CONTEXT Plant pathogens that disperse by airborne propagules may cause damage that extends beyond the borders of individual fields. Developing sound management strategies, therefore, requires consideration of heterogeneity in pathogen transmission, the effectiveness of control measures, host susceptibility and pathogen virulence, and the resulting economic outcomes that scale up at the regional level with coordinated management. OBJECTIVE We use hop powdery mildew as a motivating pathosystem to develop a coupled epidemiological-economic model to enable simulation of the impact of epidemic conditions and coordinated management interventions on profitability. This pathosystem is a well-suited case study because disease development may be limited by primary inoculum and fungicide applications, yet the pathogen can spread via long-distance dispersal between fields and rapidly damage both crop yield and quality. METHODS We parameterized the model using data collected from a census survey of commercial hop yards in Oregon during 2014 to 2017, including the monthly incidence of plants with powdery mildew, fungicides applied by growers, and estimated revenue depending on how the incidence of diseased hop cones affects yield and the likelihood of crop devaluation. We show that conditions in the early stages of epidemics related to primary inoculum dose, pathogen diversity, and the intensity of management intervention interact and determine the optimal regional control strategy. RESULTS AND CONCLUSIONS As the likelihood of primary infection increases, due to either the dose of primary inoculum or virulence of the pathogen population, mean profitability decreases. These effects are most pronounced when primary infection occurs in yards that are highly connected in the disease transmission network. The choice of how many fungicide applications to make in response to initial infection has little effect on profitability when the primary inoculum is relatively infrequent. However, as primary inoculum increases, targeted fungicide applications made in the early stages of epidemics are essential for maximizing profitability region-wide. These principles hold across a range of market demand scenarios that impose different crop quality standards, with the optimal number of early-season fungicide applications remaining largely consistent despite substantially different crop prices. SIGNIFICANCE Our analysis addresses a multifaceted challenge in agricultural disease management where epidemic control decisions must account for interactions between pathogen biology, management practices, market conditions, and regional-scale disease transmission. This research provides a framework for formally understanding factors that influence the cost of disease in complex systems where pathogens disperse across management units.

Halo blight of hop, caused by Diaporthe humulicola, was first described in 2018 and is a major concern for growers in the eastern United States and Canada. This pathogen can cause quality and yield losses by desiccating hop cones, leading to shatter. However, traditional disease diagnosis is time-consuming, with morphological features taking up to 30 days to develop in culture. To address this issue, a quantitative PCR (qPCR) assay based on the translation elongation factor 1-alpha (TEF) gene was developed. We assessed capabilities and limitations of this assay for detection of D. humulicola in plant tissue and investigated aspects of the disease through (i) testing of hop rhizomes for the presence of fungal pathogens, (ii) determining the time required to detect D. humulicola in detached hop leaves, and (iii) comparing plating methods with the qPCR assay to monitor D. humulicola in a hop yard. The limit of detection for the assay was 100 fg/μl of DNA. The assay showed no cross-reactivity with other hop pathogens, endophytes, or other Diaporthe species tested. Detection of D. humulicola occurred 1 day after inoculation. The assay detected D. humulicola in both asymptomatic and symptomatic rhizome tissue, but further investigation is required to determine the cause of the observed symptoms. The assay successfully detected the pathogen in individual hop cones and inflorescences throughout the season, with higher positive identification rates than culture-based assays. This assay will provide time-limited diagnosticians with a tool for the detection of D. humulicola.

Hop downy mildew, caused by Pseudoperonospora humuli, is routinely managed using fungicides. Plot-level data from fungicide efficacy trials (n = 44) in Oregon and Washington between 1997 and 2024 were analyzed in a one-stage, contrast-based, multi-treatment individual participant data (IPD) meta-analysis. Data were aggregated by fungicide mode of action (MOA), inferred from the Fungicide Resistance Action Committee (FRAC) group, and analyzed when a given MOA appeared >= 5 times. In Oregon, fungicide MOA was resolved into four overlapping groups, with the most effective group being FRAC 49 + 4, providing estimated disease control of 87.4%. In Washington, the four MOAs analyzed were more effective than the nontreated control but had similar efficacy, with estimated disease control of 67.4 to 74.8%. Trial-level disease severity had an additive and multiplicative interaction with MOA on estimated disease control in trials in Oregon or combined over both states. After controlling for trial-level disease severity, state had a nonsignificant additive effect on estimated disease control (95% confidence interval -130.7 to 70.7%). Analysis of design inconsistency indicated that relative efficacy was stable across study designs in Washington. However, design inconsistency was detected in trials in Oregon and over both states, indicating that estimated efficacy varied depending on the specific combinations of MOAs evaluated. Design inconsistency was related to high variance in certain trials, including FRAC 49 + 40. These analyses provide a foundation for designing fungicide programs that are effective and consistent with resistance management principles. The study also illustrates the value of one-stage, multi-treatment IPD meta-analytic approaches and assessing design inconsistency.The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.

