Plant Disease

Fusarium oxysporum Species Complex (FOSC) includes important soilborne pathogens of a range of crops worldwide. In Victoria (VIC) and New South Wales (NSW), Australia, FOSC has been identified as the cause of stunting and poor growth in processing tomato fields, resulting in significant yield losses. A total of 40 FOSC isolates were obtained from symptomatic tomato plants, irrigation water samples and culture collections, which were confirmed to be FOSC by multi-gene phylogenetic analyses based on four genomic loci: beta tubulin, calmodulin, the second largest subunit of nuclear RNA polymerase II, and translation elongation factor one-alpha. There was a high level of genetic diversity among isolates, with multiple phylogenetic lineages detected. Glasshouse bioassays demonstrated that all isolates were pathogenic to processing tomato, resulting in significant reductions in plant growth, with above ground height reduced by 11 to 26% and root dry weight by 44 to 83% compared with the control (p < 0.05). Although aggressiveness varied among isolates, growth reduction occurred irrespective of their phylogenetic placement. Moreover, the shared genetic background of isolates from irrigation water and plant samples highlights the role of irrigation water as a potential source of inoculum in Fusarium epidemics, underscoring its significance for disease management in Australian processing tomato systems.

Whitebark pine (Pinus albicaulis), a wide-ranging high-elevation conifer in western North America, is listed as threatened in the U.S. and as endangered in Canada. A major threat to whitebark pine is the non-native, invasive white pine blister rust disease, caused by the fungal pathogen Cronartium ribicola. In many pathosystems (including white pine blister rust), seedling inoculation trials are used to identify parent trees with genetic resistance. However, many of these trials use only one spore density for inoculation, and little information exists on the effectiveness of quantitative disease resistance (QDR) under varying spore densities and the corresponding implications for field performance. In this study, we examine the levels of infection and survival present within six whitebark pine seedling families previously rated for QDR (three susceptible and three resistant families) under six widely varying inoculum densities. The susceptible families showed very high infection and mortality at all inoculum densities, while performance of the resistant families varied with spore density treatment. The information gathered from the study will be useful in updating the projections of the future of whitebark pine populations under field conditions in areas of different rust hazard. The results also serve as a caution to those working in other pathosystems where seedling inoculation trials based on one spore density level are used to rate the resistance level of parent trees and their associated progeny.

Soft rot Pectobacteriaceae (SRP) are among the most economically important plant pathogenic bacteria and are especially known to be problematic in potato production. The epidemiology of disease transmission has been investigated for almost a century, and several aspects have been highlighted as plausible infection routes. However, it is generally accepted that the major source of disease is the latently infected mother tuber, but several parameters are still influencing disease prevalence including contaminated equipment, soil water status as well as temperature. Management of the disease is limited to hygiene practices, dry storage and seed certification systems but several studies have also proven biocontrol agents such as bacteriophages (phages) as promising tools. Despite the severity of SRP on potato production, little is known about the genetic diversity of SRPs in Denmark, and since only few isolates are available, the possibility to design a broadly effective phage cocktail is limited. Here we describe a three-year field study utilizing an agri-citizen science approach where Danish farmers provided symptomatic potato plants or tubers, together with metadata such as date, location, potato variety and origin. By using whole genome sequencing (Illumina and Nanopore) together with metadata we were able to investigate and monitor the epidemiological disease spread across the country using 103 complete genomes, sampled across all three years. In this study we provide epidemiological evidence of disease origins and a suite of phages that could be used as a biocontrol tool for early disease intervention. Our results revealed several clonal clades across diverse locations (SNPs < 20) which strongly indicate common origin. A total of 17 Pectobacterium phages were tested and did target > 80% of clonal clades. Based on the clonality across the soft rot isolates we propose the possibility to set in early on using phages targeting strains relevant for soft rot development, with the possibility of a surveillance program together with customizing the phage preference.

