Location: Forage Seed and Cereal Research Unit
2021 Annual Report
Objectives
The goal of this project is to maintain and enhance the competitiveness of the U.S. hop industry through development of publicly available genetic resources, tools, and knowledge-based pest management systems. This will be accomplished through interdisciplinary research that addresses high priority documented stakeholder needs. Over the next 5 years, the specific objectives to be accomplished are:
Objective 1: Develop and release new hop cultivars and germplasm possessing superior disease resistance, yield, and brewing characteristics. (Henning)
Objective 2: Identify, characterize, and validate molecular markers associated with qualitative and quantitative resistance to important foliar diseases. (Henning)
Objective 3: Identify molecular markers associated with virulence of Podosphaera macularis and use the information to rapidly determine pathogen races. (Gent)
Objective 4: Quantify the aggressiveness, fitness, and race of Podosphaera macularis isolates able to overcome partial host resistance and identify new sources of resistance to diverse strains of the pathogen in public germplasm. (Gent)
Sub-objective 4A: Characterize the aggressiveness, fitness, and race of Podosphaera macularis virulent on the cultivar Cascade. (Gent)
Sub-objective 4B: Identify and quantify the impact of supraoptimal temperature on host susceptibility to and development of powdery mildew on the cultivar Cascade. (Gent)
Sub-objective 4C: Characterize publicly available male germplasm for its reaction to multiple strains of Podosphaera macularis. (Gent)
Approach
Objective 1 Research Goal: Develop multiple pathogen resistant germplasm or cultivars. Controlled crosses of cultivars two cultivars will be made using resistant males. Progeny will be screened for disease resistance and phenotypic traits including hop aroma. Selected offspring will be advanced for further evaluation.
Objective 2 Research Goal: Identify molecular markers associated with plant resistance to P. humuli and P. macularis. Genetic maps and genome-wide surveys for marker association will be conducted using a bi-parental mapping population derived from a powdery mildew resistant female line and a downy mildew resistant male line.
Objective 3 Hypothesis: Markers associated with pathogenic variation in P. macularis can be identified. Isolates of P. macularis from Pacific NW will be collected and race-validated using differential host panels. RNA will be collected from P. macularis isolates and subsequently sequenced using next gen sequencing. SNP markers will be identified from this data. SNPs will be used to fingerprint different isolates and a set of unique markers for each isolate identified.
Sub-objective 4A Hypothesis: Strains of P. macularis virulent on Cascade are specifically adapted to this cultivar. Controlled environment experiments will be conducted to determine the aggressiveness and fitness of isolates of P. macularis originating from Cascade to provide fundamental information to guide breeding efforts and disease risk assessment. These races will also be characterized using a differential set of cultivars possessing different resistance genes.
Sub-objective 4B Hypothesis: Partial resistance to powdery mildew in the Cascade is modulated by brief exposure to supra-optimal temperature. An extensive set of controlled environment studies will be conducted to define the environmental conditions that moderate infection risk on the Cascade to derive rules for adapting the HOPS powdery mildew risk index to Cascade and similar cultivars.
Sub-objective 4C Research Goal: Characterize resistance of USDA males to multiple strains of powdery mildew. A set of 150 individuals –resistant to downy mildew--will be tested for their resistance to multiple races of P. macularis. Resistance to three different isolates-each with unique virulence genes—will be sequentially scored across all male lines. Remaining resistant individuals will be further evaluated to determine the nature of resistance.
Progress Report
Research continued on Objective 1, completing the second year of evaluating nursery seedlings for both downy mildew and powdery mildew in the field. Continual evolution of consumer tastes along with evolving plant pathogens require the development of new public cultivars possessing both disease resistance as well as other economically important traits. We observed that selection for powdery mildew resistance in the earlier greenhouse stages of this project was more successful than selection for downy mildew resistance at identifying resistant individuals and culling susceptible lines. Of the 350 female offspring advanced to field observations, only two possessed powdery mildew colonies with only one ranked as “highly susceptible”. Forty-nine of the 350 offspring exhibited symptoms of infection from downy mildew, with an average score of these non-resistant lines equaling 2.9 [Scale = 1 (highly tolerant) to 5 (highly susceptible)]. 278 lines appear to be highly tolerant under normal field practices performed by producers in Oregon. The remaining 21 lines failed to thrive during greenhouse operations and were discarded. Nevertheless, a third year of observations on disease scoring will be performed, as additional yield and chemistry data are also required for advancement to the next stage of selection. Yield and chemistry evaluations will continue on these lines. This research is vital towards the development of new public cultivars possessing disease resistance, high yields, and superior aroma and brewing characteristics for the highly successful craft brewing industry of the United States.
