Under changing climate, plants need combined ability to cope with co‐occurring biotic/abiotic stresses. Understanding simultaneous plant responses to multiple stresses offers unique insights towards developing effective strategies to mitigate effects of such stresses in plants. qRT‐PCR was used to determine and compare relative gene expression ratios (RGER) of three disease resistance related genes, CHs, GAP, PAL, and three abiotic stress related genes, RPK, HSP, TrVSP, across seven time durations in relation to infection by the root pathogen Pythium irregulare under three temperature regimes in three Trifolium subterraneum varieties of varying resistance. Temperature and genotype drove biotic and abiotic stress related gene expression in Pythium‐infected plants. RGER of tested genes and their relationships differed across varieties, temperatures and infection duration (ID). For example, RGER most upregulated were CHs then PAL and RPK at 25°C and detected by 2hr ID, while that of GAP, HSP and TrV were detected by 6hr ID at all temperatures. These are the first studies to report expression of defence related genes in relation to either biotic or abiotic stress in subterranean clover. The current study not only demonstrated how RGER of tested genes and their relationships differed across varieties, temperatures and ID, but also highlight as yet unexploited opportunities to together utilize these biotic/abiotic‐related genes to develop new varieties with combined biotic/abiotic stress resistances in forage legumes that are suitable for changing climate scenarios. Examples could include RGER of PAL to identify ‘temperature‐stable’ disease‐resistant varieties, and RGER of RPK to eliminate susceptible and temperature‐sensitive genotypes.

Canada is one of the largest wheat producers in the world, and wheat is grown over an area spanning most of the southern latitudes, with the prairie region (provinces of Saskatchewan, Alberta, and Manitoba) being the main producer. Several pathogens and pests attack wheat, but at present Fusarium head blight, stripe rust and leaf spots are the most damaging diseases to wheat production in Canada. Historically, smuts, stem rust and leaf rust caused major crop losses in Canada and can still pose serious threat if management practices are relaxed. Cropping practices used by Canadian farmers to grow and harvest wheat over the last century have influenced disease development and pathogen biology, affecting the severity, incidence, and prevalence of crop diseases over time. Changes such as reduced tillage coincide with emergence of residue born diseases, such as Fusarium head blight and leaf spots, while the deployment of resistant cultivars and increased fungicide use has resulted in the reduction of common bunt, stem and leaf rust. This mini‐review will discuss the influence of long term cropping practices, alone or in combination, on the biology, emergence, and prevalence of wheat diseases in Canada over the last century.

Soybean rust (SBR), caused by Phakopsora pachyrhizi, is the most important yield damaging fungal disease of soybean due to severe reduction in healthy leaf area and acceleration of leaf fall. In experimental research, SBR severity is estimated visually aided/trained by a standard area diagram (SAD) developed and validated during the mid‐2000s (Old SAD). In this study, we propose a new SAD for SBR with five true‐colour diagrams following linear increments (~15% increments) amended with three diagrams at low (< 10%) severities (0.2, 3, 5, 10, 25, 40, 55, 70 and 84%). For evaluation, 37 raters were split into two groups. Each assessed severity in a 50‐image sample (0.25 to 84%), firstly unaided and then using either the Old SAD or the New SAD. Accuracy, precision and reliability of estimates improved significantly relative to unaided estimates only when aided by the New SAD (accuracy > 0.95). Low precision (< 0.78) and trend of underestimation with the increase in severity were the main issues with the Old SAD, which did not differ from unaided estimates. Simulation to evaluate the impact of the errors by different methods on hypothesis tests, the new SAD was more powerful to detect the smallest difference in mean control (e.g. 70% vs. 65% disease reduction) than the Old SAD; the latter required a 2‐fold increase in sample size to achieve the same power. There is a need to improve some SADs taking advantage of new knowledge and technology to increase accuracy of the estimates and optimize both resource use efficiency and management decisions.

Citrus greasy spot (CGS), caused by Zasmidium citri, induces premature defoliation and yield loss in Citrus spp. The epidemiology of CGS is well understood in high humidity areas, but remains unaddressed in Brazil, despite differing climatic conditions and disease management practices. The spatiotemporal dynamics of CGS was characterized in the Recôncavo of Bahia (Brazil) at four hierarchical levels (quadrant, plant, grove and region). A survey conducted in 19 municipalities found the disease to be present throughout the region with an incidence of 100% in groves and plants, and higher than 70% on leaves. Index of dispersion (D) values suggest the spatial pattern of symptomatic units lies between random and regular. This was confirmed by the parameters of the binary power law for plants and their quadrants (log(A)<0 and b < 1). No consistent differences were observed in the disease incidence at different plant heights. We introduce a compartmental model synthesizing CGS epidemiology. The collected data allow such a model to be parameterised, albeit with some ambiguity over the proportion of new infections that result from inoculum produced within the grove vs. external sources of infection. By extending the model to include two populations of growers – those who control and those who do not – coupled by the airborne inoculum, we investigate likely performance of cultural controls accessible to citrus growers in Northeastern Brazil. The results show that control via removal of fallen leaves can be very effective. However, successful control is likely to require area‐wide strategies, in which a large proportion of growers actively manage disease.

Root‐lesion nematodes of the genus Pratylenchus are migratory endoparasites with worldwide economic impact on several important crops including potato, where certain species like P. penetrans, P. neglectus and P. scribneri reduce the yield and quality of potato tubers. Morphological identification of Pratylenchus spp. is challenging, and recent advancements in molecular techniques provide robust and rapid diagnostics to differentiate species without need of specialist skills. However, the fact that molecular diagnostics are not available for all Pratylenchus species means that there are limitations in worldwide application. In general, root‐lesion nematodes are difficult to manage once introduced into agricultural land and damage can be related to pathogenicity and population densities. In addition, root‐lesion nematodes interact with fungi such as V. dahliae, resulting in disease complexes that enhance the damage inflicted on the potato crop. Management interventions are often focused on limiting nematode reproduction before planting crops and include the application of nematicides, and cultural practices such as crop rotation, cover crops, biofumigation, and biological control. Understanding the limitations of the available crop protection strategies is important and there are many gaps for further study. This review discusses the status of the diagnosis, distribution, pathogenicity and management of the main species of root‐lesion nematodes, reported to infect potatoes worldwide, and highlights areas for potential future research.