Septoria nodorum blotch (SNB) and tan spot (TS) wheat diseases are caused by necrotrophic fungal pathogens Parastagonospora nodorum (Pn) and Pyrenophora tritici-repentis (Ptr), respectively. Although recognised as premier model pathosystems for our understanding of necrotrophic effectors, no resistance mechanism has been reported in both diseases. Here, two SNB and TS resistance wheat lines ( 56:ZWB11 and 105:ZIF14) derived from the Australian national germplasm evaluation programme (CAIGE) were used to develop a double haploid mapping population. Two Pn and Ptr isolates of different pathotypes, their respective culture filtrates and effector SnTox267 were evaluated on the population. Genetic analysis of Ptr conidial inoculation of race 1 and race 2 identified a major resistance quantitative trait locus (QTL) (QTs.cur-1B) on chromosome 1B, while resistance to SNB was explained by several minor QTL. SnTox267 sensitivity was mapped to six locations (2A2, 2A3, 2B1, 2D3, 5B and 7B1) with only one QTL co-localized to known corresponding gene Snn7. Sensitivity loci 5B and 7B1 also conferred SNB resistance at seedling and adult stages. Two QTL on chromosome 2D1 and 7B2 were common in both SNB and TS, associated with disease at seedling stage and culture filtrate bioactivity, respectively. Resistance responses of 56:ZWB11 and 105:ZIF14 were confirmed cytologically, however, distinct responses were observed on wounded leaves. The defence responses were more effective against Ptr, while resistance to Pn infection was likely a combination of lack of susceptibility and effective physical barriers. Overall results demonstrated the distinction between the underlying resistance mechanisms to TS and SNB.

O_LIOver the past decade, leafhoppers (Hemiptera: Cicadellidae) have gained increasing attention as pests and vectors of phytoplasma diseases in Quebec. C_LIO_LIDrawing on historical and modern reports spanning 1868 to 2025, we investigate whether leafhopper pest status has been changing in the province, focusing on two leafhopper groups: those that overwinter in Quebec (local species) and those that do not (migratory species). C_LIO_LILocal species have been reported as pests since at least 1886 and have been considered of secondary significance. Migratory species, first mentioned in 1908, have been listed more frequently as economically important. C_LIO_LIEmpoasca fabae and Macrosteles quadrilineatus were associated with 10 crops, accounting for 11-88% of adult specimens in reported crop assemblages. On the other hand, local species, such as Erythroneura ssp. and Zonocyba (= Typhlocyba) pomaria, were reported mainly on grapevines and apples, respectively. C_LIO_LIWe found that the first field reports of leafhoppers from 1997 to 2025 are advancing in crops where migratory species are most frequently reported (e.g., potato and strawberry), whereas in crops where local species appear to predominate, no significant association was found (e.g., apple and grapevine). C_LIO_LIOur findings indicate that recent changes in leafhopper pest status in Quebec are likely due to migratory species, a group that has historically been a significant component of the leafhopper assemblage on agricultural crops. In Quebec agriculture, what was once loin des yeux, loin du cur (out of sight, out of mind) appears to be shifting toward pres des yeux, pres du cur (now visible and therefore important). C_LI GRAPHICAL ABSTRACT AND HIGHLIGHTS O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/727661v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1c58d5forg.highwire.dtl.DTLVardef@c45e02org.highwire.dtl.DTLVardef@1f801ceorg.highwire.dtl.DTLVardef@13eb7e3_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIThe pest status of leafhoppers has changed in Quebec over recent decades, but whether local or migratory species are driving this shift remains unknown. C_LIO_LILocal species have been recognized as pests since at least 1886, and migratory species since 1908. However, migratory species were more frequently reported in historical documents. C_LIO_LIMigratory species (Empoasca fabae and Macrosteles quadrilineatus) appear to be driving the recent status change, as evidenced by earlier first reports and presence across multiple crops. C_LI

Breeding disease-resistant varieties (DRV) is a central strategy for reducing reliance on phytosanitary products. However, the successful deployment and long-term durability of these cultivars rely on acquiring field data across diverse production conditions, a step that remains frequently neglected, especially in perennial crops. Since 2018, the OSCAR observatory, a network of vineyard plots planted in France with varieties resistant to downy and powdery mildew, the two major pathogens of grapevine, has aimed to close this gap for viticulture. The observatory comprises over 199 commercial plots, covering 127 hectares across diverse agroclimatic conditions, all managed by winegrowers under their own production practices. The observatory currently monitors 30 disease-resistant grapevine varieties, tracking both their agronomic performance and the dynamics of key pathogens. Since 2018, while phytosanitary treatments have been reduced by an average of 79% compared to conventional plots, the incidence of downy and powdery mildew, remain low, even in years highly conducive to these diseases. However, the long-term survey also highlights the decline in efficacy of some resistances to downy mildew and the emergence of black rot, a disease effectively controlled by conventional phytosanitary programs. Beyond acting as a rapid warning system for resistance breakdown, the observatory promotes sustainable disease management in viticulture. It provides valuable insights to winegrowers on effective DRV management. It also delivers actionable feedback to breeders to guide more durable DRV breeding strategies. Highlights- OSCAR observatory monitors 199 plots of grapevine disease resistant varieties (DRV) - Grapevine DRV cuts fungicide uses by 79% while maintaining good disease control - Some resistances efficacy declines against downy mildew, but not powdery mildew - Black rot, a disease usually controlled by fungicide, is rising in OSCAR plots OSCAR provides useful feedback to breeders and winegrowers on DRV management

