Plant Disease

Late blight caused by Phytophthora infestans poses a significant global threat to potato and tomato cultivation with profound historical and ongoing impacts on food security. In Central America, particularly in Guatemala and Honduras, the disease has intensified over the last decade, possibly due to favorable climatic conditions and changes in local pathogen populations. This study identified four distinct clonal lineages of the A2 mating type, US7A2, US8A2, and 13A2, and a newly identified lineage exhibiting genetic variation. Mitochondrial haplotype analysis confirmed that the patterns aligned with those reported in previous studies, thereby reflecting the diverse genetic composition of this pathogen. The genetic variability of P. infestans, including its reduced sensitivity to fungicides such as metalaxyl, and its ability to overcome host resistance, underscores the importance of understanding its population dynamics. Approximately 61% of the genetic variation was observed between lineages, likely because of the introduction of genetically distinct propagules into infected seeds. These findings underscore the urgent need for region-specific disease management strategies guided by local genetic data to effectively mitigate the impact of late blight and suggest the need to strengthen local seed production to minimize the import of new genotypes.

Canada thistle (Cirsium arvense (L.) Scop., CT) is one of the worst weeds threatening temperate regions of the world. A host-specific rust fungus, Puccinia punctiformis (F. Strauss) Rohl., is known to cause systemic disease of CT, ultimately killing individuals and reducing stand densities. In 2013, it was demonstrated that fall inoculation of rosettes with coarsely ground leaves bearing P. punctiformis telia can successfully initiate epiphytotics. In the same year, a cooperative project between the Colorado Department of Agriculture and United States Department of Agriculture was initiated, in which CT patches across the state of Colorado (USA) were inoculated and tracked over subsequent years for changes in stem density. Here, we report our findings from 8 years (2014-2021) of monitoring effort. At most sites (N = 87), CT stem densities declined, from a mean ({+/-} SE) of 87.9 ({+/-} 6.5) stems to 44.7 ({+/-} 4.2). These declines however were spatially-autocorrelated, and likely attributable to local growing conditions, as mean annual daily maximum temperature and standard deviation of elevation, as well as climatic conditions around the times of both treatment and monitoring, were found to be important predictors of CT decline. Further, we observed that the amount of inoculum deployed, timing since last release, and method in which it was spread locally at a site were also associated with the magnitude of CT stem decline. These results are indicative of the value of P. punctiformis as a CT biological control agent. The name Cirsium arvense dieback (CADB) is proposed herein to describe the agriculturally important decline in CT stem densities attributable to this previously un-named systemic disease.

Beyond the significant impact of Cassava witches broom disease (CWBD), caused by the fungus Rhizoctonia (syn. Ceratobasidium) theobromae on cassava cultivation in French Guiana and Brazil, this disease also poses a potential threat to cacao trees in the region, since the fungus is responsible for Vascular Streak Dieback (VSD) of cacao in South East Asia. Cross-pathogenicity trials were conducted in several cassava fields in French Guiana by planting young cacao plants adjacent to diseased cassava plants. Vascular necrosis was observed in some cacao plants, and the presence of R. theobromae in the cacao tissues was confirmed through PCR diagnostics using primers specific to the fungus. Sequence analysis indicated 100% similarity between samples from both hosts and 97.53 to 99.74% identity with R. theobromae isolates previously reported from cassava in the Americas and Southeast Asia. Additionally, symptomatic cacao in a mixed cacao-cassava farm yielded R. theobromae-positive PCR results, suggesting a natural infection. Ongoing work includes artificial inoculations and controlled cross-pathogenicity trials under screenhouse conditions to attempt reproduction of the symptoms. While current data do not yet establish definitive causality, the findings indicate potential host jump and warrant rapid communication to researchers, policy makers, and farmers to safeguard cacao production and Theobroma biodiversity in the Amazon region.

