is synthesized by diguanylate cyclases (DGCs) containing the GGDEF domain and degraded by phosphodiesterases (PDEs) containing the EAL domain. However, studies on the genetic and physiological characteristics of c-di-GMP metabolism in Pantoea ananatis are lacking. In this study, we identified 26 predicted c-di-GMP metabolism-related genes in the P. ananatis PA13 genome: 9 encode GGDEF-only domain proteins, 5 encode dual GGDEF/EAL domain proteins, and 12 encode EAL-only domain proteins. We constructed overexpression strains and mutants of 26 DGC- and PDE-encoding genes, and then assessed their Congo Red binding, mucoid and rugose phenotypes, pellicle formation, and swimming motility. We identified 14 of 26 DGC and PDE proteins that affect phenotype changes. Among the 26 DGC- and PDE-overexpressing strains, 13 exhibited the phenotypic changes described above, with some showing alterations in multiple phenotypes simultaneously. Notably, overexpression of dgcM induced changes across all phenotypes. Among the 26 DGC and PDE mutants, the pdeC mutant increased pellicle formation and Congo red binding, the pdeM mutant reduced the mucoid phenotype, and the pdeS mutant, which shows high similarity to ydiV, an anti-FlhD factor, increased swimming motility. Overexpression strains and mutants of 14 DGC and PDE proteins that exhibited phenotypic changes had higher intracellular c-di-GMP levels than the wild type. This study provides important insight into the role of the c-di-GMP network in the plant pathogen P. ananatis. IMPORTANCEPantoea ananatis is a versatile bacterium that causes significant diseases in various economically important plants. To survive and infect hosts, bacteria use a key signaling molecule called c-di-GMP to switch between swimming freely and forming protective communities known as biofilms. Despite its importance, the specific genes governing this signaling network in P. ananatis remained unknown. In this study, we systematically identified and characterized 26 genes responsible for regulating c-di-GMP levels in P. ananatis PA13. By analyzing mutants and overexpressing these genes, we pinpointed 14 critical factors that control essential behaviors such as motility, pellicle formation, and colony appearance. Notably, we discovered specific genes, such as dgcM and pdeS, that act as master regulators of these traits. This comprehensive functional map of the c-di-GMP network provides essential insights into how this pathogen adapts to its environment, offering potential targets to control plant infections.

Plants employ cell surface receptors to recognize pathogen-associated molecular patterns (PAMPs) and activate pattern-triggered immunity, a crucial defense mechanism against invading pathogens. Pep-13 is a PAMP derived from a class of conserved cell wall transglutaminases present in Phytophthora species, and its receptor PERU was reported recently. In our parallel study, we observed distinct responses to Pep-13 between two diploid potato inbred lines: E454 recognizes Pep-13, whereas A018 does not. Genetic analysis demonstrated that Pep-13 recognition in E454 is controlled by a single genetic locus, tentatively designated TGER (Transglutaminase elicitor response). Through bulked segregant analysis sequencing, followed by complementation assays, we found that the TGERa gene in E454 is essential for Pep-13 recognition. Sequence alignment revealed that TGERa shares 99.91% amino acid sequence identity with PERU, indicating that TGERa and PERU are allelic variants of the same gene (PERU/TGERa). TGERb, a highly homologous gene of TGERa, was identified in the E454 genome; notably, TGERa, but not TGERb, can recognize Pep-13. We further demonstrated that TGERb exhibits defects in both ligand binding and association with the co-receptor StSERK3A. Additionally, we found that the TGERa allele in A018 is a weak allele with reduced expression levels, presumably resulting from a 3 kb DNA fragment insertion in its first intron. Heterologous introduction of TGERa into Nicotiana benthamiana and tomato significantly enhanced their resistance to Phytophthora infestans. Collectively, our findings confirm that PERU/TGERa functions as the Pep-13 receptor in potato and provide a valuable molecular target for improving Phytophthora resistance in plants.