Chia (Salvia hispanica L.) is an emerging crop in Bangladesh valued for its medicinal properties and economic significance. In March 2024, target spot-like symptoms were observed in an experimental chia field (24.75{degrees} N, 90.50{degrees} E) at Bangladesh Agricultural University in Mymensingh, Bangladesh with disease incidence ranging from 23% to 47% across approximately 0.25 ha. Initially appearing as brick-red spots, these symptoms developed into target-shaped concentric rings, affecting leaves, stems, and inflorescences. A total of 24 fungal isolates were recovered from infected tissue; two representative isolates (BGECh-3 and BGECh-4) were randomly selected for details characterization. Pathogen identity was established through morphological traits, multilocus phylogenetic analysis of internal transcribed spacer (ITS) and elongation factor 1-alpha (EF-1) genes sequence, and pathogenicity confirmation through Kochs postulates, collectively identifying the causal agent as Corynespora cassiicola. The isolates demonstrated a broad host range, successfully infecting brinjal, chili, bottle gourd, country bean, tomato, and soybean. In vitro fungicide sensitivity assays with seven commercial fungicides showed that both isolates were highly sensitive to Goldzim (50% carbendazim), which completely inhibited mycelial growth at 10 {micro}g mL-{superscript 1}. Conza (10% Hexaconazole) and Amister top (18.2% azoxystrobin + 11.4% difenoconazole) reduced growth by up to 85% and 67%, respectively at equal concentration. Other fungicides showed comparatively lower efficacy even at higher concentrations. This study represents the first report of target spot disease of chia caused by C. cassiicola in Bangladesh and provides insights for effective disease management strategies.

Soybean (Glycine max [L.] Merr.) productivity is frequently compromised by soil-borne pathogens. Macrophomina phaseolina (Mp), the causal agent of charcoal rot, can produce important soybean yield losses especially when hot and dry weather prevails. Integrating biological control agents with chemical seed treatments represents a promising strategy for improving disease management. This study aimed to (i) assess the in vitro compatibility of Trichoderma koningiopsis with commercial fungicide seed treatments, and (ii) evaluate the field performance of T. koningiopsis, alone or combined with compatible fungicides, across three soybean growing seasons. Compatibility assays revealed fungicide-specific effects, with Acronis(R) classified as non-fungitoxic and Topseed Extra as moderately fungitoxic. Across field seasons, Mp inoculation reduced seedling emergence, while several seed treatments improved emergence compared to the inoculated control, however, treatment effects varied markedly among years. Disease severity did not differ significantly among treatments in any season, and yield responses were strongly modified by environmental conditions rather than treatment effects. Temperature-response assays showed that T. koningiopsis exhibited optimal growth between 28 to 30{degrees}C and complete inhibition above 40{degrees}C, indicating high thermal sensitivity. The results demonstrate that T. koningiopsis can be integrated with compatible fungicides and may enhance early stand establishment under favorable conditions, but its field performance is strongly limited by high temperatures. These findings highlight the importance of environmental conditions when biological seed treatments are used.