Myrtle rust (Austropuccinia psidii) is an invasive species causing damage to Myrtaceae species in natural and managed ecosystems in many countries. To better understand myrtle rust epidemiology we studied latent period (LP) and ontogenic resistance in relation to temperature on three susceptible hosts (Metrosideros excelsa, hybrid Lophomyrtus bullata x L. obcordata and Syzygium jambos). The latent period curve was U‐shaped, with latent development > 0 from between 8 and 10°C, depending on the host, to 30°C. Optimum range was 22 to 28°C with minimum LP of 5 to 7 days. Peak spore production occurred over about two weeks, starting about one week after the LP ended. Some spore production continued for one to two months. Comparison of the LP data with field temperatures indicated that the uredinial stage of A. psidii can overwinter in the latent phase in temperate areas of New Zealand and southern Australia and, therefore, re‐infection via the uredinial or telial stages is not required during winter. The LP information was used to correct the LP function in a New Zealand myrtle rust climatic risk model. The transition of emergent leaf and stem tissues in susceptible Myrtaceae genotypes from susceptible to immune (ontogenic resistance) was characterised in terms of uredinium density and LP. Onset of ontogenic resistance was closely linked to the degree of leaf expansion, with fully expanded leaves being immune to infection. Because ontogenic resistance restricts infection to periods when growth flushes occur, understanding it is crucial for explaining the seasonality of myrtle rust development in the natural environment.

The objective of this study was to evaluate the potential role of gramineous weeds present near paddy fields as alternative hosts for the Fusarium graminearum species complex (FGSC) that causes Fusarium head blight (FHB) in rice. 142 weed samples were collected from 10 gramineous weed species near paddy fields from August to October 2018 in Jiangsu Province, China. Of the 145 isolates of seven Fusarium species isolated from the weed samples, F. asiaticum was the most abundant (86.9%), followed by F. fujikuroi (5.5%), F. proliferatum (2.8%), F. graminearum (2.1%), F. tricinctum (1.4%), F. acuminatum (0.7%), and F. sporotrichioides (0.7%). Genotype and mycotoxin analyses confirmed that 72.2% of F. asiaticum isolates were deoxynivalenol (DON) with 3‐acetyldeoxynivalenol (3ADON) producers, and the remainder were nivalenol (NIV) producers. Pathogenicity assays showed that both 3ADON and NIV chemotypes of F. asiaticum could cause FHB in rice, but NIV chemotypes were significantly (P < 0.05) more aggressive than 3ADON chemotypes. Three Fusarium mycotoxins, DON, NIV and zearalenone, occurred naturally at low concentrations in the weed samples. Taken together, this study provides insight into the mycotoxin production and aggressiveness of F. asiaticum isolates from gramineous weeds in China.

Glomerella leaf spot (GLS), characterized by black necrotic spots and severe defoliation, is a destructive foliar disease of apple. Widely grown cultivars such as ‘Gala’ and ‘Golden Delicious’ are highly susceptible to GLS. Currently, the infection biology of this pathogen on apple leaves is unclear. In the present study, the penetration and colonization process of Colletotrichum fructicola were characterized on apple (cv. Gala) leaves using light and transmission electron microscopy. C. fructicola conidia produced germ tubes 4 hours post inoculation (hpi) and appressoria at 8 hpi. In melanized appressoria, appressorial cones, funnel‐shaped structures formed around the penetration pore. At 12 hpi, C. fructicola produced secondary conidia. After penetration, C. fructicola began to develop infection vesicles at 36 hpi. At 48 hpi, the primary hyphae of C. fructicola were produced from infection vesicles within host epidermal cells; the host epidermal cell plasma membrane remained intact, indicating a biotrophic association. Subsequently, secondary hyphae penetrated epidermal cells and destroyed cell components, initiating necrotrophic colonization. C. fructicola also produced biotrophic subcuticular infection vesicles and hyphae. Together, these results demonstrate that C. fructicola forms special infection structures and colonizes apple leaves in a hemibiotrophic manner involving intracellular as well as subcuticular colonization strategies. Detailed characterization of the infection process of C. fructicola on apple leaves will assist in development of disease management strategies and provide a foundation for studies of the molecular mechanism of C. fructicola‐apple leaf interaction.

From 1988 to July 2019 more than 100 review articles were published, including opinion papers and book chapters, that focused on potential climate change effects on plant pathogens and the future crop disease risks. Therefore, an overview of them is presented herein, particularly helpful for beginners and non‐experts in climate change biology research. Specifically, this overview contributes to a faster and more convenient identification of appropriate review articles, for example, related to a certain crop, pathogen, plant disease or country of interest. However, not all important crops, pathogens, diseases and countries are considered specifically and in‐depth in any of these review articles, suggesting that there are still research gaps prevalent, which are also highlighted herein. Nevertheless, the overview suggests that researchers are increasingly busy and successful in summarizing the fragmented information spread throughout the international literature. Consequently, they are providing ‘step‐by‐step’ a comprehensive, in‐depth, and continuously updated knowledge platform on potential climate change effects on plant pathogens and the respective crop disease risks in the future, although some aspects will, by nature, be repeated.

Phaeomoniella chlamydospora and wood‐rotting basidiomycete fungi, namely Fomitiporia spp., are known esca pathogens. However, the effect of their mixed infections and the sequence of infection on disease development is unclear. To determine the effects of single and co‐inoculations on symptoms, potted Vitis vinifera ‘Crimson Seedless’ was inoculated with P. chlamydospora either alone or in combination with one of four basidiomycetes: Coprinellus radians, Fomitiporia langloisii, F. polymorpha and the novel species Tropicoporus texanus. Basidiomycetes were isolated from vines with foliar symptoms of esca in California and Texas. In sequential co‐inoculations, the effects of different sequences of infection (P. chlamydospora first, basidiomycete 6 months later; and vice versa) were tested, compared to simultaneous co‐inoculations. Plants inoculated with P. chlamydospora either alone or in combination with a basidiomycete (in any sequence) did not differ significantly in the length of black‐streaking lesions. In plants inoculated only with a basidiomycete, the appearance of large brown lesions, coupled with the absence of this wood symptom from control plants, suggests that C. radians, F. langloisii and T. texanus are pathogenic. Foliar symptoms resembling those of esca in the field (marginal and/or interveinal scorching, combined with red and/or yellow discoloration) were statistically more frequent among plants inoculated with F. polymorpha or T. texanus, either simultaneously or following P. chlamydospora, compared to single inoculations. Sequential co‐inoculations of a basidiomycete before or after P. chlamydospora were associated with similar lesion lengths, suggesting that basidiomycetes may not require infection by P. chlamydospora in order to extensively colonize the wood.