Hop (Humulus lupulus L.) is a long-lived perennial crop in which yield stability is critical to the economic sustainability of growers. Declining yields in established hop yards are hypothesized to be linked to pathogen buildup and cultural practices that can impact perennial carbohydrate reserves. However, there is limited multiyear field data quantifying these relationships. In this study, we assessed changes in yield and cone quality in a commercially important aroma hop cultivar (Citra) over four growing years (2020-23) in Washington State, USA, after planting with "virus- and viroid-free" material. Irrigation was delivered using two drip irrigation configurations (single- and double-tubing per row) and two harvest timings (early and late), implemented in a split-plot design. The incidence of apple mosaic virus (ApMV), hop mosaic virus (HMV), American hop latent virus (AHLV), hop latent virus (HLV), and hop stunt viroid (HSVd) was measured annually using reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR). The incidence of all viruses and HSVd increased annually, with hop latent virus (HLV) and HMV becoming widespread by 2023. However, no overall decline in yield was detected across the 4 years. Yield varied by year and exhibited a significant year 3 irrigation interaction, with double-tube irrigation increasing yield by similar to 0.16-0.20 kg/plant in 2022 and 2023 but not in earlier years. Harvest timing did not impact overall yield but significantly affected certain conequality attributes. Delayed harvest consistently increased alpha-acids concentration and reduced cone color scores across years. Effects on dry matter, Hop Storage Index, oil content, and volatile terpenoid composition were also observed but varied in magnitude by harvest year. Late-harvested hops generally contained elevated concentrations of most volatile terpenoids, whereas geraniol was higher in early-harvested hops.

A maximum residue limit (MRL) is a statutory limit of analyte concentration for a food or feed. An MRL for a given pesticide may vary from country to country, potentially creating technical barriers to trade when these limits are incongruous. Approximately half of the hops produced in the United States are exported, with the EU being the most important market and also having the most restrictive MRLs for numerous pesticides. Quinoxyfen historically has been central in fungicide programs for management of hop powdery mildew (Podosphaera macularis), but there is concern that loss of a harmonized MRL for quinoxyfen (currently 3 ppm) may create a barrier to export. We conducted 5 years of field studies to develop guidance on fungicide programs that are EU export-compliant, limit use of a single fungicide mode of action, and maximize efficacy without use of quinoxyfen. Plants that received fluopyram + tebuconazole during bloom and the juvenile stages of cone development had the least powdery mildew on cones, which were statistically comparable to disease levels when plants received quinoxyfen at the same timing. On leaves, the efficacy of MRL-compliant or MRL-exempt fungicides depended on the specific product and application interval. The most effective programs utilized trifloxystrobin on a 7-day or 10-day interval, or banda de Lupines albus doce on a 7-day interval, providing disease control comparable to a rotation of quinoxyfen and myclobutanil. These findings offer alternatives to quinoxyfen, provided that specific fungicides are used at and after bloom and that application intervals are appropriately matched for each fungicide.The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.

Powdery mildew of hop is caused by Podosphaera macularis. This disease affects all green tissue of the hop plant, forming the characteristic signs of white colonies that bear mycelia and conidia and which lead to browning, shatter, and yield damage when infection occurs on the inflorescence. This report communicates efficacy data of various fungicides against powdery mildew. This trial was conducted on the hop (Humulus lupulus) cultivar ‘Galena’ during the spring and summer of 2025, near Granger, Washington. Results from this trial will help producers develop more effective management approaches for the disease.

Hop downy mildew, caused by Pseudoperonospora humuli, is a widespread and damaging disease of hop in many production regions worldwide. In the western United States, one of the most important aspects of the disease is shoot infection in spring and early summer. This report summaries the efficacy of synthetic and biological fungicides in the suppression of hop shoots with systemic downy mildew in Humulus lupulus ‘Nugget’ in a trial conducted near Hubbard, Oregon, in 2025. Findings from this trial will help inform management of the disease and support future analyses that can mitigate crop damage and minimize use of ineffective or unnecessary pesticide applications.