Septoria nodorum blotch (SNB) is an economically important fungal disease of wheat caused by Parastagonospora nodorum. It is primarily controlled by the breeding of resistant wheat cultivars, but experience over the last 50 years shows that new pathogen populations soon evolve that are more virulent on the current popular cultivars. In this study, we assembled a panel of 360 P. nodorum isolates. The collection resolved into eight subpopulations. One core and seven transient populations were found possessing contrasting characters in term of spatial and temporal distribution, mating-type, effector haplotypes and patterns of intact and degraded copies of a Tc-1 mariner transposon, called Molly. Molly can proliferate and randomly insert throughout the fungal genome. Its multiplication in sexual population likely triggered RIP which partially explains the extensive genetic diversity and explains the ability to form new adapted lineages and the observed population structure of this important pathogen of wheat. When tested on wheat, the recently emerged groups exhibited greater pathogenicity on modern elite cultivars consistent with the low-amplitude boom-and-bust cycle observed previously. It is possible that active copies of Molly transpose and contribute to both the birth and death of the transient groups. This study identified and characterised a fungal specific transposable element (TE) which plays a vital role in shaping Australian P. nodorum population structure and creating extensive genetic diversity which potentially leads to better adaptation of the pathogen. The study suggests practical measures to improve the efficiency and longevity of resistance breeding for SNB.

Peacock eye disease, caused by Venturia oleaginea, is a major foliar disease of olive (Olea europaea) in Mediterranean regions, resulting in defoliation, reduced tree vigor, and yield losses. Effective disease management relies on precise fungicide timing. In this study, we validated a decision support system (DSS) named PedMan (Peacock eye disease Manager), designed to predict infection events and optimize fungicide application timing in highly susceptible olive cultivars based on rainfall and temperature conditions. The system was validated in seven independent grove experiments conducted during the 2023/24 and 2024/25 growing seasons in commercial olive orchards in Israel. In addition, simulation analyses were performed using weather data from 11 meteorological stations representing diverse climatic regions. Field validation showed that fungicide applications timed according to PedMan significantly reduced leaf abscission by approximately 60% compared with untreated controls. Applications made contrary to system recommendations did not improve disease control, confirming the reliability of both positive and negative predictions. Multi-season analyses indicated cumulative disease suppression, with up to 85% reduction in leaf abscission after three consecutive years of correctly timed applications. The system was implemented by olive growers in 2025/6 with applicable success. Simulation results showed that most infection events occurred in autumn and early winter, with rainfall as the primary driver in autumn and temperature as the main limiting factor in winter and spring. Across all regions and seasons, PedMan recommended 0-3 fungicide applications per season, comparable to or fewer than conventional spray programs. These findings demonstrate that PedMan is a robust, field-validated DSS that improves fungicide timing, enhances disease control efficiency, and supports sustainable management of peacock eye disease without increasing spray frequency under Mediterranean conditions.

Phytophthora cinnamomi, the causal agent of Phytophthora root rot (PRR), poses a persistent threat to the United States avocado industry, the top domestic producer and consumer. Avocado growers are facing clonal A2 P. cinnamomi populations challenging their current PRR control methods. In this study, we characterized 125 isolates collected from orchards in California, Florida, Hawaii, Texas, and Puerto Rico for radial growth per day, optimal growth temperature, in vitro fungicide sensitivity, and virulence on DAnjou pear fruit and UC2001 avocado seedlings. Across all isolates, optimal growth occurred most frequently at a range from 22 to 25{degrees}C; however, a subset of isolates from Hawaii, Florida, and California exhibited higher optimal growth temperatures (28{degrees}C and 30{degrees}C) suggesting thermal adaptation in warmer regions. Potassium phosphite EC50 values spanned from 4.61 to 763.13 {micro}g/ml, with significantly higher insensitivity in isolates from California and Florida, reflecting the continued overuse of this fungicide in these major production states. In contrast, baseline sensitivities to ethaboxam, mandipropamid, mefenoxam, fluopicolide, and oxathiapiprolin were uniformly high, with narrow, unimodal EC50 distributions across states. Finally, a wide range of virulence among isolates was detected using avocado seedlings and DAnjou pear fruits with isolates from California and Puerto Rico being the most virulent. Together, this data documents extensive phenotypic diversity within clonal A2 P. cinnamomi populations including heat-adapted and phosphite-insensitive lineages, establishes multi-state fungicide sensitivity baselines, and underscores the need for continued surveillance, integrated fungicide stewardship (especially phosphonates), and rootstock screening against phenotypically diverse populations to sustain avocado PRR management and ensure the United States avocado industry sustainability and profitability.