Cassava witches broom disease (CWBD) has emerged as a significant threat to cassava production in the Oiapoque region of Amapa, Brazil. Diseased plants exhibit stunted growth, vascular necrosis, abnormal shoot proliferation, and distinctive broom-like appearance. This study aimed to characterize the disease and identify its causal agent(s). The assessment by high-throughput sequencing of total nucleic acids (DNA and RNA) from affected cassava tissues revealed Rhizoctonia theobromae (syn. Ceratobasidium theobromae) associated with CWBD. PCR-based detection using species-specific primers confirmed the presence of R. theobromae in 74% of symptomatic samples. Genetic diversity analysis based on the Ca2+/calmodulin-dependent protein kinase gene showed low variability among Brazilian isolates compared with Asian populations, suggesting their recent introduction. This first report of R. theobromae causing CWBD in Brazil follows a recent report of the disease from French Guiana and highlights the urgent need for effective measures to prevent the further spread of this emerging pathogen, which poses a deadly threat to cassava cultivation in the rainforest, a significant risk to cassava production in Brazil, and regions with similar eco-climatic conditions.

Xanthomonas wilt (XW) of banana caused by Xanthomonas vasicola pv. musacearum (Xvm) does not spread to all plants physically interconnected through the rhizome when one or a few are diseased. However, the factors behind this incomplete systemic spread of Xvm are not fully known yet could inform XW management. This study explored the effect of Xvm inoculum amounts, number and size of suckers, sucker positioning on mother plant corms and other mother plant corm attributes on sucker colonization. A shorter (p <0.05) incubation period (17.9 vs 21.1 days) and higher (p<.001) cumulative number of symptomatic leaves (5.2 vs 1.6 leaves) was observed when all (high inoculum) compared to two leaves (low inoculum) were inoculated. Xvm was recovered in corms at 29 days post inoculation (dpi) in both treatments with no differences (p >0.05) in proportions of corms with Xvm between the treatments. However, Xvm was recovered earlier and at a higher frequency in suckers when all leaves were inoculated. Lower Xvm recoveries occurred in the lower corm sections to which most suckers were attached relative to the middle and upper corm sections. Xvm incidence in corms increased with the number of attached maiden suckers, and the dpi while it declined with increasing mother plant and corm height. Thus, Xvm spread within mats is influenced by the amount of inoculum and the physiological stage (e.g., height) of the plant and attached suckers. The position of suckers, predominantly at the bottom of corms also protects them from infection. Measures that reduce Xvm inoculum build-up in mats are thus crucial for minimizing within mat XW spread.

Foot rot is a devastating disease of faba bean crops globally, including in the United Kingdom, the worlds third largest producer. To identify the causal agents, we have sampled foot rot-affected plants and soils from faba bean crops across England. We isolated organisms associated with foot rot disease in culture and assessed pathogenicity in vivo to evaluate the infectivity of the isolates on faba bean. We identified the pathogenic isolates using DNA barcoding of the Internal Transcribed Spacer (ITS) and Translation Elongation Factor one (TEF1 ) molecular markers. A total of 113 clonal isolates were obtained from infected plants and soil samples across England. Of these, 60 were pathogenic, inducing mild to severe symptoms on faba bean. Sequencing of the ITS and TEF1 loci and comparison against sequence databases (Genbank and Fusarium_ID) enabled the identification of pathogenic isolates, in decreasing order of frequency, as Fusarium oxysporum (26.6 %), F. vanettenii (25%), F. redolens (15 %), F. solani (11.6%), F. culmorum (8.3 %), F. avenaceum (6.7 %), F. equiseti (1.7 %), F. clavum (1.7 %), Clonostachys rosea (1.7%) and Alternaria alternata (1.7%). F. oxysporum, F. redolens and F. avenaceum induced the most severe symptoms, whilst F. solani induced the least severe symptoms. Determining the most prevalent causal agents of foot rot in UK faba beans will facilitate targeted disease monitoring and intervention for enhanced productivity.