Powdery of hop, caused by Podosphaera macularis, is managed in large part on susceptible cultivars by fungicide applications applied through the growing season to minimize disease on the cones, which are the harvested product. Fungicide applications made after the juvenile stages of cone development are reported to have small or non-detectable effects on certain hop cultivars in certain environments. However, there is no information on the cultivar Nugget, a historically important cultivar in Oregon hop production regions. Until 2014, this cultivar was unaffected by powdery mildew because of R-gene-mediated resistance. However, Nugget now routinely develops powdery mildew because virulent races of P. macularis are widespread in the Pacific Northwest. To guide Oregon growers' management decisions on Nugget, we conducted field studies in small plots in commercial hop yards from 2018 to 2020 to quantify the impact and value of late-season fungicide applications typically used for powdery mildew control on cones. Under conditions of varying disease levels on cones, making one, two, or three additional fungicide applications after late July to early August did not improve control of powdery mildew (range 19.3 to 27.2% when analyzed over years); alpha-acids content, the hop storage index, and cone color also were unchanged relative to ceasing applications in late July. This finding should give confidence to Oregon producers of Nugget that late-season fungicide applications for powdery mildew can be omitted after the critical period of juvenile susceptibility in cones without compromising disease control or crop quality.

The economic value of cultivars resistant to disease is of great interest, but how growers change their fungicide use in response to host resistance may be nuanced. We draw upon a well-described data set of the incidence of hop plants with powdery mildew and associated production metadata and demonstrate the utility of Bayesian networks as a framework for quantifying causal relationships for fungicide use and cost in response to host resistance. Conditional Gaussian Bayesian network models applied to cultivars differing in race-specific resistance to powdery mildew revealed cultivar resistance to powdery mildew influenced disease levels in early spring, which had a causal effect on how often and what fungicides growers later applied. Annual costs depended on not only the number of applications made but also the specific types of fungicides growers selected. Fungicide costs were little changed on cultivars that possessed race-specific resistance to only one of two extant strains of the pathogen. For cultivars with resistance to both pathogen strains, annual costs of fungicides were reduced commensurate with the level of resistance. Predicted values from the Bayesian networks and simulation indicate that growers apply a baseline level of fungicide, independent of cultivar resistance. Fungicide cost savings result from how fungicide inputs differentially scale with the incidence of powdery mildew and the type of fungicides used. Our analyses indicate that for a high-value crop, deployment of disease resistance may cause complex and unexpected changes in growers' fungicide use patterns that may not be obvious in simplified randomized controlled trials.

Resistance to powdery mildew (caused by Podosphaera macularis) is a primary objective for hop (Humulus lupulus L.) breeding programs. However, selection efforts are challenged by the existence of multiple races and the pathogen's demonstrated ability to overcome host resistance. The need for novel sources of resistance and the recent material transfer of an extensive collection of hop germplasm from Washington State University to the USDA-ARS inspired an elimination screen of 102 hop genotypes to six races of the pathogen. Fourteen genotypes (13.7% of the collection) were resistant to the three races currently widespread in the U.S. Pacific Northwest. After inoculation with two additional races with novel virulence from Europe, seven (6.8%) were resistant. Of these, two (similar to 2%) were resistant to a third race from Europe. Of the group of seven resistant genotypes, one is already registered (21184M [PI 558601]), and the remaining six are presented here (31058M [Reg. no. GP-45, PI 706212]; W1101-001M [Reg. no. GP-46, PI 706213]; 31061M [Reg. no. GP-47, PI 706214]; W1108-002M [Reg. no. GP-48, PI 706215]; W1110-002M [Reg. no. GP-49, PI 706216]; and W1125-004M [Reg. no. GP-50, PI 706217]). The lines can be used in breeding and to further research into the genetic mechanisms underlying multi-race powdery mildew resistance in hop.

Downy mildew of hop is caused by Pseudoperonospora humuli. The foliar symptoms of the disease are characterized by chlorotic, stunted shoots with down curled leaves. This report communicates efficacy data for various fungicides against downy mildew. The trial was conducted on the hop cultivar ‘Nugget’ during the spring of 2024, near Hubbard, Oregon. Results from this trial will aid producers in the development of more efficacious disease management programs for hop downy mildew.

