Project : USDA ARS

ARS Home » Pacific West Area » Corvallis, Oregon » Forage Seed and Cereal Research Unit » Research » Research Project #445259

Research Project: Development of Superior Hops and Resilient Hop Production Systems

Location: Forage Seed and Cereal Research Unit

2025 Annual Report

Objectives
Objective 1: Breed new hop varieties possessing superior traits including disease resistance, yield, and brewing characteristics. Sub-objective 1.A: Combine multiple sources of resistance to powdery mildew disease into new germplasm. Sub-objective 1.B: Evaluate, identify, and promote superior advanced female hop germplasm from the former Washington State University breeding program for potential public variety release. Sub-objective 1.C: Generate new variation via crossing, make selections, and advance selected material. Objective 2: Characterize hop germplasm for tolerance to priority traits such as water-use-efficiency and pest and disease resistance including systematic evaluation of powdery mildew resistance in new germplasm. Sub-objective 2.A: Assess germplasm for water use efficiency characteristics and abiotic stress resiliency. Sub-objective 2.B: Evaluate male germplasm for resistance to powdery mildew. Objective 3: Identify, characterize, and validate molecular markers associated with qualitative and quantitative traits of economic importance in hop such as novel powdery mildew resistance. Sub-objective 3.A: Identify molecular markers for WUE using bi-parental mating designs, genotyping-by-sequencing (GBS) and quantitative trait loci (QTL) analyses. Sub-objective 3.B: Identify and validate QTL in the hop cultivar Comet for quantitative resistance to powdery and downy mildews in field environments. Sub-objective 3.C: Develop a multi-parent population to identify novel sources of powdery mildew resistance and create and utilize a consensus genetic map. Objective 4: Evaluate management practices that improve crop productivity and crop health using computational analyses to identify optimal control policies for powdery mildew disease at the landscape level and abiotic stress physiology and management. Sub-objective 4.A: Assess reduced late-season irrigation as a cultural management strategy to improve hop cone quality. Sub-objective 4.B: Identify determinants and model pesticide use intensity at the field level based on characteristics of growers’ production systems.

Approach
Objective 1 Research include 1) develop new disease resistant varieties possessing unique, desirable brewing qualities, and 2) evaluate germplasm from Washington State University (WSU) for the same. Germplasm with different and complementary resistance will be crossed to produce offspring to be screened for disease resistance. Resistant offspring will be field-evaluated for resistance, agronomics, aroma and brewing chemistry. Germplasm evaluation from WSU includes screening for the same metrics. Possible challenges exist with 1) ensuring successful controlled pollination; addressed using greenhouses for crosses if necessary, and 2) inoculation for disease resistance screening; alleviated by multiple inoculation attempts. Objective 2 posits 1) hop varieties with higher water-use efficiency (WUE) can be identified, and 2) newly acquired male hop germplasm exhibits varying levels of powdery mildew resistance. Experiments to test hypotheses include 1) evaluating four hop varieties over two growth seasons near Prosser, WA for WUE, along with agronomic, physiological assessments, and brewing quality metrics, and 2) employing an elimination screening procedure with diverse isolates of the powdery mildew fungus. Contingencies include alternative strategies such as broadening hop variety evaluations and additional germplasm sources for Hypothesis 1, while Hypothesis 2 may involve additional genetic analyses or functional investigations. Objective 3 posits 1) WUE under drought conditions is under polygenic control, 2) quantitative trait loci (QTL) for resistance to downy and powdery mildew are consistent between greenhouse and field environments and 3) resistance to powdery mildew in male hops is heritable and novel. Bi-parental crossing schemes will be used to develop multiple populations. Populations will be phenotyped for WUE in the greenhouse or disease resistance in the field or via high-throughput systems. Germplasm will be genotyped using molecular methods. QTL statistical analyses will be performed to identify significant QTL. Contingencies for addressing problems range from use of increased water for WUE, use of spatial adjustment of phenotypic data for differences environmental conditions, and use of larger population sizes and/or increased depth of DNA sequencing. Objective 4 involves 1) developing late-season irrigation guidelines to improve hop quality, and 2) hypothesizes that production efficiency and pesticide use levels vary among farms and are explained by pathogen, host, and environment. Field studies will compare regular irrigation to reduced late-season irrigation for improving hop quality. Soil water will be monitored to maintain deficit water conditions. Yield and brewing quality metrics will be quantified. In 4.B data from industry cooperators or developed in-house will be used to identify determinants of pesticide use on commercial farms. Machine learning will be used to identify factors predicting pesticide use. Contingencies include increasing biological replicates to resolve irrigation effects and developing additional weather or biological variables to refine models if results do not describe pesticide use intensity.