In support of Objective 2, we completed the first and second rounds of scoring to determine the genetics of downy mildew tolerance. We also completed the genetic map for a mapping population and used it to identify genomic regions affiliated with quantitative resistance to powdery mildew possessed by the hop cultivar, ‘Comet’. We successfully identified putative genetic markers for use in molecular assisted breeding for quantitative powdery mildew resistance. This is the first molecular characterization of quantitative disease resistance in hop. These results have importance for hop breeders as quantitative resistance is significantly more durable than qualitative, or gene-for-gene, resistance. Historical evidence in hop had documented the rapid loss of resistance across multiple cultivars possessing the same R-gene when qualitative resistance was the primary defense against infection. Conversely, quantitative resistance in other crops has proven to be more durable, typically providing protection against pathogens many years beyond that observed for qualitative resistance. The characterization of quantitative resistance along with identification of molecular markers for this trait will enable breeders to develop cultivars with potentially more durable resistance than what is currently available.
In support of Objective 3, we completed development of a simple and rapid diagnostic assay that can differentiate between two widely prevalent disease-causing races of the hop powdery mildew fungus. Differentiating the races is beneficial for the industry, as only one of the three prevailing races is currently able to defeat the hop disease resistance gene widely found in cultivated hop varieties in the Pacific Northwest. This assay will potentially provide an early warning system on the prevalence of infectious races of the powdery mildew fungus in a region. We adapted the DNA test for a platform that is scalable and able to detect the genetic variant associated with virulent strains of the fungus in hundreds of samples. In this high-throughput platform, the DNA test had the perfect ability to differentiate strains of the fungus that derived from cultivars with or without the powdery mildew resistance of interest. This is a major advancement over traditional methods that may take weeks to determine the race of a given strain of the fungus. From a single diseased leaf, we can now predict pathogen virulence in hours, which is critical for knowing which cultivars may be susceptible to infection by a particular isolate of the pathogen.
The cultivar ‘Cascade’ has been grown in the U.S. hop industry for decades but historically was not seriously affected by powdery mildew due to its partial resistance to the disease. New, virulent strains of the hop powdery mildew fungus emerged in sync with expansion of the cultivar Cascade over the past decade, requiring growers to implement cost control measures where none were required previously. In support of Sub-objective 4A, we expanded the scope of this research to determine if the powdery mildew fungus develops local adaptation for increased aggressiveness on any cultivar, even those that do not possess known resistance to the disease when a given cultivar is widely grown in the landscape. Using the cultivar Citra as a contemporary example, we discovered that there is variation in virulence among strains of the hop powdery mildew fungus derived from Citra as compared to strains derived from other cultivars. At present, though, none of the pathogen isolates evaluated are able to cause severe disease on this cultivar. This has important implications for how, when, and where host resistance is developed and deployed in the landscape to maximize the durability of genetic disease resistance.
In support of Sub-objective 4B, given that powdery mildew resistance in the cultivar Cascade was overcome by a host-adapted strain of the hop powdery mildew fungus, there is an urgent need for growers to manage the disease to minimize crop damage. In previous years, we synthesized information from the field and controlled environment studies to develop a powdery mildew risk index to estimate disease hazards on the cultivar Cascade based on current and forecasted weather. A beta version of a web application and an automated email notification system was developed with university collaborators and revised based on usability testing with stakeholders. We planned, initiated, and conducted field studies to validate the decision aid. Under disease-favorable conditions during the 2020 growing season, the decision aid tool correctly predicted high hazards from the disease. The second year of validation is underway.