Brewers are seeking new public hop (Humulus lupulus L.) cultivars that exhibit desirable tropical and stone-fruit aroma profiles for use in hop-forward beer styles. 'USDA-ARS Vera' (Reg. no. CV-31, PI 707888) is a new hop developed in collaboration between USDA-ARS and Washington State University and released by USDA-ARS in 2025. USDA-ARS Vera resulted from a cross made between Brewer's Gold and a powdery mildew-resistant male hop of Wild American descent, USDA 64103M, in 2011. USDA-ARS Vera was tested under the experimental name W1108-333 and later HRC003. The cultivar is low in alpha acids (3.79%-5.44%) and is mid-to-late maturing (median harvest date September 20 in Washington and Idaho), with on-farm yields between 1723 and 3049 kg ha(-1) when mature (>= 2 years). The aroma of USDA-ARS Vera is described as tropical, stone fruit, and citrus, and the descriptors are consistent from dry rub to the final beer. The cultivar possesses resistance to the predominant races of the causal pathogen of hop powdery mildew present in the U.S. Pacific Northwest and moderate susceptibility to hop downy mildew. This release provides brewers and growers with a new, fruit-forward aroma hop with powdery mildew resistance that is freely available to the public and absent of intellectual property restrictions.

The two-spotted spider mite (Tetranychus urticae Koch) is a globally significant agricultural pest with high reproductive capacity, rapid development, and frequent evolution of miticide resistance. Breeding and selection of resistant host cultivars represent a promising complement to chemical control, but widespread adoption is limited primarily due to the labor-intensive nature of conventional in vitro phenotyping methods. Here, we present a high-throughput, semi-automated image analysis pipeline integrating the Blackbird CNC Microscopy Imaging Robot with computer vision models for mite life stage identification. We developed a publicly available dataset of over 1,500 annotated images (nearly 32,000 labeled instances) spanning five biologically relevant classes across 10 host species and >25 cultivars. Three YOLO11-based object detection models (three-, four-, and five-class configurations) were trained and evaluated using real and synthetic data. The three-class model achieved the highest overall performance on the hold out test set (precision = 0.875, recall = 0.871, mAP50 = 0.883), with detection accuracy robust to host background and moderate object densities. Application to miticidal assays demonstrated reliable fecundity estimation but reduced accuracy for mortality assessment due to misclassification of dead mites. In hop cultivar assays, the pipeline detected significant differences in fecundity, aligning with manual counts (R2 [Formula: see text] 0.98). Performance declined on hosts absent from training data and at densities exceeding [Formula: see text]80 objects per image, underscoring the need for host-specific fine-tuning and density-aware assay experimental design. By enabling rapid, standardized, and reproducible quantification of mite life stages, this system offers a scalable alternative to manual scoring, particularly for resistance breeding programs targeting antibiosis traits. Our approach addresses major throughput bottlenecks in T. urticae phenotyping and establishes a framework for integrating automated imaging into broader pest management and plant breeding pipelines. Dataset, code, and trained models are publicly available to facilitate adoption and extension.

Plant disease monitoring metadata are a rich source of information for predicting pesticide use and costs on individual fields, farms, or regionally. Pesticide use patterns for management of hop powdery mildew (Podosphaera macularis) in Oregon were summarized by frequency of use of active ingredients and Fungicide Resistance Action Committee (FRAC) code. There was extensive variation in the frequency of use of specific active ingredients and FRAC codes among growers, ranging from a mean of 0 to 2.41 applications per yard. All growers used fungicides with FRAC codes 7/11 and 13; all but one grower used fungicide FRAC codes M02, NC, 3, and 11. Among fungicides with a moderate to high risk of developing resistance (FRAC codes 3, 5, 7, 7/11 premix, 11, or 13), the mean number of applications was ≤1.35 per yard across all growers and never exceeded four applications within a given yard. Hierarchical cluster analysis identified that the diverse use patterns could be categorized into three groups, which we define as pesticide programs. We fitted a random forest regression model and used Shapley values to quantify the importance of fungicide program in predicting the number of active ingredients applied and their costs relative to other known factors that influence these outcomes in individual yards. Pesticide program was the third most important variable predicting annual costs and the fifth most important predictor for the number of active ingredients applied. We also found hints that growers may switch between one of the three pesticide programs depending on the incidence of powdery mildew.