Watermelon is an important specialty crop in the USA. Fungal diseases primarily challenge the production and productivity of watermelon. The understanding of prevailing diseases, gained through genotypic and phenotypic techniques, eventually helps researchers develop disease management strategies. This study involved scouting and sampling of a watermelon research field in Southwest Mississippi for diseases. Nine distinct potential pathogenic fungi were identified from symptomatic leaves and fruits through development of pathogen pure cultures followed by PCR amplification of internal transcribed spacer regions and sequencing. The identified fungi were Didymella americana, Diaporthe melonis, Fusarium incarnatum, Alternaria longissima, Curvularia pseudobrachyspora, Xylaria multiplex, Phoma sp., Nigrospora sphaerica, and Fusarium chlamydosporum. The fungal isolates were ascomycetes at the phylum-level and belonged to the orders of fungi: Pleosporales, Hypocreales, Diaporthales, Xylariales, and Trichosphaeriales. Future research studies include pathogenicity assays with a broader host range, whole genome sequencing to develop deeper understanding of the pathogenic fungi, and formulation of disease management strategies for high-yielding, superior quality, and profitable watermelon production.

Late blight, a destructive disease affecting potatoes, is caused by the oomycete Phytophthora infestans and remains a critical threat worldwide. The potential for sexual reproduction in production areas near the Peru-Bolivia border remains high due to the historical presence of mating type A2 in Bolivia and the current presence of mating type A1 in Peru. In Ecuador, there has been a past coexistence of A1 (P. infestans) and A2 (P. andina), while in Colombia, P. infestans has mainly exhibited mating type A1. These neighboring countries were compared with strains from Uruguay, which historically had A2 but now shows A1. We examined the genetic structure of South American P. infestans populations using 182 isolates: 97 from Bolivia and southern Peru, 14 from Colombia, 57 from Ecuador (1993-2022), and 14 from Uruguay. The isolates were characterized by clonal lineage, mitochondrial haplotype, and mating type. In Bolivia, only the lineage/haplotype 2A1/Ia was identified, whereas Peru exhibited both 2A1/Ia and EC1/IIa, all of which were mating type A1. Puno was the sole department where both lineages were present. In older Ecuadorian populations, we found US1/Ib and EC1/IIa (P. infestans), as well as EC2/Ic and EC3/Ia (P. andina), while recent populations showed only US1. In Colombia, EC1/IIa and a new lineage, CO4 (Ia), were discovered. In Uruguay, 2A1/Ia was predominant. These results offer updated insights into the genetic diversity and geographic distribution of P. infestans across South America and aid in the development of enhanced late blight management strategies.

Ascochyta Blight (AB), caused by Ascochyta rabiei (syn Phoma rabiei), is the major endemic foliar fungal disease affecting the Australian chickpea industry, resulting with potential crop loss and management costs. This study was conducted to better understand the risk posed by the Australian A. rabiei population to current resistance sources and to provide informed decision support for chemical control strategies. Recent changes in the pathogenicity of the population were proposed based on disease severity and histopathological observations on a host set. Controlled environment disease screening of 201 isolates on the host set revealed distinct pathogenicity groups, with 41% of all isolates assessed as highly aggressive and a significant increase in the proportion of isolates able to cause severe damage on resistant and moderately resistant cultivars since 2013. In particular, the frequency of highly aggressive isolates on the widely adopted PBA HatTrick cultivar rose from 18% in 2013 to 68% in 2017. In addition, isolates collected since 2016 caused severe disease on Genesis 090, another widely adopted moderately resistant cultivar and on ICC3996, a commonly used resistance source. Of immediate concern was the 10% of highly aggressive isolates able to severely damage the recently released resistant cultivar PBA Seamer (2016). Histopathology studies revealed that the most aggressive isolates were able to germinate, develop appressoria and invade directly through the epidermis faster than lower aggressive isolates on all hosts assessed, including ICC3996. The fungal invasion triggered a common reactive oxygen species (ROS) and hypersensitive response (HR) on all assessed resistant genotypes with initial biochemical and subsequent structural defence responses initiated within 24 hours of inoculation by the most highly aggressive isolates. These responses were much faster on the less resistant and fastest on the susceptible check host, indicating that speed of recognition was correlated with resistance rating. This will inform fungicide application timing so that infected crops are sprayed with prophylactic chemistries prior to invasion and with systemic chemistries after the pathogen has invaded.Competing Interest StatementThe authors have declared no competing interest.View Full Text