In support of Sub-objective 4C, powdery mildew screening of 136 male accessions of hop in the USDA germplasm collection was completed, and resistance to all known extant strains of the powdery mildew fungus was identified in a subset of germplasm. We began work to expand the screening to include germplasm that the USDA recently acquired from the former Washington State University hop breeding program. Further, we expanded a collaboration with researchers at the University of Minnesota to validate molecular markers associated with an important source of resistance to powdery mildew, called R1. This research should lead to a novel DNA-based approach that can quickly identify R1-based resistance in plants without the need for laborious and time-consuming methods based on inoculation.
Accomplishments
1. Decision aid for spider mite damage to hop cones. Twospotted spider mites are cosmopolitan pests in agriculture, including on hop. Routine management of spider mites with synthetic pesticides is common in commercial hop production to maintain crop quality and yield. However, there is likely widespread overuse of pesticides because no formal guidelines exist on when the pest actually is most likely to cause crop damage. ARS researchers at Corvallis, Oregon, and university collaborators, identified risk factors for pest outbreaks and developed mathematical risk algorithms to predict when hops are most likely to suffer damage from the pest. The risk algorithm can form the basis of a decision aid to estimate when and where control of pests is warranted and safely reduce unnecessary inputs and enhance the overall sustainability of the industry.
2. Genetic characterization of durable resistance to hop powdery mildew. Hop breeding has traditionally focused on implementation of non-durable, qualitative, or gene-for-gene, resistance. This focus resulted in cycles of new resistant cultivars losing resistance over time as the pathogen evolves and responds accordingly. ARS researchers at Corvallis, Oregon, and university collaborators, identified and genetically characterized one source of quantitative resistance to powdery mildew and identified putative molecular markers for this trait. Quantitative resistance appears to be under the control of three separate regions of the hop genome, with each region possessing multiple copies of genes similar to plant resistance genes found in other crop plants. Markers for quantitative resistance to powdery mildew in hop may enable breeders to select for and incorporate this trait into new varieties.
3. Scalable molecular markers for pathogen genotyping. Management of emerging and endemic plant diseases often is limited by a lack of knowledge of which strains of the pathogen are present and traits associated with the strain’s geographic origin, fungicide resistance, and host range. This is the case with the hop powdery mildew fungus, which exists in unique populations in different parts of the United States and world, and where knowledge of pathogen genotype could greatly inform appropriate disease mitigation efforts. Researchers with ARS in Corvallis, Oregon, Geneva, New York, and university collaborators, identified a set of molecular markers that can predict whether a given strain of the hop powdery mildew fungus is endemic to the western United States or exotic, and virulent on a widely deployed hop resistance gene. The markers were successfully adapted for a high throughput genotyping system that can simultaneously evaluate hundreds of markers on hundreds of samples. This technology will be foundational for rapidly responding to new outbreaks of the disease and tailoring management to match the specific strain of the fungus present.
4. Genomic regions controlling sex expression in hop characterized. Breeders of other Cannabaceae crops chemically induce female cultivars to produce male flowers and pollen, enabling breeders to directly combine the characteristics of developed cultivars and obtain only female offspring from the cross. This technique has not been successful in hop. Understanding the genetic control of sex in hop would potentially provide breeders tools to perform similar techniques in hop. ARS researchers at Corvallis, Oregon, and university collaborators, identified regions of sex chromosomes that do not recombine and contain concentrations of genes controlling flowering or pollen action. This basic information provides a first look at the genetic control of flowering in hop and will ultimately aid breeders to make crosses resulting only in female offspring.
Review Publications
Altendorf, K.R., Dehaan, L.R., Heineck, G.C., Zhang, X., Anderson, J.A. 2020. Floret site utilization and reproductive tiller number are primary components of yield in intermediate wheatgrass spaced plants. Crop Science. 61(2):1073-1088. https://doi.org/10.1002/csc2.20385.
Block, M., Knaus, B.J., Wiseman, M., Grunwald, N.J., Gent, D.H. 2021. Development of a diagnostic assays for race differentiation of Podophaera macularis. Plant Disease. 105(4):965–971. https://doi.org/10.1094/PDIS-06-20-1289-RE.