Progress Report
This report documents FY 2025 progress for project 2072-21000-061-000D, “Development of Superior Hops and Resilient Hop Production Systems”, which began in March 2023. In support of Sub-objective 1.A, from the initial 1,000 offspring from the cross ‘Cascade x USDA 19058M”, previously challenged in the greenhouse with non-V6 isolates of powdery mildew (PM) followed by V6-isolates, ARS researchers in Corvallis, Oregon, selected approximately 200 for resistance. Selected offspring were transferred to the ARS hop farm during spring 2025 where they were subsequently placed in a selection nursery for a second round of PM selection along with selection for sex, cone (flower) morphology, aroma, and overall plant vigor. For Sub-objective 1.B, ARS evaluated approximately 56 advanced lines derived from crosses made with germplasm originating from a former Washington State University (WSU) program in replicated plots with commercial checks Cascade and Zeus in Prosser, Washington. Plots were evaluated for powdery mildew and downy mildew resistance, yield, full chemical analyses, cone morphology, and aroma characteristics, and a number were submitted for brewing evaluations. W1108-333 was an elite line from the WSU program, which was released in June 2025 as ARS Vera. The second line from the historical germplasm that is being pursued for release is continuing to be evaluated in a one-acre plot in Toppenish, Washington. Under Sub-objective 1.C, 29 successful crosses were made including parents with variable sources of powdery mildew resistance, producing 3540 seedlings. Seedlings were inoculated with V6- and Cascade-adapted isolates and susceptible individuals were culled, sexed using a molecular marker, and 989 seedlings were planted in Oregon to screen for downy mildew, and Washington to collect pollen (males) and evaluate for aroma, cone morphology, a visual estimate of yield, and vigor (females). Approximately 100 offspring originating from the W2023 seedling population were selected, cloned, and subjected to additional disease resistance screening in the greenhouse. After screening, approximately 28 lines were selected and propagated, and established in seven-hill plots in Prosser, Washington, for evaluation. In support of Sub-objective 2.A, research efforts continued for a second consecutive year to evaluate water use efficiency and abiotic stress resilience in three hop cultivars: Cascade, Citra, and Mosaic. These observations were assessed through a combination of yield and quality data, along with seasonal physiological monitoring, as plants were subjected to proper, excess, and deficit irrigation regimes. Yield data indicated that hop cone production remained stable as long as soil moisture levels stayed within the plant-available water range. However, among the cultivars, Citra exhibited a slightly higher sensitivity to yield reduction under deficit irrigation conditions. Intrinsic water use efficiency, a measure of how much carbon a plant can produce per unit of water it transpires through its leaves, was not substantially affected by either deficit or excess irrigation. For Sub-objective 2.B, studies continued on a subset of hop plants identified as resistant to all pathogenic races of the hop powdery mildew fungus that prevail in the western United States. These 13 hop accessions were challenged by three new isolates with novel virulences not present in the U.S. Among these 13, ARS identified seven with resistance that is not based on two known and widely deployed resistance genes (termed R1 and R2). They then challenged these seven resistant accessions with a different isolate of the fungus with a novel virulence dubbed VWH18. Two of the seven accessions were resistant to all isolates used for inoculation. Of the group of seven resistant genotypes, one was already publicly available, and the remaining six will be released to the public in 2025 and were deposited in the ARS National Clonal Germplasm Repository in Corvallis, Oregon. Importantly, these seven lines possess two distinct sources of resistance that appear novel and are resistant to all extant isolates of the pathogen in the United States. Under Sub-objective 3.A, ARS researchers identified approximately 265K high-quality markers across 220 offspring for use in developing a genetic map for the cross, “Cascade x USDA 19058M”. Of these markers, about 5,900 markers across all chromosomes were selected and utilized to develop genetic maps for QTL studies on drought. The 220 individuals along with parents were transferred into the greenhouse from overwintering at the hop farm during spring 2025. The first round of parents and 220 offspring were subsequently cloned for replicated trials and a controlled irrigation system set up to deliver water once plants reach the appropriate developmental style. In support of Sub-objective 3.B, the Comet x 64035M bi-parental population was maintained in a randomized complete block design in Washington for field evaluation of powdery mildew resistance. Disease incidence and severity in 2024 was high and two disease ratings were collected on the population. Marker analysis using the phenotype and genotype data demonstrated that the same markers were identified in the field as were reported previously, suggesting the marker is associated with a form of resistance that is reliable in a field setting. Various combinations of KASP markers are currently being evaluated for use in marker-assisted-selection, and the population is being monitored currently for an additional rating opportunity. For Sub-objective 3.C, ARS researchers curated all phenotypic data from the population resulting from the Blackbird image capture system and human raters and calculated summary statistics. Whole genome sequencing data was obtained on the five parental lines used in the population, and a targeted genotyping-by-sequencing approach was carried out on the progeny. Markers were identified, filtered, and curated, and population structure analyses were completed. Further analyses will be underway in the coming year to develop a genetic map and conduct QTL mapping to elucidate the genetic control of presumably novel forms of resistance to powdery mildew. Under Sub-objective 4.A, ARS completed the final steps for this study and published the results in the Journal of the American Society for Horticultural Science. This study examined the effects of late-season irrigation lapses on hop physiology, cone yield, and brewing quality using the Cascade cultivar in Washington’s Yakima Valley. Irrigation was withheld either 15 or 30 days prior to harvest and compared to fully irrigated controls. ARS found that even brief irrigation lapses induced significant physiological stress, including reduced stomatal conductance, lower photosynthetic efficiency, and increased leaf temperatures, despite soil moisture levels remaining above critical thresholds. Yield declined by 9.5% with a 15-day lapse and by 28.8% with a 30-day lapse, underscoring the heightened sensitivity of hops to early stress during cone development. While a- and ß-acid concentrations remained stable, total oil content and essential oil profiles were markedly affected with individual terpenes either declining or increasing under water stress. These findings underscore the importance of maintaining near-optimal soil moisture through cone maturation to safeguard yield and aroma quality, particularly under increasing climate variability. In support of Sub-objective 4.B, ARS researchers extended modeling analyses using a data set of powdery mildew incidence on hops from yards in Oregon during 2014 to 2017 and associated metadata on grower cultural practices, cultivar susceptibility to powdery mildew, and pesticide application records. This is one of the most extensive data sets of this type in plant pathology, and a rich source of information for predicting pesticide use and costs in individual fields, farms, or regionally. Scientists analyzed pesticide use patterns by frequency of use of active ingredients and fungicide mode of action. They applied a machine learning method (hierarchical cluster analysis) and identified that the diverse pesticide-use patterns followed by growers fell into three groups defined as “pesticide programs”. Predictive machine learning methods indicated that growers’ general fungicide program was among the most important factors influencing how much pesticide they applied and the annual costs they incurred. This indicates that growers may be able to both reduce pesticide use and costs by adopting one of the lower input pesticide programs that are already in use. Models were developed for estimating the probability that growers would apply a more potent and more expensive synthetic fungicide rather than a non-synthetic alternative. Overall, growers switch from non-synthetic fungicides to more active and expensive synthetic fungicides at critical periods of crop susceptibility, and when expected or observed disease incidence increases. Reducing use of synthetic fungicide input appears to be closely linked to disease risk mitigation, as risk mitigation is linked to growers’ decision to switch to these more potent fungicides or fungicide mixtures. In the second analysis in support of Sub-objective 4.B, ARS researchers identified 30 commercial hop yards for field surveys to acquire data on pesticide use determinants in Washington State, a distinct environment and production region from that used earlier. They collected disease data and grower production meta-data from these yards in 2024. From this data set, scientists will conduct analyses to validate the findings from the data set collected in Oregon and develop models to predict pesticide use intensity and management factors that can reduce pesticide use and costs.