The hop powdery mildew fungus, Podosphaera macularis, has overcome host resistance when cultivars with a given form of genetic resistance are broadly deployed, as most recently experienced in the partially resistant hop cultivar Cascade. Hop is a long-lived perennial grown under production contracts; therefore, growers of Cascade hops must now manage powdery mildew because of contractual obligations. We developed and validated a modified powdery mildew risk index to aid in matching fungicide application intervals for foliar powdery mildew to weather favorability specifically for this cultivar. The modified risk index preserves the form and logic of the original hop powdery mildew risk index but lowers the cardinal temperature from 30 to 28 degrees C and introduces a low-temperature rule that reduces estimated daily risk points when temperatures are <= 4 degrees C for >= 2 h. During eight location-years of validation in commercial yards in Washington State, the modified disease risk index resulted in disease control comparable to fungicide applications made at regular intervals yet with up to two fewer applications in years predicted to be less favorable to powdery mildew. We separately evaluated the benefit of fungicide applications made after bloom for managing the cone phase of powdery mildew. In 5 years of studies, fungicide applications ceasing in mid-July yielded disease control and hop brewing quality metrics similar to applications made into mid-August. An effective and minimal input program for the cultivar Cascade can be achieved by adjusting fungicide application intervals appropriately in spring and omitting unnecessary fungicide applications 4 to 6 weeks before harvest.

Powdery mildew of hop is caused by Podosphaera macularis. This disease affects all green tissue of the hop plant, forming the characteristic signs of white colonies that bear mycelia and conidia and which lead to browning, shatter, and yield damage when infection occurs on the inflorescence. This report communicates efficacy data of various fungicides against powdery mildew. This trial was conducted on the hop cultivar ‘Zeus’ during the spring and summer of 2024, near Toppenish, Washington. Results from this trial will help producers develop more effective management approaches for the disease.

The Pacific Northwest (PNW) of the United States (Idaho, Oregon, and Washington) is the most important hop-producing region both nationally and internationally. However, little research on plant-parasitic nematodes has been conducted in the region. In this study, a total of 185 soil samples representing 93 hopyards were collected in 2021 and 2022 to characterize the plant-parasitic nematodes associated with this crop in the PNW. Ten different genera of plant-parasitic nematodes were found, with the hop cyst nematode, Heterodera humuli, second-stage juveniles (J2s) being the most frequently encountered (54% of the total samples and 65% of surveyed hopyards). The identity of selected H. humuli populations was confirmed by Sanger sequencing of the 28S rRNA gene. Other nematode taxa encountered in order of frequency of occurrence were Helicotylenchus, Telotylenchinae, Xiphinema, Paratylenchus, Pratylenchus, Trichodoridae, Ditylenchus, Gracilacus, and Mesocriconema. Heterodera humuli J2 densities were positively correlated with sand content based on the Spearman correlation coefficient. The host status of four hop cultivars ('Cascade', 'Centennial', 'Mosaic', and 'Citra') to three Meloidogyne species was also assessed under greenhouse conditions. Meloidogyne incognita reproduced on all four hop cultivars, with reproduction factor values (RF = final population density/initial population density) ranging from 5 to 40. The hop cultivars were non-hosts for M. chitwoodi (RF <= 0.1) and varied from non-host to host (RF = 0.1 to 3) for M. hapla. This study demonstrates the wide distribution of the most important plant-parasitic nematode in hop production, H. humuli, in the PNW and the host status of hop cultivars to different Meloidogyne spp.

Fusarium sambucinum is a plant pathogen involved in multiple pathosystems, including dry rot of potato (Solanum tuberosum) and Fusarium canker of hop (Humulus lupulus). As a causal agent of Fusarium canker, the pathogen is becoming increasingly important in the Pacific Northwest due to rising disease incidence over the last decade. To better understand the pathogen and facilitate future genomics research, two F. sambucinum isolates originally obtained from two common hosts in the United States, hop and potato, were sequenced and assembled using long-read sequencing technology. Four chromosomes were identified along with a mitochondrial genome sequence, resulting in a total genome size of 38 Mb. The hop-derived genome assembly, OSU_Fsam_1.1, is the first F. sambucinum genome associated with Fusarium canker of hop and is of high quality, with 89x coverage, a BUSCO completeness of 99.7%, and an N50 of 9.53 Mb. A total of 13,388 genes were annotated, including 39 secondary metabolite biosynthetic gene clusters, 1,219 carbohydrate-active enzymes, and 474 candidate effectors. The potato-derived genome, OSU_Fsam_2.1, has 185x coverage, 97.3% completeness, and N50 of 9.65 Mb. OSU_Fsam_1.1 and OSU_Fsam_2.1 are the first publicly available chromosome-level assemblies for F. sambucinum and the first assembled mitochondrial genome of F. sambucinum. These resources will greatly enhance future genomics research in the Fusarium sambucinum species complex.The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.