Eriksen, R.L., Padgitt-Cobb, L., Townsend, M., Henning, J.A. 2021. Gene expression for secondary metabolite biosynthesis in hop (Humulus lupulus L.) leaf lupulin glands exposed to heat and low-water stress. Scientific Reports. 11. Article 5138. https://doi.org/10.1038/s41598-021-84691-y.
Weldon, W.A., Marks, M.E., Gevens, A.J., D'Arcangelo, K., Quesada-Ocampo, L.M., Parry, S., Gent, D.H., Cadle Davidson, L.E., Gadoury, D.M. 2021. A comprehensive characterization of ecological and epidemiological factors driving perennation of Podosphaera macularis chasmothecia. American Phytopathological Society. https://doi.org/10.1094/PHYTO-11-20-0492-R.
Gent, D.H., Claassen, B.J., Massie, S.T., Phillips, C.L., Shellhammer, T.H., Trippe, K.M., Twomey, M.C. 2021. Delayed early season irrigation: impacts on hop yield and quality. Journal of the American Society of Brewing Chemists. 80:62-65. https://doi.org/10.1080/03610470.2021.1915053.
Purayannur, S., Gent, D.H., Miles, T.D., Radisek, S., Quesada-Ocampo, L. 2021. The hop downy mildew pathogen Pseudoperonospora humuli. Molecular Plant Pathology. 22(7):755-768. https://doi.org/10.1111/mpp.13063.
Weldon, W.A., Knaus, B.J., Grunwald, N.J., Havill, J.M., Block, M.H., Gent, D.H., Cadle Davidson, L.E., Gadoury, D.M. 2020. Transcriptome-derived amplicon sequencing (AmpSeq) markers elucidate the U.S. podosphaera macularis population structure across feral and commercial plantings of Humulus lupulus. Phytopathology. 111:194-203. https://doi.org/10.1094/PHYTO-07-20-0299-FI.
Block, M., Wiseman, M.S., Gent, D.H. 2021. Characterization of Podosphaera macularis derived from the hop cultivar ‘Strata’ and resistance to powdery mildew. Plant Health Progress. 22(2):154-156. https://doi.org/10.1094/PHP-11-20-0095-BR.
Crandall, S.G., Ramon, M.L., Burkhardt, A.K., Bello, J.C., Adair, N., Gent, D.H., Hausbeck, M.K., Quesada-Ocampo, L.M., Martin, F.N. 2021. A multiplex TaqMan qPCR assay for detection and quantification of clade 1 and clade 2 isolates of Pseudoperonospora cubensis and Pseudoperonospora humuli. Plant Disease. https://doi.org/10.1094/PDIS-11-20-2339-RE.
Wiseman, M., Ocamb, C., Bates, T., Garfinkle, A., Gent, D.H. 2021. First report of powdery mildew caused by Golovinomyces ambrosiae on Cannabis sativa in Oregon. Plant Disease. https://doi.org/10.1094/PDIS-11-20-2455-PDN.
Woods, J.L., Iskra, A.E., Gent, D.H. 2021. Predicting damage to hop cones by Tetranychus urticae (Acari: Tetranychidae). Environmental Entomology. 50(3):673-684. https://doi.org/10.1093/ee/nvab008.
Padgitt-Cobb, L.K., Kingan, S.B., Wells, J., Elser, J., Kronmiller, B., Moore, D.L., Concepcion, G., Peluso, P., Rank, D., Jaiswal, P., Henning, J.A., Hendrix, D.A. 2021. A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. The Plant Genome. 14(1). Article e20072. https://doi.org/10.1002/tpg2.20072.
Henning, J.A., Townsend, M., Gent, D.H., Wiseman, M., Walsh, D., Groenendale, D., Randazzo, A. 2021. Registration of high-yielding aroma hop (Humulus lupulus L.) cultivar, ‘USDA Triumph'. Journal of Plant Registrations. 15(2):244-252. https://doi.org/10.1002/plr2.20138.