Rice blast, caused by the fungus Magnaporthe oryzae, can result in notable yield losses in rice production. The objective of this study was to investigate the potential of a rice endophytic isolate, Streptomyces albidoflavus OsiLf‐2, on the control of rice blast and the possible mechanisms involved. In vitro assays displayed a variety of antagonistic effects of OsiLf‐2 against different physiological races of M. oryzae, with peak mycelial growth inhibition ranging from 74.1% to 83.0%. In vivo tests of OsiLf‐2 showed 18.0% and 19.6% reduction in disease index in greenhouse and field conditions, respectively. The stable active metabolites in its cell‐free culture filtrate inhibited the mycelial growth, spore germination and appressorial formation of M. oryzae in a dose‐dependent manner. They also possessed strong antifungal capacities toward various phytopathogens in vitro. OsiLf‐2 secreted multiple antimicrobial compounds, cell wall degradation enzymes, siderophore, plant hormones, and 1‐aminocyclopropane‐1‐carboxylate deaminase, which might function in direct or indirect resistance to M. oryzae. In addition, a variety of defence responses were induced in OsiLf‐2‐treated rice, including hydrogen peroxide (H2O2) accumulation, callose deposition, defence‐related enzymes activation, and elevated expression of salicylic acid (SA) and jasmonic acid (JA) pathways genes, which might contribute in resisting pathogen attack. The significant biological control activity and host defence‐stimulation ability of OsiLf‐2 suggest that this endophytic actinobacterial strain could be a promising candidate in the management of rice blast disease.

The application of disinfectants through drip irrigation could be a feasible practice against verticillium wilt (Verticillium dahliae) of olive. OX‐VIRIN (activated peroxide) and OX‐AGUA AL25 (quaternary ammonium compounds) are two disinfectants that have shown efficacy against V. dahliae in irrigation water and potential for reducing the disease in young olive plants. In this work, various post‐planting application strategies incorporating OX‐VIRIN (once a month, or twice a month on alternate or successive weeks) or OX‐AGUA AL25 (once a month, or twice a month on alternate weeks) were assessed for their effect on V. dahliae in soil, disease in olive trees, and olive yield, in a 2‐year pot‐experiment under natural environmental conditions. The disinfectants were injected via metering pumps into a drip irrigation system that irrigated olive trees planted in V. dahliae‐inoculated soil. All the application strategies significantly reduced the total inoculum density in soil compared to controls with no disinfectants and noninoculated soil. The microsclerotia density was also significantly reduced in disinfested soils by 73.6–86.8%, depending on the strategy. The symptoms and infection incidence were always lower in treatments subjected to disinfestation. The treatment with OX‐AGUA AL25 applied twice a month on alternate weeks most reduced the symptoms (by 53.0%) and colonization index (by 70.8%) with respect to untreated water control. This soil disinfestation also significantly strengthened the symptom remission. Tree growth and production were negatively affected by soil inoculation (reduced by 45.6% and 88.7%, respectively), but not so by disinfectants, which even relieved the reduction in inoculated soils, especially when OX‐AGUA AL25 was applied.

Alternative hosts of Spongospora subterranea may allow multiplication and survival of the pathogen over time; thus, host range is important from an epidemiological aspect. Weeds and rotational crops, such as wheat and barley, were sampled from potato fields with a history of powdery scab (PS) and examined for the presence of S. subterranea by root staining followed by microscopic observations and by qPCR analysis after DNA extraction. The pathogen was detected in plants of 16 weed species from eight families and in volunteer plants of potato and wheat. The ability of the pathogen to infect weeds and rotational crops was further examined by artificial inoculations with sporosori in pot experiments. Successful inoculations occurred with 13 weed species from eight families and with 12 rotational crops from five families. The findings of this study indicate a wide host range in Israel; the families Malvaceae and Zygophyllaceae and the following species are reported for the first time as S. subterranea hosts: Solanum elaeagnifolium, Triticum aestivum, Cynodon dactylon, Phalaris paradoxa, Phalaris minor, Setaria verticillata, Rostaria cristata, Sinapis nigra, Arachis hypogaea, Medicago sativa, Astragalus hauraensis, Amaranthus albus, Chenopodium murale, Chenopodium opulifolium, Salsola soda, Malva nicaeensis, Chrysanthemum segetum, Verbesina encelioides, Ammi majus and Tribulus terrestris. Controlling weeds and avoiding the relevant rotational crops observed to be S. subterranea‐positive and thus potential hosts, should be taken into consideration in the management of PS, to reduce pathogen inoculum build‐up.

Plum pox virus (PPV) strain D is globally distributed and causes serious losses in stone fruits in over 40 countries. Here, full‐length genomic sequences were analysed for 44 PPV‐D isolates from all regions of Turkey, together with partial sequences for a larger number of isolates. PPV‐D isolates from Turkey are similar to other PPV‐D isolates in all major genomic features. However, the majority of Turkish PPV‐D isolates form separate phylogenetic clusters from all other isolates and show a geographical clustering tendency, suggestive of limited movement between regions. In particular, PPV‐D isolates from Thrace and Central Anatolia formed a monophyletic sister cluster to the cluster that includes all previously known PPV‐D isolates. Two isolates with strong evidence of recombination with the PPV‐T strain were identified, together with two isolates with weaker evidence for intra‐D strain recombination. The genetic diversity of PPV‐D was found to be particularly high in Turkey (0.017 ± 0.001%), close to that observed for PPV‐D world diversity once the over‐represented isolates from Japan, the USA and Canada have been excluded (0.020 ± 0.001%). Taken together, these results suggest a long and largely isolated evolutionary history of PPV‐D in Turkey and further extend knowledge of the diversity of this highly successful strain. The high diversity of PPV‐D in Turkey, together with the basal phylogenetic position of Turkish isolates, are compatible with a hypothesis making Turkey the centre of origin of the D strain.

In Argentina, infections by alfalfa dwarf virus (ADV) affect the cultivation of alfalfa, which is globally one of the most important forage plants. The main objective of this study was to improve current understanding of the underlying mechanisms related to the dwarfism phenotype developed during viral infection. Hydrogen peroxide production, callose deposition and PR5 gene expression levels were evaluated to determine if ADV induces plant defence responses. At the morphological level, higher epicuticular wax production and an increase in proliferation of cells from the fundamental parenchyma were observed when plants were infected by ADV. Infected plants had reduced photosynthesis, stomatal conductance and transpiration/evaporation rate, but interestingly the production of chlorophylls was induced. Finally, using transcriptional analysis, ADV was observed to negatively affect the expression of genes related to synthesis of auxins, cytokinins and brassinosteroids. These results suggest that ADV infection induces a hormonal imbalance leading to an increase in chlorophyll pigment synthesis, stomatal closure and generation of tissue deformation. Overall, the results show a morphological, physiological and photosynthetic characterization of dwarf plants affected by ADV.