Ralstonia pseudosolanacearum (Rps) belongs to the Ralstonia solanacearum species complex (RSSC). It is a vascular pathogen that causes lethal bacterial wilt disease in many plants, including tomato and eggplant. In this study, we infiltrated tomato leaves with the phytopathogenic bacterium at 109 CFU/mL and observed the development of necrotic scars in the infiltrated area at 48 hours post-infiltration. Interestingly, this response was followed by petiole bending toward the ground of the compound leaf. This was followed by the gradual senescence of the infiltrated leaflet only. In addition, the terminal leaflet infiltrated with the pathogen exhibited epinasty. None of the above symptoms were observed in leaves infiltrated with the known virulent deficient hrpB::{Omega} mutant. Surprisingly, all of the above symptoms were observed in leaves infiltrated with another well-known virulence-deficient mutant phcA::{Omega}. It indicated that the necrotic lesion caused in tomato leaves was hrp-dependent. Infiltration in eggplant leaves caused necrotic scarring and leaf senescence, which were relatively delayed. Necrotic scarring without petiole bending or senescence in tomato leaves was also observed due to infiltration of Pseudomonas aeruginosa SPT08, a tomato endophyte having plant growth promotion activity. The patho-phenotypes such as petiole bending, epinasty, and senescence observed in the case of tomato in this study were not reported earlier. We believe these phenotypes produced in tomato after leaf infiltration may be useful to study the virulence of this pathogen.

Longitudinal data on disease susceptibility in forest trees are rare but essential for understanding host-pathogen dynamics and genetic variation in susceptibility traits. We present a long-term multisite common garden dataset quantifying susceptibility of Scots pine (Pinus sylvestris) to Dothistroma needle blight. The dataset comprises annual disease assessments collected from the same trees across 11 years, spanning 168 families and 21 Scottish provenances. This design enables partitioning of genetic and environmental sources of variation, evaluation of temporal stability in host response, and estimation of variance components and narrow-sense heritability of susceptibility. The data support analyses of phenotypic plasticity, provenance-level responses, and interactions between disease susceptibility and other adaptive traits. This resource will facilitate predictive modelling of host susceptibility under current and future environmental conditions.

Bacterial leaf blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), causes yield losses exceeding 50% in affected areas, including the Bagre rice plain in Burkina Faso. Genome-edited (GEd) rice lines have been successful in tackling BB. Modifications in the Xoo virulence protein target site upstream of three SWEET susceptibility genes in two elite rice varieties, IR64 and Ciherang-Sub1, have been demonstrated to confer broad-spectrum resistance to Asian and East African Xoo strains. Here, we evaluate the potential of the GEd lines as a solution for BB management in Burkina Faso. We challenged the GEd lines against five locally collected Burkinabe Xoo strains under controlled green-house conditions and assessed their agro-morphological performance under field conditions representative of local agroecological conditions. Greenhouse pathogen assays demonstrated that GEd IR64 and Ciherang-Sub1 lines were resistant to all tested local Xoo strains across three successive generations. We identified TalC as the primary disease-causing effector in the local Xoo populations. Irrigated field trials conducted over two seasons in the Kou Valley, Burkina Faso, revealed absence of agro-morphological penalties in GEd lines compared to their parental wild-type lines. Observed trait variation was attributable to environmental fluctuations rather than genomic modifications. Collectively, our findings demonstrate that genome editing of the rice lines does not impose growth penalties, and support the suitability of GEd IR64 and Ciherang-Sub1 for large-scale adoption in Burkina Faso, pending multi-location validation and introgression into locally adapted varieties.

Endophytic biocontrol agents may contribute to grapevine health, but their ability to establish, persist, and move within woody tissues remains poorly understood. In this study, a stem injection method was developed to introduce Pseudomonas chlororaphis M71 and Trichoderma atroviride SC1 into rooted and grafted grapevine plants, and their spatial and temporal colonization patterns were compared with the movement of a dye tracer. The dye tracer moved rapidly through xylem tissues, whereas both microorganisms showed more restricted early distribution. Over time, M71 and SC1 displayed distinct colonization patterns. M71 persisted after injection, but remained localized near the inoculation site, with limited movement toward roots or distal aerial tissues. In grafted plants, M71 recovery depended on the injection site and declined more markedly after rootstock injection than after scion injection. In contrast, SC1 showed broader and more persistent colonization. In rooted cuttings, SC1 was recovered from stem and root tissues up to 56 days post-injection, and in grafted plants it was recovered across the graft union, particularly after scion injection. Microscopy supported internal localization of both microorganisms. GFP-labelled M71 and SC1 hyphae were observed mainly within xylem vessels, and viable microorganisms were recovered from corresponding wood tissues. No contamination was observed in control plants. These results show that beneficial microorganisms can be introduced into grapevine tissues by stem injection and that bacterial and fungal biocontrol agents differ markedly in their internal movement and persistence. IMPORTANCEIntroducing beneficial microorganisms directly into plant tissues could help in establishing protective endophytic populations, but little is known about how such microorganisms move and persist inside grapevine. This study shows that stem injection can deliver Pseudomonas chlororaphis M71 and Trichoderma atroviride SC1 into grapevine tissues without visible phytotoxicity. The two microorganisms followed different colonization patterns. M71 remained mostly localized near the injection site, whereas SC1 spread more broadly and persisted in both rooted and grafted plants. These findings provide a basis for developing targeted endophytic biocontrol strategies in grapevine propagation and early plant establishment. This approach may be particularly relevant for grapevine trunk diseases and other vascular disorders, in which pathogens colonize internal woody tissues.