Accomplishments
1. New guidelines to mitigate yield and quality losses during late-season irrigation lapses in hops. Drought-driven reductions in late-season water availability increasingly threaten high-value crops like hops, which rely on irrigation during cone maturation. In a two-year study, ARS scientists in Prosser, Washington, found that withholding irrigation 15 to 30 days before harvest caused significant physiological stress in Cascade hops and led to yield losses of almost 30%. Although bittering compounds (a- and ß-acids) remained stable there were changes to the essential oil profile, which is critical to brewing quality. These changes have serious implications for hop growers, brewers, and stakeholders in the Yakima Valley, where over 70% of U.S. hops are produced. Maintaining stable yield and aroma profiles is essential to meet brewing industry demands and sustain economic viability. This research provides actionable evidence to support irrigation decisions that reduce the risk of quality and yield loss, helping ensure the resilience of hop production.

2. Release of a new public hop variety, USDA-ARS Vera. Brewers and hop growers alike seek new aroma hops with improved disease resistance. ARS researchers in Prosser, Washington, developed USDA-ARS Vera, a new aroma hop that offers resistance to hop powdery mildew and a unique and complex tropical, stone-fruit and citrus aroma. This variety release emerged from a large-scale effort to evaluate germplasm from a former Washington State University hop breeding program. Brewers that have used USDA-ARS Vera in pilot brews have reported positive internal reviews while growers have identified good yields with reduced pesticide inputs. Clean plant stock of USDA-ARS Vera has been created and is publicly available and free of intellectual property rights restrictions and serves as a new option for brewers and growers.

3. Release of six new powdery mildew resistant hop genotypes for use in breeding. Hop powdery mildew is one of the most important diseases of hop and the causal pathogen has been known to overcome many forms of host plant resistance. Breeding for novel sources of resistance is a major objective in hop as it is one of the most effective and efficient ways of reducing disease losses. ARS researchers in Corvallis, Oregon, and Prosser, Washington, identified seven lines possessing resistance to five of six isolates of the pathogen, and two lines with resistance to all isolates tested. The powdery mildew isolates used in our study represent the known pathogenic diversity in the U.S. and Europe. The newly released lines can be used by hop breeding and research community to breed novel sources of resistance for hop production.

U.S. DEPARTMENT OF AGRICULTURE

Forage Seed and Cereal Research Unit: Corvallis, OR