Austropuccinia psidii causes rust disease on species within the family Myrtaceae and was first detected in Australia in 2010, with the first detection in Western Australia in 2022. While species within the genus Melaleuca from Eastern Australia show variable responses to the pathogen, little is known of the response of species from Western Australia. This study established that 13 previously unscreened species of Melaleuca, including Threatened and Priority species that were grown from seeds sourced from Western Australian populations, were susceptible to the pandemic strain of the pathogen. The proportion of highly susceptible plants within a single species ranged from 2% - 94%, with several species displaying highly variable levels of resistance to A. psidii. These results highlight the importance of disease screening and may direct conservation efforts.

Phytophthora ramorum (Pr) is an invasive oomycete in Europe and North America and the causal agent of sudden oak death (SOD), which occurs along the coastal fog belt of California and southwestern Oregon, and it also causes sudden larch death in the UK. The Macaronesian laurel forest (MLF), a relict subtropical evergreen forest of the North Atlantic islands, shares climatic and some taxonomic affinities with those areas affected by SOD. To assess the disease risk, we tested the foliage susceptibility of MLF species and their capacity to sustain Pr sporulation and compared the climatic suitability with other areas where the pathogen is established. Detached leaves of 15 species were inoculated with zoospores and mycelium (through wounding) with five Pr isolates belonging to the EU1 and NA1 clonal lineages. MLF species showed diverse responses to Pr, ranging from extensive necroses on Viburnum tinus to asymptomatic sporulation on Picconia excelsa. Eleven species developed necrotic lesions to different degrees through zoospore inoculation while this increased to 13 species through wound treatment. Overall, small necrotic lesions (i.e. tolerance) were predominant, but Pr was rather aggressive to V. tinus, Arbutus canariensis and Ilex canariensis. Although the mean sporangial production was generally low (25-201 sporangia) in all species, the number of sporangia per leaf in five MLF species was similar to those reported for Umbellularia californica, a key host driving the SOD epidemics in California. Climatic suitability indexes in MLF areas were similar to those where SOD is found in California. Our results indicate a moderate to high risk of Pr establishment if the pathogen is introduced in the MLF.

Management of widespread plant pathogens is challenging as climatic differences among crop growing regions may alter key aspects of pathogen spread and disease severity. Xylella fastidiosa is a xylem-limited bacterial pathogen that is transmitted by xylem sap feeding insects. Geographic distribution of X. fastidiosa is limited by winter climate and vines infected with X. fastidiosa can recover from infection when held at cold temperatures. California has a long history of research on Pierces disease, and significant geographic and climatic diversity among grape-growing regions. This background in combination with experimental disease studies under controlled temperature conditions can inform risk assessment for X. fastidiosa spread and epidemic severity across different regions and under changing climate conditions. Californias grape growing regions have considerable differences in summer and winter climate. In northern and coastal regions, summers are mild and winters cool, conditions favoring winter recovery of infected vines. In contrast, in inland and southern areas summers are hot and winters mild, reducing likelihood of winter recovery. Here, winter recovery of three table grape cultivars (Flame, Scarlet Royal, and Thompson seedless) and three wine grape cultivars (Sauvignon Blanc, Cabernet Sauvignon, and Zinfandel) were evaluated under temperature conditions representative of the San Joaquin Valley, an area with hot summers and mild winters that has been severely impacted by Pierces disease, and contains a large portion of California grape production. Mechanically inoculated vines were held in the greenhouse under one of three warming treatments to represent different seasonal inoculation dates prior to being moved into a cold chamber. Winter recovery under all treatments was generally limited, but with some cultivar variation. Given hot summer temperatures of many grape-growing regions worldwide, as well as increasing global temperatures overall, winter recovery of grapevines should not be considered a key factor affecting X. fastidiosa spread and epidemic severity in the majority of cases.

