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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Research Project #432469

Research Project: Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

2021 Annual Report

Objective 1: Describe the pathogen biology and disease epidemiology of exotic and emerging plant pathogens affecting horticultural crops. Sub-objective 1A: Comparative genomics of Phytophthora pathogens. Sub-objective 1B: Population genomics and evolution of Phytophthora pathogens. Sub-objective 1C: Characterize the fungal, oomycete and bacterial microbiome associated with horticultural crops. Sub-objective 1D: Disease surveys of small fruits in the Pacific Northwest. Objective 2: Develop improved integrated disease management of pathogens of horticultural crops. Sub-objective 2A: Integrate disease risk forecasters with models for air turbulence to predict pathogen dispersal and spatially explicit disease risk. Sub-objective 2B: Develop methods to monitor presence of fungicide resistance in pathogen inoculum. Sub-objective 2C: Optimize fungicide selection and application timing to manage powdery mildew on grape berries. Sub-objective 2D: Identify inoculum sources of Botrytis cinerea in caneberry fields and evaluate methods to reduce overwintering populations. Sub-objective 2E: Develop and evaluate alternative control measures for management of diseases that reduce fruit yield or quality.

The long-term goal of this project is to develop the knowledge and tools needed to respond to plant disease epidemics using approaches that are economically and environmentally sustainable, with emphasis on increasing our ability to respond to exotic, emerging, and re-emerging pathogens. This will be accomplished through trans-disciplinary approaches that increase our knowledge of pathogen genetics, biology, and disease epidemiology and incorporates this information into decision support aids for horticultural crops. The biology of exotic, emerging, and re-emerging plant pathogens is either poorly understood or inadequate to enable economic and environmentally sustainable management. We will develop and test methods for monitoring pathogen dispersion and describe the genomes, evolutionary history, population structure, genetics, epidemiology, and ecology of these pathogens. This knowledge will then be used in Objective 2 to develop decision support tools for producers of horticultural crops. Once there is a more detailed understanding of pathogen ecology, this knowledge will be translated into disease management strategies that are continually optimized and/or improved to address changing climate, market and regulatory pressures. We will develop and improve disease management strategies for select pathogens affecting horticultural crops. The development and improvement of integrated disease management strategies for endemic pathogens will also improve our ability to respond to changing climatic conditions while enhancing the economic and sustainable production of horticultural crops.

Progress Report
In support of Sub-objective 1A, related to comparative genomics of Phytophthora pathogens, whole genomes of five P. ramorum strains were sequenced using Pacific Biosciences long-read technology and assembled. This technology allows assembly of a much more contiguous genome assembly with less missing data. In support of Sub-objective 1B, related to population genomics and evolution of Phytophthora pathogens, we identified two new invasions of the sudden oak death pathogen into U.S. forests, including the EU1 and NA2 clonal lineages. This result documents that we are seeing continued migration of the sudden oak death pathogen in the nursery industry. Sub-objective 1C relates to characterizing the fungal, oomycete and bacterial microbiome associated with horticultural crops. Red raspberry samples that were collected in 2019, freeze dried, and stored at -80 C were processed and total DNA was extracted from nearly 400 samples. We sequenced the microbiome of year one red raspberry samples and found that over 98% of reads were from amplification of raspberry DNA; too few of the sequences were from the microbes residing in or on plant tissues for statistical analyses. We designed new peptide nucleic acid (PNA)-clamps to block amplification of raspberry DNA. Consequently, we have increased depth of sequencing of bacteria, fungi and yeasts in the raspberry tissues to levels appropriate for statistical analyses of the changing microbiome from bloom to berry harvest. Sub-objective 1D relates to disease surveys of small fruits in the Pacific Northwest. Disease surveys were limited this past year to a few blackberry, blueberry, and cranberry fields in Oregon due to pandemic-related out-of-state travel and staffing restrictions. We isolated a fungal pathogen causing cane canker and wilt in blackberries that has not been previously reported in this region. From blueberry, we isolated the unique aerial stem gall bacterial pathogen by generating tissue culture explants, which reduced environmental contaminants and permitted isolation from developing galls on a general microbiological medium. From cranberry, we isolated several fungal fruit rot pathogens known to cause disease in other areas of the United States. Labor-intensive fungicide resistance assays are underway, but progress is slow due to pandemic-related limits on staffing of labs. Sub-objective 2A relates to integrating disease risk forecasters with models for air turbulence to predict pathogen dispersal and spatially explicit disease risk. Fortunately, we had been able to move particle release experiments planned for 2020 to 2019 and were thus not impeded by the pandemic restriction. The Quick Urban and Industrial Complex (QUIC) 3D wind model simulations were improved, such that we could make predictions on the source probability for particles captured by an impaction sampler and allow for assessment of how sampler placement (height or location) impacts probability of detection. A new software tool was developed that simulates disease epidemics and assesses probability of visual or impaction sampler sampling strategies. Sub-objective 2B relates to developing methods to monitor presence of fungicide resistance in pathogen inoculum. We demonstrated that the glove sampling technique we have been developing was more sensitive and cost effective to detecting disease in the field than visual scouting or spore samplers. Additionally, we demonstrated SDHI (succinate dehydrogenase inhibitors; FRAC group 7) resistance in grape powdery is likely developing and could become a management issue in the coming years. We also developed DNA methods for monitoring SDHI resistance in addition to molecular markers for resistance to quinone outside inhibitor (QoI) and demethylation inhibitor (DMI) fungicides. The results have been widely disseminated through numerous talks and popular press presentations, as well as by making protocols available for sampling molecular detection of resistance alleles. Sub-objective 2C relates to optimizing fungicide selection and application timing to manage powdery mildew on grape berries. We completed research and published a manuscript on targeted application of redistributing fungicides for management of grape powdery mildew. We also delivered several presentations on these results and improved management recommendations. Sub-objective 2D relates to identifying inoculum sources of Botrytis cinerea in caneberry fields and evaluating methods to reduce overwintering populations. We initiated research to evaluate methods to detect overwintering inoculum of Botrytis in caneberry fields. The full experiment was postponed due to reduced laboratory time in order to maintain pandemic mitigation protocols. Sub-objective 2E relates to developing and evaluating alternative control measures for management of diseases that reduce fruit yield or quality. We found that Botrytis cinerea is very sensitive to aluminum salts. Low concentrations of 1 part per million aluminum sulfate were lethal to the pathogen in culture. In a field trial on blackberry, we found that three applications of aluminum sulfate or aluminum potassium sulfate (Alum) reduced the incidence of yellow rust on blackberry fruits by 30% and the incidence of gray mold by 50% compared to the water-treated control, but the differences were not significant, likely due to low disease incidence. Berry weight and yield was significantly greater on aluminum sulfate treated plants compared to water-treated plants. We also initiated evaluation of six multi-fungicide tolerant isolates of Aureobasidium pullulans and the commercial biocontrol agent, Botector (A. pullulans, fungicide sensitive, Westbridge Agricultural Products), for gray mold management in blackberry. The incidence of gray mold was significantly reduced by approximately 50% on plants treated once with Botector or one of the six fungicide-tolerant yeast isolates. Mean berry weight was not significantly different among treatments. We will continue to evaluate the efficacy of these alternative control measures for gray mold.

