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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

2018 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
Under Objective 1, ARS scientists in Corvallis, Oregon, described the pathogen biology and disease epidemiology of exotic and emerging plant pathogens affecting horticultural crops to develop improved understanding of pathogen emergence and help guide research on disease management. Under Sub-objective 1A, ARS researchers focused on a comparative genomic analysis of Phytophthora pathogens. The genomes of Phytophthora rubi and P. fragariae were sequenced and distinct genomic features were analyzed. In Sub-objective 1B, ARS scientists characterized the population genomics and evolution of Phytophthora pathogens. This research documented that a new clonal lineage was introduced into Oregon forests. Similarly, population of the raspberry pathogen Phytophthora rubi, were shown to migrate on the West coast. This work directly relates to characterizing the pathogen biology of exotic and emerging plant pathogens affecting horticultural crops. These results are being used by state and federal agencies, the private sector, and crop consultants to manage outbreaks in forests along the west coast of the United States, to manage quarantine in nurseries growing host plants susceptible to this pathogen, and to manage pathogen in production systems. Identification of specific pathways of migration of the pathogen have aided in a more rational design of federal and state quarantine programs. In Sub-objective 1C, ARS researchers characterized the fungal, oomycete and bacterial microbiome associated with horticultural crops. The fungal and oomycete microbiome was characterized for variation among cultivars, nurseries and potted versus field-grown plants. This work lays the foundation for understanding what a healthy microbiome looks like and provides new insights into which members of the microbiome are highly variable and what factors influence microbiome assembly. In Sub-objective 1D, ARS scientists conducted disease surveys of small fruit crops, which provided a means to meet with stakeholders and hear their concerns and challenges. Gray mold, caused by the fungus Botrytis cinerea, is a perennial concern for production of soft-skinned small fruits. Fungicides are applied frequently from bloom to harvest to control gray mold. This research found resistance to three of the five classes of fungicides commonly used for gray mold control was detected in isolates of the pathogen from small fruit fields, leaving growers with fewer options for disease control. Disease surveys revealed a) a new floral disease of raspberry and blackberry, in which a fungus identified as a Monilinia spp. was isolated from diseased tissues; b) a damaging outbreak of aerial crown gall of blueberry caused by the bacterium Agrobacterium tumefaciens, was recorded in several mature fields; c) a lethal stem disease called silver leaf caused by the fungus Chondrostereum purpureum was observed in several young blueberry fields; and d) cane blight symptoms were noted in mechanically-harvested raspberry and blackberry fields. Currently, few options exist for management of these diseases, except for removal of the symptomatic plants. Research to improve diagnosis of the diseases and management strategies is underway. Under Objective 2, ARS researchers developed improved integrated disease management of pathogens of horticultural crops. Under Sub-objective 2A, particle release and capture experiments were conducted that measured plume spread and air turbulence 180 meters from point of release. These data sets are being analyzed to aid in the development of spatial disease risk for disease forecasting models. This data will also aid in research to understand and estimate risk of fungicide resistance development. In Sub-objective 2B, two quantitative polymerase chain reaction (qPCR) assays were developed to examine E. necator samples for genetic markers associated with fungicide resistance to FRAC 11 and FRAC 3 fungicide classes. FRAC is number/letter system assigned by the Fungicide Resistance Action Committee to group active ingredients that exhibit probability for cross resistance. Examination of a collection of 73 isolates of E. necator for resistance to FRAC 3 and FRAC 11 fungicides demonstrated isolates that were resistant to one fungicide in a FRAC class were also resistant to the other fungicides in that class. For FRAC 11 chemistries, the isolate had a lethal dose that caused death in half of the group (LD50’s) when more than 2 milligrams/milliliters (ml) was used, while isolates resistant to FRAC 3 chemistries had LD50’s ranging from 0.01 to 36 micrograms/ml. These data and assays were used to support development of a monitoring program to inform growers of the risk of E. necator and reduce the chance of control failures. For Sub-objective 2C, field, greenhouse and lab experiments were conducted examining fungicide mobility and timing passed on grape vine phenological growth stage. These greenhouse and lab experiments indicated that some fungicides thought to be relatively immobile were mobile on grapes. Field experiments indicated that timing highly mobile fungicide to berry set significantly improve disease management on harvested clusters.

1. Development of computational tools for estimating the copy number of genes based on analysis of whole genome sequencing. Inference of the genome copy number presents a technical opportunity because traditional software typically requires the copy number of a genome or genomic region to be known before analysis. ARS scientists in Corvallis, Oregon, developed a method to infer copy number that uses sequence data as input. The method infers ploidy based on the relative frequency of each allele sequenced at heterozygous positions throughout the genome without assuming ploidy a priori. The approach was validated with yeast as a model system and applied to the oomycete plant pathogen, Phytophthora infestans. This novel tool will have broad application to characterize genomes of microbes and plants and is particularly useful for characterizing emerging plant pathogens.