Members of the genus Trichoderma are widely recognized as beneficial fungi and frequently applied as biocontrol agents. However, recent studies have identified Trichoderma afroharzianum as a pathogenic species, capable of infecting maize, wheat, and barley under greenhouse conditions. Its pathogenic potential in small-grain cereals under field conditions, however, has been so far unexplored. To evaluate its pathogenic potential, two-year field trials (2023 and 2024) were conducted using ten wheat, five barley, two rye, and one triticale cultivar. Artificial inoculation was carried out at full flowering using a spray inoculation with pathogenic T. afroharzianum isolates obtained from maize and water as control. Three fungicides were applied: untreated control, foliar treatment before inoculation, and ear application after inoculation. Disease development was assessed based on colonization rate of harvested kernels, and thousand kernel weight (TKW). The results showed significant differences in susceptibility between and within cereal species. T. afroharzianum was able to colonize wheat and barley ears under field conditions, with some cultivars showing significant reduction in TKW and high colonization rate. In contrast, rye and triticale exhibited much lower infection rates. Fungicide treatments had varying levels of efficacy. Ear application after flowering was most effective in reducing colonization and preventing yield loss, whereas early foliar treatment showed limited effect. These findings indicate that T. afroharzianum may represent a relevant pathogen in cereal production adding a new ear disease in cereals and requiring monitoring and enhanced fungicide applications in the future, unless less susceptible cultivars are identified and utilized in practice.

Over the past two decades, dieback of Pinus sylvestris L. stands has increased across Europe, largely due to mass outbreaks of the bark beetle, in particular, Ips acuminatus Gyll. (Coleoptera: Curculionidae). This beetle causes mechanical damage and vectors pathogenic fungi, including ophiostomatoid species that induce blue-stain. Ophiostoma clavatum Math.-Kaarik is the most frequently reported fungal associate, yet its occurrence had not been documented in Ukraine. While ophiostomatoid fungi are well studied in pine pathogenesis, the role of fast-growing associates such as Fusarium spp., remains poorly understood. This study aimed to identify the dominant Ophiostoma and Fusarium species associated with I. acuminatus in western Ukraine and to evaluate their pathogenicity on pine seedlings. Isolates from beetle abdomens and blue-stained wood were identified as O. clavatum based on morphology and molecular markers (ITS, TUB, TEF1-). Pathogenicity tests showed that O. clavatum acts as a weak phytopathogen. The dominant Fusarium morphotype from blue-stained wood was identified as Fusarium verticillioides (Sac) Nirenberg, which induced necrosis and tissue maceration on pine seedlings. In dual culture, F. verticillioides displayed strong competitive dominance over O. clavatum. This study provides the first record of O. clavatum associated with I. acuminatus in Ukraine, extending its known European distribution. The observed pathogenicity and competitive ability of F. verticillioides suggest it may contribute to Scots pine decline, warranting further investigation.