Dieback and wilt caused by Erwinia psidii is an emerging disease that has been causing considerable damage in eucalypt plantations. Because it is a recently emerged disease, several aspects of the bacterium interaction with its host still remain to be elucidated. In this work, we studied the E. psidii colonization and biofilm formation in eucalypt tissues by specific detection using the polymerase chain reaction (PCR) and scanning electron microscopy (SEM). The results indicate that the bacterium is able to translocate in stem tissue mainly acropetally, although movement to a lesser extent in the basipetal direction was also observed, always through the xylem. No colonization of phloem tissues was observed. In addition to colonizing the xylem, E. psidii colonized the parenchymatous tissue. The bacterium formed cell aggregates enveloped by fibrillar material that evolved into complex, well‐structured biofilms in stem and leave tissues. In contrast, no biofilm formation was observed on abiotic surfaces. These observations suggest that biofilm formation plays an important role in the elicitation of dieback and wilt symptoms caused by E. psidii on eucalypt plants. This study not only shows ultrastructural aspects of the E. psidii communities but also tissue damage in eucalypt plants that was associated with the presence of bacterial aggregates and tyloses formation.

Maize lethal necrosis (MLN) is emergent in East Africa, first reported in 2011 in Kenya, and is devastating to maize production in the region. MLN is caused by co‐infection of maize with the emergent maize chlorotic mottle virus (MCMV) and any of several maize‐infecting potyviruses endemic in East Africa and worldwide. Here, we examine the distribution of MCMV and sugarcane mosaic virus (SCMV), the major viruses contributing to MLN in Rwanda. These and other viruses in maize across Rwanda were further characterized by deep sequencing. When identified, MCMV had high titers and minimal sequence variability, whereas SCMV showed moderate titers and high sequence variability. Deep sequencing also identified maize streak virus and other maize‐associated viruses, including a previously described polerovirus, maize yellow mosaic virus; barley yellow dwarf virus; diverse maize‐associated totiviruses; maize‐associated pteridovirus; Zea mays chrysovirus 1; and a maize‐associated betaflexivirus. Detection of each virus was confirmed in maize samples by reverse transcription polymerase chain reaction.

Kauri (Agathis australis), which is one of the world's largest and longest‐living conifer species, is under threat from a root and collar dieback disease caused by the oomycete pathogen Phytophthora agathidicida. The noted incidence of kauri dieback has increased in the past decade, and even trees >1000 years old are not immune. This disease has profound effects on both forest ecosystems and human society, particularly indigenous Māori, for whom kauri is a taonga or treasure of immense significance. This review brings together existing scientific knowledge about the pathogen and the devastating disease it causes, as well as highlighting important knowledge gaps and potential approaches for disease management. The life cycle of P. agathidicida is similar to those of other soilborne Phytophthora pathogens, with roles for vegetative hyphae, zoospores and oospores in the disease. However, there is comparatively little known about many aspects of the biology of P. agathidicida, such as its host range and disease latency, or about the impact on the disease of abiotic and biotic factors such as soil health and co‐occurring Phytophthora species. This review discusses current and emerging tools and strategies for surveillance, diagnostics and management, including a consideration of genomic resources, and the role these play in understanding the pathogen and how it causes this deadly disease. Key aspects of indigenous Māori knowledge, which include rich ecological and historical knowledge of kauri forests and a holistic approach to forest health, are highlighted.

Myrtle rust (caused by Austropuccinia psidii) affects more than 500 known host species in the Myrtaceae family. Three different modelling approaches (CLIMEX, MaxEnt and Multi‐Model Framework) were used to project the habitat suitability for myrtle rust at both global and local scales. Current data on the global occurrence of myrtle rust were collected from online literature and expert solicitation. Long‐term averages of climate data (1960–1990) were sourced from WorldClim and CliMond websites. Recent reports of myrtle rust in New Zealand were used for validation of model outputs but not in model training and testing. The model outputs were combined into a consensus model to identify localities projected to be suitable for myrtle rust according to two or three models (hotspots). In addition to the locations where the pathogen is currently present, all models successfully projected independent occurrence data in New Zealand suitable for establishment of the pathogen. Climate suitability for the pathogen was primarily related to temperature followed by rainfall in MaxEnt and the CLIMEX model. The results confirmed the optimum temperature range of this pathogen in the literature (15–25 °C). Additional analysis of the precipitation variables indicated that excessive rain (more than 2000 mm in warmest quarter of the year) combined with high temperatures (>30 °C) constrain pathogen establishment. The results of the current study can be useful for countries such as New Zealand, China, South Africa and Singapore where the pathogen has not fully spread or established.

The Eucalyptus stem canker pathogens Teratosphaeria gauchensis and T. zuluensis (Capnodiales, Teratosphaeriaceae) are found in many tropical regions of the world where their hosts are cultivated for plantation forestry. Population genetic analyses have suggested that some populations undergo recombination, even though their sexual states have never been observed. Against this background, the aim of this study was to characterize the mating type (MAT) locus of these species and thus to better understand the basis of their diversity. Known Mycosphaerellaceae MAT genes were used to identify and investigate the MAT locus in the T. gauchensis and T. zuluensis genomes. Both species were found to be heterothallic and primers were designed to amplify the opposite MAT idiomorphs as well as conserved regions within the MAT1‐1‐1 and MAT1‐2‐1 genes. Each Teratosphaeria MAT idiomorph was defined by either the MAT1‐1‐1 or the MAT1‐2‐1 gene, and an idiomorph‐specific hypothetical protein (MAT1‐1‐10 and MAT1‐2‐12). Populations of T. zuluensis from Asia and southern Africa were dominated by a single mating type, whereas the proportions of the different idiomorphs for T. gauchensis in South America and southern Africa were similar. There was no physical evidence of sexual reproduction for either species and it is argued that although recombination may be possible, it is unlikely to form an important part of their life cycles in diseased Eucalyptus plantations. Instead, continuous human‐mediated multiple introductions of these species have probably resulted in the current genetic structure of their populations, which holds risk for future disease outbreaks and interspecific hybridization.