The fungal pathogen Zymoseptoria tritici poses a major global threat to wheat production, causing severe yield losses and necessitating intensive and costly fungicide applications. The increasing demand for durable genetic resistance has intensified interest in quantitative resistance loci, particularly those exhibiting multi-stage resistance (MSR), which suppress pathogen development continuously throughout the wheat life cycle. Many previously effective resistance genes are now showing declining efficacy, underscoring the urgent need for novel and long-lasting sources of resistance. In this study, we report the identification and genetic mapping of two quantitative resistance loci that address this need. The first locus, designated Stb23, is a major QTL on chromosome 1DS, with LOD scores exceeding 9 and explaining 6-36% of phenotypic variation at the seedling stage and 2-16% at the adult-plant stage. The second locus, designated Stb24, is a major QTL on chromosome 3DL, with LOD scores of approximately 10 and accounting for 11-30% of seedling-stage variation and 9-23% of adult-plant variation. Furthermore, two tightly linked KASP markers-snp_1D1217527 for Stb23 and snp_3D1077880 for Stb24-were developed and validated across three popular Australian bread wheat cultivars, providing practical tools for deploying these loci in breeding programs targeting improved resistance to Z. tritici. Key messageTwo significant major-effect resistance loci on chromosomes 1DS (proposed as Stb23) and 3DL (proposed as Stb24) were identified and characterized. Two tightly linked KASP markers with these loci were also discovered and validated for molecular-assisted breeding programs.

Light leaf spot (LLS), caused by subcuticular hemibiotrophic ascomycete fungus Pyrenopeziza brassicae, is a major constraint on oilseed rape (Brassica napus) production, yet the genetic and biochemical mechanisms of quantitative disease resistance (QDR) remain poorly defined. Here, disease phenotyping, pathogen quantification, microscopy, gene expression profiling and glucosinolate (GSL) analysis were integrated to dissect resistance mechanisms in B. napus. Disease assays of 19 diverse lines revealed clear contrasts between susceptible and resistant genotypes, with the commercial cultivar Ambassador showing a phenotype inconsistent with the UK Recommended List rating. Microscopy demonstrated that resistance within doubled haploid line Cubs Root does not inhibit spore germination or penetration but restricts hyphal branching and subcuticular colonisation from 4 to 8 days post-inoculation. Expression profiling of seven candidate gene expression markers (GEMs) and pathogenesis-related PR1 showed that cinnamate-4-hydroxylase, phospholipase C4, {beta}-adaptin, universal stress protein and the 40S ribosomal subunit protein S24 were strongly pathogen-induced in resistant lines, whereas a BAHD acyltransferase, a putative susceptibility factor, was induced only in susceptible cultivars. GSL profiling identified negative correlations between disease severity and total GSLs, particularly aliphatic and aromatic GSLs, with 2{square}phenylethyl and 7-methylsulfinyl heptyl GSLs showing the strongest associations with resistance. Together, these results highlight coordinated transcriptional and metabolic responses that limit pathogen proliferation and provide targets for breeding durable LLS resistance in B. napus.