Grapevine downy mildew, caused by the oomycete Plasmopara viticola, is one of the most devastating diseases of grapevine worldwide. Primary inoculum (i.e. oospores) play a decisive role in downy mildew epidemics, but we still know very little about its abundance in vineyard soil. This study presents a novel molecular method for quantifying P. viticola oospore concentration in vineyard soil using digital droplet PCR (ddPCR). The development of this method enabled characterization of both the abundance and spatial distribution of oospores in a vineyard at the onset of the growing season. Following a regular grid, a total of 198 soil samples (0-15cm horizon) were collected in March 2022 in grapevine rows in a 0.22 ha vineyard planted with cv. Merlot and conducted according to French organic viticulture specifications. Additional samples were collected from the same field within five nested sampling plots with three distance levels, including samples collected in the inter-rows. Using ddPCR, we found P. viticola DNA in all soil samples except one, and we estimated that oospore concentration ranged from 0 to 1858 oospores per gram of soil (303 {+/-} 308 on average). The distribution of oospores at field scale was not random but characterized by 15 m-diameter patches of concentrically increasing oospore concentration. Oospores accumulated 5 times more below the vine stocks than in the inter-row. Using a leaf disc bioassay, we found that soil infectious potential significantly increased with oospore concentration assessed by ddPCR. However, the low coefficient of determination of the relationship indicated that DNA-based oospore quantification lacked clear epidemiological significance. Both ddPCR and bioassay methods are valuable tools that could be used to assess reservoirs of P. viticola primary inoculum across different agroclimatic contexts, thereby bringing greater genericity. Further methodological improvement will also help refine the accuracy of DNA-based assessment of primary inoculum reservoir and improve our understanding of the relationship between primary inoculum reservoir and epidemic dynamics. Ultimately, these data will be essential for improving epidemic risk models and evaluating new preventive disease management strategies targeting the primary inoculum. ImportanceGrapevine downy mildew caused by the oomycete Plasmopara viticola, affects leaves and bunches, and leads to important economic losses for viticulturists. Recently, evidences have accumulated that soilborne primary inoculum (i.e. oospores in the soil) importantly contributes to disease progress. The significance of our work is in presenting a direct and sensitive method for assessing soil oospore concentration, as well as quantitative and spatially-explicit data on downy mildew primary inoculum. This opens the way to new research, the evaluation of new disease control strategies based on primary inoculum management and the improvement of epidemic risk models, which will potentially contribute to lower fungicide use in viticulture in fine.

AbstractGrapevine downy mildew, caused by Plasmopara viticola, is one of the most destructive diseases in viticulture. Resistance-based management strategies rely on grapevine varieties carrying major resistance loci (Rpv). Although breakdown of several loci has been reported, Rpv1 had remained effective until now. Here, we provide the first evidence of Rpv1 breakdown by P. viticola in Cilaos on Reunion Island (France) and the first case of a strain simultaneously overcoming three resistances of grapevine. We combined pathogenicity assays with whole-genome sequencing to characterize a P. viticola strain collected in Cilaos in 2023, alongside a panel of eight reference strains of known virulence. Hypersensitive response and sporulation were assessed for each strain on Chardonnay (susceptible variety) and four resistant varieties carrying Rpv1, Rpv3.1, Rpv10, or Rpv12. The strain collected in Cilaos was able to overcome not only Rpv1 but also Rpv3.1 and Rpv10. On Rpv1, we observed a complete loss of host recognition with high sporulation. On Rpv3.1, the phenotype was consistent with previous breakdowns, and the strain carried the vir1 allele previously described in France. By contrast, the breakdown of Rpv10 differed from that reported in European populations: whereas European strains displayed only partial breakdown of resistance, the strain of Cilaos showed complete loss of host recognition with high sporulation. Moreover, genomic analyses revealed a novel mutation, a large homozygous deletion in the corresponding avr locus. Our genomic data analyses further suggests that this P. viticola strain shares a genetic background with populations from mainland France, raising serious concerns about the potential emergence and spread of multivirulent lineages in Europe. These findings highlight the need for large-scale virulence monitoring of P. viticola and improved strategies for the sustainable management of grapevine resistance in Europe.