Our findings confirm that CIRA15A / LEUCINE ZIPPER-EF-HAND CONTAINING TRANSMEMBRANE PROTEIN1 (LETM1) is critical for Trichoderma-induced growth biostimulation in sugar beet and the Cellulase-Induced Resistance to Alamethicin (CIRA) response in Arabidopsis. Notably, this plant homolog of a gene associated with human disease plays a vital role in both defense against Trichoderma antimicrobial peptides and the biostimulation of plant growth. We identified AtCIRA15A/LETM1 and AtCIRA15B/LETM2 as key genetic determinants of CIRA through Arabidopsis analysis and comparative studies of sugar beet inbred lines. BvLETM1 allelic variations correlated with differential biostimulation responses, and complementation confirmed functional LETM1 alleles restore CIRA in Arabidopsis mutants. These findings highlight LETM1 as a crucial factor in Trichoderma-plant interactions, with potential applications in breeding for enhanced microbial-induced plant biostimulation and agricultural productivity.

RNA interference (RNAi) shows great potential to protect crops against fungal diseases, yet reported protection efficiencies vary greatly, and our understanding of the factors responsible for this variance remains limited. In this meta-analysis, we evaluated 89 studies that compare the efficiency of host-induced gene silencing (HIGS) and spray-induced gene silencing (SIGS) in controlling fungal diseases, focusing on biotrophic, hemibiotrophic, and necrotrophic fungi, the use of formulations, and the dsRNA design as explanatory factors for differences between reported efficiency values. Our results indicate that SIGS is slightly more effective, particularly in biotrophs. Surprisingly, SIGS studies using formulations did not outperform those applying naked dsRNA. We also assessed parameters of RNA design. Differences in dsRNA length and the number of constructs, and number of targets showed no consistent significant effect on resistance in either HIGS or SIGS. Interestingly, however, HIGS studies reported significantly higher efficiency when targeting genes closer to the 3 end and SIGS when targeting genes closer to the 5 end. We discuss potential reasons for the reported patterns, such as variability in dsRNA uptake mechanisms, intercellular trafficking and Dicer processing, and conclude that more research is needed to understand the biological mechanisms determining RNAi efficiency for fungal control.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), remains a major global constraint to wheat production. Rapid pathogen evolution, exemplified by the recent breakdown of Yr15 in Europe, underscores the need to identify diverse and durable resistance loci. The A.E. Watkins landrace collection represents a globally diverse pre-breeding resource with substantial untapped variation for stripe rust resistance. In this study, 297 Watkins landraces were evaluated against six diverse Pst isolates (representing six races and three North American lineages) and subjected to genome-wide association analysis using high-density whole-genome resequencing data. Continuous phenotypic variation was observed across isolates, with several accessions displaying stable resistance across all lineages. A total of 87 QTLs were identified across all 21 wheat chromosomes. Ten loci co-localized with designated or cloned Yr genes, including Yr84, Yr85, Yrq1, Yr71, Yr60, Yr62, Yr50, Yr68, Yr34, and Lr34/Yr18/Sr57. An additional 34 loci overlapped previously reported stripe rust QTL, whereas the majority did not coincide with known loci, suggesting potential novel resistance regions. Eighteen QTLs were supported by multiple isolates, and fourteen showed supports across statistical models, indicating robust genomic signals. Several Watkins accessions carried favorable alleles that co-localized with multiple Yr-aligned loci, identifying promising donor candidates for validation and pre-breeding. Key MessageGenome-wide association mapping of 297 Watkins wheat landraces across diverse stripe rust races & genetic lineages identified 87 QTL, including 10 formally designated Yr genes and 46 novel loci, highlighting Watkins landraces as valuable pre-breeding donors for novel all-stage stripe rust resistance.