Key message Characterized and unknown septoria nodorum blotch susceptibility/resistance genes were identified in contemporary U.S. hard winter wheat. The necrotrophic fungus Parastagonospora nodorum is the causal agent of septoria nodorum blotch (SNB) of wheat. To determine the prevalence of SNB sensitivity genes in a contemporary U.S. hard winter wheat (HWW), we evaluated a panel of 619 breeding lines and cultivars against five P. nodorum isolates and five necrotrophic effectors (NEs), SnToxA, SnTox1, SnTox3, SnTox267 and SnTox5, and genotyped the panel using genotyping-by-sequencing (GBS) markers and diagnostic Kompetetive-allele specific PCR (KASP) markers for the sensitivity genes Tsn1-B1, Snn1-B1, and Snn3-B1/B2. GBS analysis identified 34,357 GBS-single nucleotide polymorphism (SNP) markers. Evaluations against P. nodorum isolates showed that 40-67% of the genotypes were susceptible in the panel. Toxin infiltration assays showed that 54%, 2%, 37%, 13%, and 15% of the genotypes were sensitive to SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5, respectively. Diagnostic KASP markers for Tsn1-B1, Snn1-B1, and Snn3-B1/B2 showed prediction accuracies of 98%, 75%, and 92% for the corresponding effectors SnToxA, SnTox1, and SnTox3, respectively. Genome-wide association studies (GWAS) not only confirmed the presence of the previously characterized sensitivity genes Tsn1-B1, Snn1-B1, Snn2, Snn3-B1/B2, and Snn5-B1, but also identified new loci to be associated with responses to P. nodorum isolates and NEs. Of which, Qsnb.osu-2AS on chromosome 2AS was associated with responses to all five isolates. We developed KASP markers KASP_S4B_643615365, KASP_ S2D_16184991, and KASP_S2A_9833162 linked to Snn5-B1, Snn2, and Qsnb.osu-2AS, respectively. These findings should guide breeding for SNB resistance in hard winter wheat.

Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), one of the most destructive diseases of wheat worldwide. Although the Z. tritici genome encodes hundreds of predicted effector proteins, functional characterization through the use of genome-editing techniques has been limited due to low homologous recombination efficiency and extensive effector redundancy. In this study, we established and evaluated a CRISPR/Cas9-based genome editing procedure for targeted effector gene disruption in Z. tritici using in vitro-assembled Cas9-sgRNA ribonucleoprotein (RNP) complexes combined with short (60 bp) homologous donor DNA flanks. Using this approach, we successfully generated knockout mutants for a selected candidate effector gene, the Hce2 domain-containing effector Mycgr3107904. Virulence assays on the susceptible wheat cultivar Taichung 29 revealed that two independent{Delta} Mycgr3107904 mutants exhibited a pronounced delay in symptom development compared to the wild-type strain IPO323, with disease onset and progression delayed by approximately 4-5 days. While mutant strains ultimately followed a similar disease trajectory, wild-type-infected leaves displayed extensive necrosis and pycnidia formation at earlier time points, indicating a significant reduction in virulence upon loss of Mycgr3107904. Together, our results demonstrate the feasibility of CRISPR/Cas9-mediated effector gene knockout in Z. tritici and provide functional evidence that Mycgr3107904 contributes to timely disease progression. This work advances genome editing tools for Z. tritici and facilitates systematic dissection of effector functions underlying fungal virulence.

Citrus yellow vein clearing virus (CYVCV) is the causal agent of an emerging disease representing a potentially high-impact threat for citrus production. Despite remaining outside Europe for decades, CYVCV has now expanded towards two important European citrus producers, Italy and, more recently, Spain. The presence of this virus in the EPPO region represents a current threat with unpredictable and potentially devastating consequences for European citriculture. Therefore, urgent protective measures need to be taken to prevent CYVCV spread and minimize its impact. Diagnostics is a key measure in the management of viral diseases, highlighting the need for harmonized methods suitable for reliable routine detection of the currently known CYVCV diversity. In this study, an inclusive, efficient and highly sensitive real-time RT-qPCR for the detection of CYVCV in plant material and transmission vectors has been developed and validated according to EPPO standards. Moreover, the validated method has been successfully adapted to both PCR digital platforms, that allow high-sensitive absolute quantitative detection, essential in the diagnostics at low viral concentrations; and PCR portable tools, that can be applied in a real diagnostic context for on-site detection. This versatility combines standard validated performance, absolute sensitive quantitation and real on-site detection. The study has also addressed sampling strategies to support reliable molecular diagnostic performance. Our results represent an improvement in the detection of CYVCV to be applied in epidemiological studies and different real diagnostic contexts for the containment of this important citrus pathogen.