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

Location: Horticultural Crops Disease and Pest Management Research Unit

2019 Annual Report

Objectives
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.

Approach
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 addressing Objective 1, ARS researchers in Corvallis, Oregon, described the pathogen biology and disease epidemiology of exotic and emerging plant pathogens affecting horticultural crops. Under Sub-objective 1A, comparative genomic analyses were conducted of Phytophthora pathogens. An expansion and divergence of Argonaute genes in the Oomycete genus Phytophthora were documented. This knowledge provides novel insights into the silencing machinery available in oomycetes. ARS researchers also sequenced the whole genome of the raspberry and strawberry pathogens Phytophthora rubi and P. fragariae. This work provides a novel tool for effector-mediated plant breeding. For Sub-objective 1B, ARS researchers conducted a population genomics study characterizing Phytophthora plurivora. This study provides novel information that is useful in managing Phytophthora pathogens and assessing cultivar resistance. In Sub-objective 1C, the fungal and oomycete microbiome associated with Rhododendron was characterized with analyses. ARS researchers are just beginning to determine how the microbiomes shift in time. The fungal, yeast, and bacterial microbiome of flowers and fruit of red raspberry (sampled in year 1) was also characterized. Bacteria were found to be most abundant on open flowers, but the fungal pathogen, Botrytis cinerea, was most abundant on flower buds prior to bloom and before the application of fungicides. Between 15 to 40% of red raspberry fruit harvested from study sites were infected with B. cinerea. A species of yeast (Aureobasidium pullans) used for biological control of gray mold was common on developing berries, but earlier in the season when the pathogen was first present. Sampling of red raspberry tissues for analysis of the microbiome and microbial interactions during the 2019 growing season is underway. Under Sub-objective 1D, ARS scientists conducted disease surveys of small fruit crops in the Pacific Northwest. Gray mold, a pathogen caused by the fungus Botrytis cinerea, is a perennial concern for production of soft-skinned small fruits. Similar to the previous year, gray mold was commonly isolated from small fruits near harvest. In some fields, up to 80 percent of fruit sampled were infested with the pathogen. The high incidence of Botrytis in fruit indicates that current conventional chemical disease control programs are not providing sufficient management of this fungal pathogen. Aerial crown gall of blueberry caused by Agrobacterium tumefaciens is a re-emerging disease in Oregon and sporadically observed in Washington. The disease was more commonly observed in machine-harvested fields compared to those that were hand-picked. Heavily-galled blueberry stems had 50 percent fewer fruit compared to asymptomatic canes and the berries on galled stems were smaller. Silver leaf of blueberry, caused by the fungus Chrondrostereum purpureum, is an emerging disease in young blueberry fields. The disease reduces blueberry yield and quality, while slowly killing the plant. ARS scientists found that a polymerase chain reaction (PCR) assay is effective to detect the silver leaf fungus. The PCR assay will be used to examine the efficacy of removing infected canes to save blueberry plants. Under Objective 2, ARS researchers developed improved integrated disease management of pathogens of horticultural crops. Under Sub-objective 2A, ARS scientists are conducting data analyses that are continuing to refine the models from particle dispersion in complex canopies. Models can now more accurately predict airmass turning and flow under vines, which allows for improved description of particle plumes from point releases. These models are aiding research on monitoring fungicide resistance and developing a probabilistic sensor deployment system to optimize placement of meteorological sensors, pest and disease monitoring devices or scouting activities. In Sub-objective 2B, ARS scientists developed and tested a rapid sampling technique to detect presence of grape powdery mildew and assess the presence of fungicide resistance genetic markers. Swabbing worker gloves after conducting routine canopy maintenance was shown to be more sensitive and cost effective than classical visual disease scouting, even with the added costs of PCR detection assay, and had the added benefit of identifying the presence of fungicide resistance markers for Fungicide Resistance Action Committee (FRAC) group 3 and 11 fungicides. FRAC has a number and letter system assigned by the FRAC to group active ingredients that exhibit probability for cross resistance. An improved bioassay for determining fungicide resistance phenotype was developed that decreases the time required to examine an isolate for resistance or tolerance to a fungicide by 400 percent. For Sub-objective 2C, field, greenhouse and lab experiments were conducted to examine fungicide mobility and timing based on grape vine phenological growth stage. The results from these experiments continue to indicate that some fungicides previously thought to be relatively immobile are in fact mobile. Field experiments also indicated that timing highly mobile fungicide to berry set and to early berry development significantly improved disease management on harvested berry clusters.