2. Development of rapid assessment techniques for strobilurin resistant grape powdery mildew. Fungicide resistance to strobilurin fungicides was causing control failures of grape powdery mildew in western viticulture production regions, which resulted in complete crop loss. ARS scientists in Corvallis, Oregon, in collaboration with Washington State University and Michigan State University, developed rapid sampling and detection methods for a genetic mutation associated with qualitative strobilurin resistance in grape powdery mildew. These methods allowed growers to rapidly test for the presence of strobilurin resistance in their fields and adjust fungicide selection accordingly. In 2017 and 2018, over 3,000 samples were assessed from California, Washington, and Oregon, with greater than 85% of samples having strobilurin resistant grape powdery mildew. The rapid detection system has allowed viticulturists to reduce crop loss due to strobilurin resistant powdery mildew.

Review Publications
Yan, Q., Lopes, L., Shaffer, B.T., Kidarsa, T.A., Vining, O., Philmus, B., Song, C., Stockwell, V.O., Raaijmakers, J., McPhail, K.L., Andreote, F., Chang, J.H., Loper, J.E. 2018. Secondary metabolism and interspecific competition affect accumulation of spontaneous mutants in the GacS-GacA regulatory system in Pseudomonas protegens. mBio. 9(1):e01845-17.
Mideros, M.F., Turissini, D.A., Guayazán, N., Ibarra-Avila, H., Danies, G., Cárdenas, M., Myers, K., Tabima, J., Goss, E.M., Bernal, A., Lagos, L.E., Grajales, A., Gonzalez, L.N., Cooke, D.E., Fry, W.E., Grunwald, N.J., Matute, D.R., Restrepo, S. 2018. Phytophthora betacei, a new species within Phytophthora clade 1c causing late blight on Solanum betaceum in Colombia. Persoonia: Molecular Phylogeny and Evolution of Fungi. 41:39–55.
Thiessen, L.D., Neill, T.M., Mahaffee, W.F. 2018. Development of a quantitative loop-mediated isothermal amplification assay for the field detection of Erysiphe necator. PeerJ. 6:e4639.
Thiessen, L., Neill, T.M., Mahaffee, W.F. 2018. Interruption and reduction of Erysiphe necator cleistothecia development utilizing fungicidal oil. Plant Health Progress. 19:153-155.
Thiessen, L., Neill, T.M., Mahaffee, W.F. 2018. Assessment of Erysiphe necator ascospore release models for use in the Mediterranean climate of western Oregon. Plant Disease. 102(8):1500-1508.
Knaus, B.J., Fieland, V.J., Graham, K., Grunwald, N.J. 2015. Diversity of foliar Phytophthora species on Rhododendron in Oregon nurseries. Plant Disease. 99(10):1326-1332.
Press, C.M., Rolfe, K.J., Weiland, G.E., Grunwald, N.J. 2017. Efficacy of management tools for control of Phytophthora plurivora leaf spot of Rhododendron, 2014. Plant Disease Management Reports. 11:OT035.
Chang, J.H., Putnam, M.L., Grunwald, N.J., Savory, E.A., Fuller, S.L., Weisberg, A.J. 2018. Response to comments on “Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management”. eLife. 7:e35852.
Savory, E., Fuller, S., Weisberg, A., Thomas, W., Gordon, M., Stevens, D., Creason, A., Belcher, M., Serdani, M., Wiseman, M., Putnam, M., Grunwald, N.J., Chang, J. 2017. Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management. eLife. 6:e30925.
Brar, S., Tabima, J.F., Mcdougal, R.L., Dupont, P.Y., Feau, N., Hamelin, R.C., Panda, P., Leboldus, J.M., Grunwald, N.J., Hansen, E.M., Bradshaw, R.E., Williams, N.M. 2018. Genetic diversity of Phytophthora pluvialis, a pathogen of conifers, in New Zealand and the west coast of the United States of America. Plant Pathology. 67:1131–1139.
Tabima, J.F., Coffey, M.D., Zasada, I.A., Grunwald, N.J. 2018. Populations of Phytophthora rubi show little differentiation and high rates of migration among states in the Western United States. Molecular Plant-Microbe Interactions. 31(6):614-622.
Shakya, S.K., Larsen, M.M., Condoy Cuenca, M.M., Lozoya-Saldana, H., Grunwald, N.J. 2018. Variation in genetic diversity of Phytophthora infestans populations in Mexico from the center of origin outwards. Plant Disease. 102(8):1534-1540.
Knaus, B.J., Grunwald, N.J. 2018. Inferring variation in copy number using high throughput sequencing data in R. Frontiers in Genetics. 9:123.
Foster, Z.S., Chamberlain, S., Grunwald, N.J. 2018. Taxa: An R package implementing data standards and methods for manipulation of taxonomic data. F1000Research. 7:272.
Wong, J., Cave, A., Lightle, D., Mahaffee, W.F., Naranjo, S.E., Wiman, N., Woltz, M., Lee, J.C. 2018. Drosophila suzukii flight performance reduced by starvation but not affected by humidity. Journal of Pest Science. 91(4):1269-1278.
Miller, N., Stoll, R., Mahaffee, W.F., Neill, T.M. 2018. Heavy particle transport in a trellised agricultural canopy during non-row-aligned winds. Agricultural and Forest Meteorology. 256-257:125-136.
Grunwald, N.J., Everhart, S.E., Knaus, B.J., Kamvar, Z.N. 2017. Best practices for population genetic analyses. Phytopathology. 107(9):1000-1010.