Phyllosticta cavendishii has been recorded in the Northern Territory (NT) of Australia occurring on non‐Cavendish bananas since 1991. The race of P. cavendishii that infects Cavendish bananas is considered exotic to Australia and classified as an emergency plant pest. In July 2013, P. cavendishii was detected on Cavendish bananas near Darwin, NT. Here, the diagnoses and field observations carried out during the Incident Definition Phase of the national biosecurity response, from July 2013 to October 2014, are reported. Of 1395 banana samples collected from 676 properties, 480 were positive for freckle disease, including 463 samples with P. cavendishii and 17 samples with P. maculata. Phyllosticta cavendishii was detected in 256 properties, including 62 properties where it was detected on Cavendish banana plants, within six distinct geographical zones across the NT. Phyllosticta cavendishii was detected on two cultivars within the Cavendish subgroup and six non‐Cavendish cultivars. Multigene characterization of Phyllosticta cultures showed that P. cavendishii was isolated from both Cavendish and non‐Cavendish cultivars. Multilocus phylogeny analyses also revealed that the P. cavendishii strain in the outbreak had identical sequence similarity to the holotype (CBS H‐20918) clade 2 P. cavendishii isolates that infect both Cavendish and non‐Cavendish cultivars in Southeast Asia and Oceania. The genetic data in this study showed that there was one P. cavendishii strain infecting both Cavendish and non‐Cavendish cultivars in the outbreak. However, historical data and field observations provided anecdotal evidence for the existence of two races of P. cavendishii, including one that does not infect Cavendish bananas.

Sigatoka leaf diseases are a major constraint to banana production. A survey was conducted in Tanzania and Uganda to assess the distribution of Pseudocercospora species and severity of Sigatoka leaf diseases. Pseudocercospora species were identified using species‐specific primers. Sigatoka‐like leaf diseases were observed in all farms and on all cultivars, but disease severity varied significantly (P < 0.001) between countries, districts/regions within countries, altitudinal ranges and banana cultivars. In all regions except Kilimanjaro, P. fijiensis, the causal agent of black Sigatoka, was the only pathogen associated with Sigatoka disease. Mycosphaerella musae was associated with Sigatoka‐like symptoms in Kilimanjaro region. Black Sigatoka disease was more severe in Uganda, with a mean disease severity index (DSI) of 37.5%, than in Tanzania (DSI = 19.9%). In Uganda, black Sigatoka disease was equally severe in Luwero district (mean DSI = 40.4%) and Mbarara district (mean DSI = 37.9%). In Tanzania, black Sigatoka was most severe in Kagera region (mean DSI = 29.2%) and least in Mbeya region (mean DSI = 11.5%). Pseudocercospora fijiensis, the most devastating sigatoka pathogen, was detected at altitudes of up to 1877 m a.s.l. This range expansion of P. fijiensis, previously confined to altitudes lower than 1350 m a.s.l. in East Africa, is of concern, especially for smallholder banana farmers growing the susceptible East African Highland bananas (EAHB). Among the banana varieties sampled, the EAHB, FHIA hybrids and Mchare were the most susceptible. Here, the loss of resistance in Yangambi KM5, a banana variety previously resistant to P. fijiensis, is reported for the first time.

Apple is a seasonal product that is stored for long periods of time, during which fungal‐caused decay can occur. Previous infection experiments of intact Jonagored apple with Botrytis cinerea displayed apparent differences in lesion expansion rate with respect to inoculation position on the fruit (on, above or below the equator). The goal of this study was to investigate whether these differences are consistent or not and if so, to relate them to fruit characteristics. The study involved measuring the hue angle of the intended inoculation spots prior to inoculation, and firmness and total soluble solids content of fruit from the same batch. Results showed that firmness correlated somewhat (−0.55 and −0.72 for shadow and sun side, respectively) with lesion diameter expansion rate. In a subsequent step, X‐ray imaging was carried out for samples from each position. Analysis of 3D reconstructions by microcomputed tomography of these diffraction images showed that cell size was strongly correlated (0.996) to lesion diameter expansion rate. Finally, it was investigated if cell size could also be used to rank different apple cultivars for their susceptibility to B. cinerea. The result shows that there is a clear distinction between Jonagold and Golden Delicious (non‐blushing variety), which have a smaller cell size, and Braeburn and Kanzi, which have a larger cell size (overall correlation of 0.87). This indicates that cell size may also be an important factor in determining susceptibility across cultivars.

Demethylation inhibitor (DMI) fungicides are used to control brown rot in stone fruit worldwide. However, their specific mode of action can select resistant isolates of Monilinia fructicola. Monilinia fructicola resistant to DMI fungicides are associated with a fitness cost in the absence of selective pressure, indicating that the sensitive population can be re‐established when discontinuing the fungicide in the field. This work aimed to build up the sensitive population of M. fructicola after discontinuing the use of tebuconazole for successive crop seasons. The sensitivity of M. fructicola to tebuconazole was assessed in four commercial peach orchards in Paraná and São Paulo States from 2012/13 to 2015/16. Different fungicide programmes were used and DMI fungicides were discontinued from 2013/14. The sensitivity of M. fructicola to tebuconazole was assessed by a mycelial growth assay in vitro and by determining the frequency of the G461S mutation in the MfCYP51 gene. The isolates from Paraná had high sensitivity to the fungicide across all seasons and the frequency of the G461S mutation remained below 5%. The isolates from São Paulo were highly resistant in the 2012/13 season; however, there was a gradual decline until 2015/16. In addition, the G461S mutation frequency in Sao Paulo State was about 80% in the 2012/13 season, but reduced until it was completely undetectable in 2015/16. These results provide evidence that resistance can be managed in orchards with high selective pressure to tebuconazole after discontinuing the use of the fungicide for at least 3 years.

Biotic and abiotic factors from soils have been implicated in the disease suppression of Rhizoctonia solani. This study included a Eucalyptus twig baiting assay, disease index and qPCR quantification of R. solani, and physicochemical analysis of 10 tobacco soils from five different locations (V: Vaqueros, C: Cerrillos, R: Rosario de Lerma, SA: San Agustín, CH: Chicoana) in the northwest of Argentina. Levels of Rhizoctonia soil inoculum quantified by baiting assay and qPCR were positively correlated. However, there was no correlation with root rot disease index in tobacco fields. Soils from V1, SA2 and CH2 fields, which reduced root rot disease on tobacco plants, were suppressive to R. solani infection. High clay, pH, organic matter content and physical stability in tobacco soils were the main physicochemical properties that limited Rhizoctonia development. Interestingly, growth of R. solani subgroups AG4‐HGI and AG4‐HGIII was highly suppressed in V1 and CH2 fields, and in SA2 fields, respectively. Undisturbed soil from a local forested mountain also resulted in reduction of growth of AG4‐HGIII and AG4‐HGI, while AG2‐1 was less affected, suggesting that high soil organic matter contributed to suppression of R. solani. Soils highly suppressive of R. solani had significantly different populations of culturable bacteria, Pseudomonas and fungi, but populations of actinobacteria and Trichoderma spp. did not differ. These different populations may be involved in the inhibition of fungal growth. The results demonstrated that physicochemical and biological properties of soil suppressive to R. solani could act as an alternative for controlling Rhizoctonia diseases on tobacco.