1.Wheat stem rust (Puccinia graminis f. sp. tritici) is a major global threat to wheat production, driven by rapid shifts in virulence and race diversity. This study aimed to identify physiological races of stem rust pathogens in Ethiopias irrigated wheat-growing areas. Surveys and race analyses were conducted during the 2020/21-2023/24 large-scale wheat expansion periods, alongside a systemic review of rust dynamics from 2012 to 2022. Results revealed significant shifts in stem rust races, with an increasing dominance of virulent races over the last decade. TKTTF dominated from 2012 to 2016, succeeded by TTTTF in 2017, and TKKTF in 2019-2020. By 2021-2022, TTKTT and TTKTF races were prevalent, affecting 90% of wheat fields. From 2020 to 2024, five major races were identified: TTKTT, TTKTF, TTTTF, TKKTF, and TKTTF, with TTKTT, a virulent Ug99 mutant, emerging as the most dominant. This race exhibits a 95% virulence spectrum, overcoming resistance genes such as Sr24, widely used in commercial cultivars. The study highlights the urgent need to prioritize resistance breeding against virulent races, particularly in irrigated wheat regions, which serve as hotspots for pathogen evolution. Strategic rust intervention and improved screening are essential for protecting both irrigated and rain-fed wheat crops, ensuring sustainable wheat production in Ethiopia and the globe under climate change. 1. AbstractWheat stem rust (Puccinia graminis f. tritici) is a significant concern for farmers and agricultural communities around the world. It is essential to monitor the changes in virulence among these infections, as understanding these shifts can help prevent unexpected epidemics that impact livelihoods and food security. ObjectiveThis study seeks to compassionately uncover the physiological races of stem rust pathogens present in irrigated wheat-growing regions of Ethiopia, recognizing the vulnerability of local farmers to these challenges. Materials and MethodsWe conducted thorough surveys and surveillance, accompanied by detailed physiological and genetic race analyses. The insights gained from this research will be instrumental in guiding the large-scale demonstration and expansion of irrigated wheat from 2020/21 to 2023/24. Furthermore, we conducted comprehensive reviews of the dynamics of stem and yellow rust races affecting wheat production in Ethiopia over the past decade, from 2012 to 2022. Results and DiscussionOur findings reveal that changes in stem rust pathogen races, with a wider pathogenicity spectrum, are prevalent in both rain-fed and irrigated wheat-growing areas of Ethiopia. The rise of virulent races in affected fields has understandably raised concerns among farmers, with frequencies reaching up to 50%. Over the last ten years, the dynamics of wheat rust races illustrate a troubling shift toward more virulent strains. For example, the TKTTF race, virulent to resistance gene 85, was predominant from 2012 to 2016 but was subsequently replaced in 2017 by the more aggressive TTTTF race, which is harmful to gene 90. In 2018, we observed that TTTTF, along with TKTTF and TKKTF (virulent to gene 80), became equally common, creating additional challenges for our farming communities. The TKKTF race held dominance in 2019 and 2020, while from 2021 to 2022, TTKTT (virulent to gene 95) and TTKTF (virulent to gene 85) became more widespread, affecting around 90% of wheat fields.During the years 2021/22 to 2023/24, we carefully collected and analyzed 51 field rust samples to understand the situation better. We identified seven Pgt pathotypes in irrigated wheat in the 2021/22 season: TTKTT, TTKTF, TKKTF, TTRTF, TTTTF, TKTTF, and TKPTF. The emergence of the TTKTT race, a pathogenic Ug99 mutant, particularly in regions like Jimma, Buno Bedale, West Arsi, and East Shoa, is particularly concerning for the local farmers who depend on stable crops. In 2020/21, five stem rust races TTKTT, TTKTF, TTTTF, and TKTTF were identified, with TTKTF and TTKTT showing dominance in geographic distribution. Many popular varieties are now susceptible to these races, adding to the anxiety of farmers who rely on these crops for their livelihoods. The TTKTT race has been particularly alarming, with a 49% prevalence in Ethiopia for the first time, and it has shown varying reactions ranging from susceptible to moderately susceptible among different wheat types. Importantly, the resistance gene Sr24, which many farmers have relied upon in their cultivars, has unfortunately been rendered ineffective against this race. ConclusionTo develop durable resistance, it is crucial to introduce a transgene cassette containing five resistance genes into bread wheat as a single locus within the wheat production area. Integrating robust resistance genes from wild grass relatives with modern scientific breakthroughs is essential. Consequently, breeding programs should focus on identifying additional sources of resistance to counter the more virulent races of the pathogen. Special attention must be given to irrigated wheat production, which harbors virulent and genetically diverse races, threatening the belg and main season wheat crops, as well as the green bridge. The background data collected from this study will aid in strategic rust intervention, screening, and guidance for resistance breeding among wheat breeders and seed technology multiplication units in the area addressing the climate change.