The biotrophic pathogen Puccinia triticina is the causative agent of the most vulnerable foliar disease, namely leaf rust disease of wheat. The pathogen-secreted effectors are essential in modulating fungal virulence and host immune responses. Despite their significance, potential effectors and their underlying mechanisms governing host susceptibility remain elusive. In the present study, we employed an in silico approach to identify and characterise effector proteins from the P. triticina proteome. Later, performed temporal expression profiling to prioritise effector candidates associated with rust disease. Here, a total of 273 high-confidence effector candidates were identified and analysed their physicochemical properties, domains, motifs, and functional annotations, to assess their conservation and dynamics. Although most of the effectors were uncharacterised, the conserved motif virulence-associated [YFW]xC was notably enriched in the effector repertoire. Comparative PHI-base annotation highlighted similarities with known fungal virulence factors involved in host susceptibility. Effectors harbouring CAZyme activity indicate involvement in host cell wall modification. Promoter analysis identified multiple stress- and defence-related transcription factor binding sites, suggesting regulated expression during infection. Transcriptome analysis revealed that 20 effector genes were significantly upregulated during P. triticina infection. qRT-PCR validated the expression of 4 highly induced effector transcripts following P. triticina infection in susceptible wheat variety. Specifically, two of these candidates demonstrated biphasic expression pattern that aligns contrasting PTI- and ETI-mediated defense mechanisms critical for sustained virulence. Overall, this study provides a comprehensive framework for identifying functionally relevant P. triticina effectors and offers insight for future effector-target studies and effector-based leaf rust management strategies.

Cucurbit yellow vine disease (CYVD), caused by the bacterium Serratia ureilytica, is a phloem-associated disease of cucurbits. This study characterized the spatial and temporal distribution of S. ureilytica in Cucurbita pepo cultivar Delicata plants under greenhouse conditions using a GFP-tagged isolate (P01). Seedlings were sampled weekly for four weeks. Transverse sections from the stem, petiole, leaf, shoot apex, and root were imaged by laser scanning confocal and fluorescent dissecting microscopy. In parallel, bacterial abundance in each plant tissue was assessed by quantifying colony-forming units (CFU) via droplet plating over a 4-week time course. Across plant tissues and time points, S. ureilytica fluorescent signal was primarily concentrated in the inner and outer periphery of the bicollateral vascular bundles, with higher magnification images revealing mainly symplastic localization within phloem-associated cells. Consistent with the imaging results, bacterial quantification data showed a high abundance of CFUs in the main stem across weeks, with an irregular pattern of presence in the distal tissues at later time points. These results suggest that S. ureilytica is predominantly localized within phloem-associated cells and spreads both acropetally and basipetally during infection.

O_LISalicylic acid (SA) and auxin are key regulators of plant immunity and development. The clubroot pathogen Plasmodiophora brassicae encodes PbGH3, an effector related to the GH3 family involved in phytohormone homeostasis. Although PbGH3 was proposed to conjugate auxin in vitro, its biological function in planta has remained unclear. This study aimed to determine the in vivo role of PbGH3 during host colonization. C_LIO_LIWe generated Arabidopsis thaliana and Brassica napus lines overexpressing PbGH3 and characterized their developmental phenotypes, hormone profiles, gene expression, and susceptibility to infection. Structural modeling was performed to assess PbGH3 similarity to plant GH3 proteins, and functional complementation was tested using the Arabidopsis gh3.12 mutant. C_LIO_LIThe expression of PbGH3 in Arabidopsis induced auxin-related developmental phenotypes without detectable accumulation of auxin conjugates. Instead, PbGH3 structurally and functionally resembled GH3.12/PBS3 inducing increased conjugated SA levels, reduced jasmonic acid, suppressed PIN2 expression, and increased root hair number and infection. PbGH3 complemented SA-related defects in the gh3.12 mutant. C_LIO_LIPbGH3 functions as a modulator of SA metabolism rather than an auxin-conjugating enzyme, likely competing with host GH3.12/PBS3 to constrain effective SA accumulation. This reveals a novel strategy by which P. brassicae disrupts SA-auxin homeostasis to promote host colonization and ensure disease development. C_LI PLAIN LANGUAGE SUMMARYThis study shows that the clubroot pathogen uses a protein called PbGH3 to modify the plants salicylic acid balance. This alters root traits and increases susceptibility to infection. Arabidopsis and canola plants engineered to produce PbGH3 showed similar changes, revealing that the pathogen uses this protein to disrupt hormone regulation and create conditions that support its colonization.