Until recently, Fusarium fujikuroi was widely described as a non‐producer or a producer of little B‐series fumonisin toxins despite having a complement of fumonisin biosynthetic genes similar to those in F. verticillioides and F. proliferatum. Although high and low fumonisin‐producing F. fujikuroi strains have been shown to induce typical disease symptoms, the relationship between fumonisin production and virulence in F. fujikuroi has not been fully established. Following recent reports on the roles of bacterial endosymbionts in influencing the biology of their fungal hosts, including virulence, reproduction and the production of secondary metabolites, this study investigated the association of two strains of bacteria of the genus Enterobacter with a F. fujikuroi strain isolated from wheat in Nebraska. Results demonstrated the intracellular localization of bacteria within the hyphae of the fungus. The association with the bacteria was also correlated with macroconidia production and higher levels of virulence in the fungus. Additionally, fumonisin production was consistently and significantly (α = 0.05) higher in the bacteria‐containing F. fujikuroi strain compared with the bacteria‐free strain. Furthermore, higher levels of fumonisin production by bacteria‐containing F. fujikuroi correlated with higher expression levels of the fumonisin biosynthetic genes fum1, fum8 and fum21 under fumonisin‐inducing and non‐inducing conditions. Expression of fum15, which encodes a P450 monooxygenase, was similarly observed to be significantly (α = 0.05) higher in the bacteria‐containing fungus. Analysis of transcripts also revealed significantly (α = 0.05) higher expression of the sexual and asexual development activator protein, VeA, in the bacteria‐containing F. fujikuroi under fumonisin‐inducing conditions.

Wheat sharp eyespot, caused by the soilborne basidiomycete fungus Rhizoctonia cerealis group D subgroup I (AG‐DI), is a common disease of wheat stems that has increased in global importance in recent years. The disease caused a severe and extensive epidemic throughout the Willamette Valley of Oregon in 2014 and has remained one of the most important wheat diseases in this region subsequently. The population structure of this pathogen is still not well understood. In this study, 572 pure cultures of R. cerealis AG‐DI were isolated from five commercial fields and two experimental fields in the Willamette Valley, Oregon, in the spring of 2017 and 2018. Population structure studies were conducted using six microsatellite markers. Polymorphisms were observed at all six loci, and all seven subpopulations showed moderate gene and genotype diversity. Most of the loci were in Hardy–Weinberg equilibrium in the subpopulations, the entire population combined over locations and five of seven subpopulations were in gametic equilibrium, and the AMOVA and Mantel’s test demonstrated no differentiation among subpopulations. Though direct evidence is currently lacking, these results suggest that the sexual stage of the pathogen may be having a significant impact on pathogen population structure, and that the presence of basidiospores could be contributing to the extensive spread of this disease in the Willamette Valley in recent years.

Plant‐based antifungal agents offer an alternative to synthetic fungicides in amenity turfgrass disease management. Poacic acid is a by‐product of the biofuel production process that has exhibited antifungal activity, and the objective of this research was to determine its ability to serve as an effective management tool for economically important turfgrass diseases such as dollar spot and snow moulds. In vitro and field tests were conducted in Wisconsin and Michigan, USA from 2015 to 2017 to determine the efficacy of poacic acid in suppressing the economically important turfgrass pathogens Clarireedia jacksonii and Microdochium nivale. Poacic acid demonstrated strong antifungal activity against both pathogens in vitro, inhibiting growth of C. jacksonii and M. nivale by 93% and 74% relative to nonamended media, respectively. Poacic acid reduced dollar spot in the field in one of two years, but failed to suppress snow mould when applied alone. Poacic acid was an effective mix partner for snow mould control when combined with a synthetic fungicide, an important attribute because no single fungicide currently on the market provides acceptable snow mould control under heavy disease pressure. Future research should focus on improving poacic acid field efficacy so that it can be incorporated into plant‐based disease management strategies for amenity turfgrass.

Pseudomonas syringae pv. actinidiae (Psa) is a causal agent of kiwifruit bacterial canker worldwide, which has affected kiwifruit vines in China since 1996 and has subsequently spread to the main cultivation areas. Based on occurrence of Psa and pseudo‐absences randomly generated in China, the consensus‐based modelling technique was used to estimate the spatial spread of Psa epidemics within China. Environmental variables that related to Psa development were identified, and their contributions to Psa development were evaluated. Three modelling algorithms, namely generalized boosting models (GBM), random forests (RF) and classification tree analysis (CTA) within the BIOMOD2 framework, were employed to construct the model. The ensemble models weighted by the true skill statistic (TSS) value were used to predict the current habitat suitability of Psa, and were projected using the four general circulation models (GCMs) to assess range shifts under two types of representative concentration pathways (RCP 4.5 and RCP 8.5) by 2050. The results indicated that precipitation in March and mean temperature of warmest quarter were the most important limiting factors for distribution of Psa. The predictive accuracy of the ensemble model showed acceptable predictive powers (TSS = 0.852). Under future climate conditions, substantial net loss of suitability for Psa was estimated to be 3.03–12.5% under RCP 4.5 (except one GCM), and 2.46–9.89% under RCP 8.5. Shrinkage of suitable habitats was detected mainly in the areas currently infected by Psa. Special attention should be given to recent infectious regions in south and southwest China, considering the locally expanding kiwifruit commercial plantations.

Huanglongbing (HLB), associated with a non‐culturable bacterium ‘Candidatus Liberibacter asiaticus’ (CLas), is a highly destructive citrus disease with a long but poorly documented history in China. No effective treatment for HLB is available. The identification of new prophages in abundant CLas genomic sequence data provides new insights into both the diversity of CLas strains and HLB management. In this study, CLas populations from nine provinces were surveyed for the presence of prophage. Two major prophage typing groups (PTGs) were discovered to be associated with two different altitude regions: strains of CLas in PTG1 from high altitude regions (HAR) mainly contained prophage Type 1 only or Types 1 and 3, whereas strains of CLas in PTG2 from low altitude regions (LAR) mainly contained prophage Type 2. The discovery of these CLas population patterns provides evidence for independent origins of HLB in HAR and LAR. Guangdong province is the generally recognized domestic region of origin for HLB and is primarily responsible for the dissemination of HLB in LAR through transport of seedlings. Both Yunnan and Sichuan provinces are the probable regions of origin for HLB in HAR. PTG2 was further divided into two subgroups: PTG2‐1, found in Guangdong, Fujian and Guangxi and PTG2‐2, found in Jiangxi, Zhejiang and Hunan. These regions and prophage types are correlated with early and late introductions of HLB in LAR. These molecular analyses were supported by studying the history of the dissemination of HLB in historical documents.