The characterization of virulence frequencies has to be regularly updated to identify which genes are currently efficient and use this information to advise gene deployment by choosing varieties depending on the current composition of local pathogen population. In L. maculans on Brassica napus, because different genes were characterized by different teams, because new interactions are continuously identified and seed of differentials are difficult to obtain, we today still lack isolates characterized on all current resistance genes. On the one hand, we assembled a set of 12 isolates characterized on 13 of the 17 described resistance genes, having clearly compatible and clearly incompatible isolates for each interaction. This set can be used to characterize the L. maculans - B. napus interaction at cotyledon stage. Expanding the set of isolates with clearly virulent ones allowed us to detect inconsistent behaviour or intermediate (avirulent) phenotypes. On the other hand, we used this set of isolates as controls to identify virulence frequencies in a current French L. maculans population sampled in 2018 at Le Rheu. We provide the current status for 13 avirulence frequencies, including LepR1, LepR2 and LepR3 available in near isogenic lines of spring canola but not yet documented in France. Avirulence frequencies on the genes Rlm1, Rlm2, Rlm3, Rlm4, Rlm7, Rlm9 and LepR3 were low, indicating the lack of efficacy of these genes against the current population. In the opposite, all or most of isolates were avirulent for the genes Rlm5, Rlm6, Rlm10, Rlm11, LepR1 and LepR2. An optimistic point of view could conclude that there are ample resources for oilseed rape breeding. However, as compared to previous studies, so far all the resistance genes used on significant acreage without additional management practices have lost efficacy and only avirulences corresponding to resistance genes not deployed in France retain efficacy. While the call to wisely manage the available host resistance genes is not recent, it is still relevant. Adding, management practices to the deployment of resistance genes in order to reduce inoculum carry-over from one growing season to the next and to lower population sizes is key to maintain their efficacy over time.

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are to some degree all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomato, several species cause early blight, leaf spot, and other diseases. We collected Alternaria-like infection lesions from the leaves of eight wild tomato species from Chile and Peru. Using molecular barcoding markers, we characterized the pathogens. The infection lesions were caused predominantly by small-spored species of Alternaria of the section Alternaria, like A. alternata, but also by Stemphylium spp., Alternaria spp. from the section Ulocladioides, and other related species. Morphological observations and an infection assay confirmed this. Comparative genetic diversity analyses show a larger diversity in this wild system than in studies of cultivated Solanum species. As A. alternata has been reported to be an increasing problem on cultivated tomato, investigating the evolutionary potential of this pathogen is not only interesting to scientists studying wild plant-pathosystems. It could also inform crop protection and breeding programs to be aware of potential epidemics caused by species still confined to South America.

Field Pennycress (Thlaspi arvense) is gaining attention in the US Midwest as a potential oilseed cover crop for their corn-soybean systems. Field research with breeding trials have shown that pennycress is susceptible to major fungal diseases affecting Brassica crops. In this study, we identified two pathogens: Alternaria japonica and Sclerotinia sclerotiorum which cause Alternaria black spot and Sclerotinia white mold diseases, respectively. Both fungi infect pennycress leaves and pods, with S. sclerotiorum also able to infect stems of the two pennycress accessions tested. We found accession 2032 to be more susceptible than MN106. Traditional visual methods to estimate disease severity could not capture the differential progression of Alternaria black spot in the two pennycress accessions. To address this, we developed a cost-effective DNA-based qPCR-based assay that can detect differential growth of both A. japonica and S. sclerotiorum on leaves and pods of two pennycress accessions. This method also provided more precise quantification of A. japonica and S. sclerotiorum at early infection stages than was possible visually. This assay could be helpful in evaluating various pennycress cultivars and other crops affected by these pathogens.