Accomplishments
1. Resources for breeding pathogen-resistant raspberry and strawberry selections. Whole genome sequences of the Phytophthora rubi and Phytophthora fragariae provide a new resource for breeding pathogen resistant raspberry and strawberry selections. Phytophthora root rot is a pathogen that drastically reduces crop yields of raspberries and strawberries each year. ARS researchers in Corvallis, Oregon, sequenced the genomes of Phytophthora rubi and Phytophthora fragariae. Several classes of pathogen effectors (genes necessary to cause disease) were identified. Availability of these genomes provides a new resource for understanding pathogen evolution and adaptation. This ultimately improves crop breeding.

Review Publications
Tabima, J.F., Grunwald, N.J. 2019. effectR: An expandable R package to predict candidate effectors. Molecular Plant-Microbe Interactions. 32(9):1067-1076. https://doi.org/10.1094/MPMI-10-18-0279-TA.
Bollman, S.R., Press, C.M., Tyler, B.M., Grunwald, N.J. 2018. Expansion and divergence of Argonaute genes in the Oomycete genus Phytophthora. Frontiers in Microbiology. 9:2841. https://doi.org/10.3389/fmicb.2018.02841.
Smits, T., Duffy, B., Blom, J., Ishimaru, C., Stockwell, V.O. 2019. Pantocin A, a peptide-derived antibiotic involved in biological control by plant-associated Pantoea species. Archives Of Microbiology. 201(6):713-722. https://doi.org/10.1007/s00203-019-01647-7.
Thiessen, L.D., Neill, T.M., Mahaffee, W.F. 2019. Formation of Erysiphe necator Chasmothecia in the Pacific Northwest United States. Plant Disease. 103(5):890-896. https://doi.org/10.1094/PDIS-06-18-1012-RE.
Tabima, J.F., Kronmiller, B.F., Press, C.M., Tyler, B.M., Zasada, I.A., Grunwald, N.J. 2017. Whole genome sequences of the raspberry and strawberry pathogens Phytophthora rubi and P. fragariae. Molecular Plant-Microbe Interactions. 30(10):767-769. https://doi.org10.1094/MPMI-04-17-0081-A.
Arsenault-Labrecque, G., Sonah, H., Lebreton, A., Labbé, C., Marchand, G., Xue, A., Belzile, F., Knaus, B.J., Grunwald, N.J., Bélanger, R.R. 2018. Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates. BMC Biology. 16:80. https://doi.org/10.1186/s12915-018-0549-9.
Davis, E.W., Tabima, J.F., Weisberg, A.J., Lopes, L.D., Wiseman, M.S., Wiseman, M.S., Pupko, T., Belcher, M.S., Sechler, A.J., Tancos, M.A., Schroeder, B.K., Murray, T.D., Luster, D.G., Schneider, W.L., Rogers, E.E., Andreote, F., Grunwald, N.J., Putman, M.L., Chang, J.H. 2018. Bacteriophage NCPPB3778 and a type I-E CRISPR drive the evolution of the U.S. biological select agent Rathayibacter toxicus. mBio. 9:e01280-18.
Martin, F.N., Zhang, Y., Cooke, D.E.L., Coffey, M.D., Grunwald, N.J., Fry, W.E. 2019. Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs. PLoS One. 14(1):e0208606. https://doi.org/10.1371/journal.pone.0208606.
Carleson, N.C., Fieland, V.J., Scagel, C.F., Weiland, G.E., Grunwald, N.J. 2019. Population structure of Phytophthora plurivora on Rhododendron in Oregon nurseries. Plant Disease. 103(8):1923-1930. https://doi.org/10.1094/PDIS-12-18-2187-RE.
Wöhner, T., Richter, K., Sundin, G.W., Zhao, Y., Stockwell, V.O., Sellmann, J., Flachowsky, H., Magda-Viola, H., Peil, A. 2017. Inoculation of Malus genotypes with a set of Erwinia amylovora strains indicates a gene-for-gene relationship between the effector gene eop1 and both Malus floribunda 821 and Malus 'Evereste'. Plant Pathology. 67(4):938-947. https://doi.org/10.1111/ppa.12784.
Klein, J.M., Wong, P., Loper, J.E., Stockwell, V.O. 2017. Nutritional environment influences transcription of a pantocin A biosynthesis gene in Pantoea vagans strain C9-1. Journal of Plant Pathology. 99:99-103. https://doi.org/10.4454/jpp.v99i0.3911.
Klein, J.M., Loper, J.E., Stockwell, V.O. 2017. Influence of endogenous plasmids on phenotypes of Pantoea vagans strain C9-1 associated with epiphytic fitness. Journal of Plant Pathology. 99:81-89. https://doi.org/10.4454/jpp.v99i0.3914.