Chickpea chlorotic dwarf virus (CpCDV; genus Mastrevirus, family Geminiviridae) is one of the most important legume‐infecting viruses with a wide host range and geographic distribution in Africa and Asia. In Iran, CpCDV is common in chickpea (Cicer arietinum), but there is limited information about diversity and infections in plants of other legume species. In the current study, a total of 1671 leaf samples from different pulse crops with symptoms were collected in nine provinces of Iran, and the CpCDV infection status was tested by PCR and/or rolling circle amplification (RCA), resulting in the detection of CpCDV in samples of chickpea, lentil (Lens culinaris) and faba bean (Vicia faba) from different regions. Sequence analysis of complete genomes of 18 isolates recovered by digestion of RCA products revealed infection with isolates of the strains CpCDV‐A and CpCDV‐F in chickpea, lentil and faba bean. Phylogenetic analysis showed that the Iranian isolates of CpCDV were closely related to previously sequenced isolates of CpCDV‐A and CpCDV‐F. To the authors' knowledge, this is the first report of CpCDV‐F in Iran. Using agroinoculation with infectious clones for one isolate each of CpCDV‐A and CpCDV‐F, infectivity was confirmed in both faba bean and chickpea, with plants developing leaf curling and/or yellowing. Both infectious clones also successfully infected Nicotiana benthamiana resulting in mild yellowing and intensive leaf curling for CpCDV‐A, and dark‐green mosaic, dwarfing and mild leaf curling for CpCDV‐F.

Efforts to control viral diseases of grapevine include the production of certified material and development of virus‐resistant transgenic grapevines. However, effective antiviral agents, once the viruses have infected the plants, are still lacking. This study shows that a crude garlic extract has significant antiviral activity against grapevine viruses. Replication of grapevine leafroll‐associated virus 2 (GLRaV‐2) was obviously inhibited in grapevine cv. Cabernet Sauvignon calli treated with diluted (1:100) garlic extract. The relative RNA levels of GLRaV‐2 and grapevine fleck virus (GFkV) in cv. Summer Black grapevine in in vitro‐grown plantlets 10 days after treatment with diluted (1:100) garlic extract were about 22% and 20%, respectively, of that in controls. The viral RNA accumulation of GLRaV‐2, GFkV, grapevine virus A (GVA), grapevine fanleaf virus (GFLV) and grapevine rupestris stem pitting‐associated virus (GRSPaV) in field‐grown grapevine cv. Centennial Seedless plants sprayed with diluted (1:100) garlic extract were about 31–40%, 26–38%, 18–31%, 17–42% and 15–18%, respectively, of that in controls. Moreover, the garlic extract treatment led to a significant decrease in viral RNA accumulation of GLRaV‐3, GLRaV‐2, GVA, GFkV, GFLV, GRSPaV and grapevine Pinot Gris virus in pot‐grown grapevine cv. Shine Muscat plants, and viral disease symptoms in these plants were obviously attenuated. In addition, this extract significantly induced expression of pathogenesis‐related protein genes and stimulated activity of antioxidant enzymes in grapevines. Taken together, these results indicate that the crude garlic extract acts as a significant inhibitor against a broad range of grapevine viruses.

Aphelenchoides besseyi is a major nematode pathogen in rice known as the causal agent of white tip disease. In the present study, A. besseyi was recovered from 32 seed samples collected from the major rice‐growing regions in China. Nine mitochondrial COI haplotypes and 95 ITS genotypes were identified, suggesting a high genetic diversity and endemism level of A. besseyi in China. Therefore, A. besseyi is likely to have experienced a long history of host–parasite coevolution in China, rather than being recently introduced from other countries. The results of population structure analysis indicated the presence of four clusters within Chinese A. besseyi, but these did not correspond to their geographic distribution. Haplotype H2 was found to be the most widespread. Haplotypes H9 and H13 were most genetically divergent and have been recognized as two cryptic species by molecular species delimitation methods, and with limited support from morphometric measurements. The COI‐based phylogeny suggested the ability to parasitize rice has independently evolved at least four times in the genus Aphelenchoides.

The recent ban of the most efficient chemical nematicides has left growers without methods for controlling the carrot cyst nematode Heterodera carotae. This phytoparasitic nematode species has a very narrow host range and causes severe crop losses in the main carrot‐growing regions worldwide. The development of alternative means of management of H. carotae is thus essential, and knowledge is required about the adaptive abilities of H. carotae, which mainly depend on gene flow among populations. The goal of this study was to describe the genetic structure of H. carotae populations at the spatial scale of the main infested French carrot‐producing region, i.e. Lower Normandy, and to disentangle the causes of the heterozygote deficit in this polyvoltine species. Microsatellite genotyping of populations collected at both the plant and field scales showed that: (i) the heterozygote deficit is mainly due to substructure; and (ii) there is strong gene flow among populations, leading to low FST and to no clear genetic structure at the spatial scale explored here. Soil transport through both agricultural machinery and the transport of leek seedlings is probably responsible for the very strong H. carotae migration among fields and production areas. Measures should be considered to limit the passive spread of H. carotae.

Cassava brown streak disease (CBSD) caused by Cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV) is a major constraint to cassava production in Mozambique. Full genome sequences of CBSD-associated virus isolates contribute to the understanding of genetic diversity and the development of new diagnostic primers that can be used for early detection of the viruses for sustainable disease management. This study determined seven new whole CBSV genomes from total RNA isolated from cassava leaves with CBSD symptoms collected from Nampula and Zambezia in Mozambique. Phylogenetic analyses of the new genomes with published CBSV and UCBSV sequences in GenBank grouped the CBSV isolates from Mozambique into two distinct clades together with CBSV isolates from Tanzania. Clade 1 and 2 isolates shared low nucleotide (79.1-80.4%) and amino acid (86.5-88.2%) sequence identity. Further, comparisons within the seven new CBSV isolates, and between them and the single published complete CBSV sequence (CBSV_MO_83_FN434436) from Mozambique, revealed nucleotide sequence identities of 79.3-100% and 79.3-98%, respectively, and amino acid identities of 86.7-100% and 86.7-98.8%. In addition, using RDP4, a recombination analysis comprising all CBSV and UCBSV genome sequences from GenBank detect 11 recombination events. Using several comprehensive evolutionary models and statistical programs, it was confirmed that CBSV and UCBSV are distinct virus species, with an additional probable new species (clade 2).