1. Sctillometery for assessment of temperature and vapor flux over vineyards. Laser-based methods (Sctillometery) for assessing temperature and moisture changes over large heterogeneous vineyards were developed by ARS researchers in Corvallis, Oregon. These techniques allow for long term measurement of fine scale changes in vineyards without interfering with vineyard operations. This approach will aid the development of improved predictive models for pest and pathogen spread and disease development as well as improved assessment of water use and developing predictive models for plant growth that will aid vineyard managers’ decision making.

2. Improved sampling technique for monitoring grape powdery mildew in vineyards. Grape powdery mildew is a problem for grape growers. ARS researchers in Corvallis, Oregon, demonstrated that a cotton swab could be used to collect grape powdery mildew spores from worker gloves or other materials that came in contact with the plant canopy. The swabs can then be processed for molecular detection and quantification of the pathogen and to determine the presence of fungicide resistance markers. This method was cheaper and more easily deployed than current spore samplers and had similar results. The glove swab method was significantly more sensitive at detection than traditional visual disease scouting and is more time efficient. Results will be used by growers to improve sampling for this important pathogen of grapevines.

3. Identification of novel variants to the sudden oak death pathogen in U.S. forests. Sudden oak death caused by the water mold Phytophthora ramorum continues to invade U.S. forests. ARS scientists in Corvallis, Oregon, detected novel variants of the sudden oak death pathogen using genetic analysis. This analysis identified novel introductions of two clonal lineages into U.S. forests. This information provides insights for regulatory agencies and forest managers to understand pathways of introduction of the sudden oak death pathogen.

Review Publications
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.
Oliver, C.L., Cooper, M., Lewis-Ivey, M.L., Brannen, P., Miles, T., Mahaffee, W.F., Moyer, M.M. 2021. Assessing the wine grape industry’s understanding of fungicide resistance mitigation practices for grapevine powdery mildew (erysiphe necator) in the United States. American Journal of Enology and Viticulture. 72(2):181-193.
Wiman, N.G., Andrews, H., Rudolph, E., Lee, J.C., Choi, M.Y. 2020. Fatty acid profile as an indicator of larval host for adult drosophila suzukii. Insects. 11(11). Article 752.
Garbelotto, M., Schmidt, D., Dovana, F., Lee, C., Fieland, V.J., Grunwald, N.J., Valachovic, Y. 2021. First reports of phytophthora ramorum clonal lineages NA1 and EU1 from tanoaks in Del Norte county, California. Plant Disease.
Weisberg, A.J., Putnam, M.L., Grunwald, N.J., Savory, E.A., Chang, J.H. 2021. Genomic approaches to characterize plant pathogen epidemiology and develop diagnostics. Annual Review of Phytopathology. 59:311-332.
Rasmussen, D.A., Grunwald, N.J. 2020. Phylogeographic approaches to characterize the emergence and spread of plant pathogens. Phytopathology. 111(1):68-77.