The Rlm7 gene in Brassica napus is an important source of resistance for control of phoma stem canker on oilseed rape caused by the fungus Leptosphaeria maculans. This study shows the first report of L. maculans isolates virulent against Rlm7 in the UK. Leptosphaeria maculans isolates virulent against Rlm7 represented 3% of the pathogen population when cultivars with the Rlm7 gene represented 5% of the UK oilseed rape area in 2012/13. However, the Rlm7 gene has been widely used since then, representing >15% of the UK oilseed rape area in 2015/16. Winter oilseed rape field experiments included cultivars with the Rlm7 gene, with the Rlm4 gene or without Rlm genes and took place at five sites in the UK over four cropping seasons. An increase in phoma leaf spotting severity on Rlm7 cultivars in successive seasons was observed. Major resistance genes played a role in preventing severe phoma leaf spotting at the beginning of the cropping season and, in addition, quantitative resistance (QR) in the cultivars examined made an important contribution to control of phoma stem canker development at the end of the cropping season. Deployment of the Rlm7 resistance gene against L. maculans in cultivars with QR in combination with sustainable disease management practices will prolong the use of this gene for effective control of phoma stem canker epidemics.

Understanding how disease foci arise from single source lesions has not been well studied. Here, single wheat leaves were inoculated with Puccinia striiformis f. sp. tritici urediniospores, and all wheat leaves within two intersecting 0.3 × 3.0 m transects were sampled in eight replicates over three years. The lesions observed on each of the top three leaves on plants within 1.5 m from the source lesion were three-dimensionally mapped. The total number of lesions within a 1.5 m radius was estimated by dividing the number of lesions observed within each 0.025 m-wide annulus by the fraction of the annulus sampled. The estimated total number of lesions produced within 1.5 m of a single source lesion ranged from 27 to 776, with a mean of 288 lesions. Eighty percent of the lesions were recorded within 0.69 m of the source infection. The proportion of total lesions observed at a given distance from the source was fitted well by the Lomax and Weibull distributions, reflecting the large proportion of lesions arising close to the source, and when fitted to an inverse-power distribution had a slope (b) of 2.5. There were more lesions produced on leaves higher in the canopy than on lower leaves, with more lesions being detected above than below the point of inoculation. Simultaneous measurement of lesion gradients and spore dispersal in the final year of the study suggests that this pattern is due to greater susceptibility of upper leaves, rather than increased dispersal to upper leaves.

The veA or velvet gene is necessary for biosynthesis of mycotoxins and other secondary metabolites in Aspergillus species. In addition, veA has also been demonstrated to be necessary for normal seed colonization in Aspergillus flavus and Aspergillus parasiticus. The present study shows that veA homologues are broadly distributed in fungi, particularly in Ascomycetes. The Fusarium verticillioides veA orthologue, FvVE1, is also required for the synthesis of several secondary metabolites, including fumonisin and fusarins. This study also shows that maize plants grown from seeds inoculated with FvVE1 deletion mutants did not show disease symptoms, while plants grown from seeds inoculated with the F. verticillioides wildtype and complementation strains clearly showed disease symptoms under the same experimental conditions. In this latter case, the presence of lesions coincided with accumulation of fumonisins in the plant tissues, and only these plant tissues had elevated levels of sphingoid bases and their 1-phosphate derivatives, indicating inhibition of ceramide synthase and disruption of sphingolipid metabolism. The results strongly suggest that FvVE1 is necessary for pathogenicity by F. verticillioides against maize seedlings. The conservation of veA homologues among ascomycetes suggests that veA could play a pivotal role in regulating secondary metabolism and associated pathogenicity in other fungi.

Bacterial canker is a major disease of Prunus avium (cherry), Prunus domestica (plum) and other stone fruits. It is caused by pathovars within the Pseudomonas syringae species complex including P. syringae pv. morsprunorum (Psm) race 1 (R1), Psm race 2 (R2) and P. syringae pv. syringae (Pss). Psm R1 and Psm R2 were originally designated as the same pathovar; however, phylogenetic analysis revealed them to be distantly related, falling into phylogroups 3 and 1, respectively. This study characterized the pathogenicity of 18 newly genome-sequenced P. syringae strains on cherry and plum, in the field and laboratory. The field experiment confirmed that the cherry cultivar Merton Glory exhibited a broad resistance to all clades. Psm R1 contained strains with differential specificity on cherry and plum. The ability of tractable laboratory-based assays to reproduce assessments on whole trees was examined. Good correlations were achieved with assays using cut shoots or leaves, although only the cut shoot assay was able to reliably discriminate cultivar differences seen in the field. Measuring bacterial multiplication in detached leaves differentiated pathogens from nonpathogens and was therefore suitable for routine testing. In cherry leaves, symptom appearance discriminated Psm races from nonpathogens, which triggered a hypersensitive reaction. Pathogenic strains of Pss rapidly induced disease lesions in all tissues and exhibited a more necrotrophic lifestyle than hemibiotrophic Psm. This in-depth study of pathogenic interactions, identification of host resistance and optimization of laboratory assays provides a framework for future genetic dissection of host-pathogen interactions in the canker disease.

High elevation spruce forests of the European Alps are frequently infected by the needle rust Chrysomyxa rhododendri, a pathogen causing remarkable defoliation, reduced tree growth and limited rejuvenation. Exact quantification of the disease severity on different spatial scales is crucial for monitoring, management and resistance breeding activities. Based on the distinct yellow discolouration of attacked needles, it was investigated whether image analysis of digital photographs can be used to quantify disease severity and to improve phenotyping compared to conventional assessment in terms of time, effort and application range. The developed protocol for preprocessing and analysis of digital RGB images enabled identification of disease symptoms and healthy needle areas on images obtained in ground surveys (total number of analysed images n = 62) and by the use of a semiprofessional quadcopter (n = 13). Obtained disease severities correlated linearly with results obtained by manual counting of healthy and diseased needles for all approaches, including images of individual branches with natural background (R2 = 0.87) and with black background (R2 = 0.95), juvenile plants (R2 = 0.94), and top views and side views of entire tree crowns of adult trees (R2 = 0.98 and 0.88, respectively). Results underline that a well-defined signal related to needle bladder rust symptoms of Norway spruce can be extracted from images recorded by standard digital cameras and using drones. The presented protocol enables precise and time-efficient quantification of disease symptoms caused by C. rhododendri and provides several advantages compared to conventional assessment by manual counting or visual estimations.