Source: AGRICULTURAL RESEARCH SERVICE submitted to NRP
EXOTIC AND EMERGING PLANT DISEASES OF HORTICULTURAL CROPS
Sponsoring Institution
Agricultural Research Service/USDA
Project Status
ACTIVE
Funding Source
Reporting Frequency
Annual
Accession No.
0423109
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
May 14, 2012
Project End Date
May 13, 2017
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
AGRICULTURAL RESEARCH SERVICE
(N/A)
CORVALLIS,OR 97331
Performing Department
(N/A)
Non Technical Summary
(N/A)
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2121131116014%
2121139116012%
2122110116015%
2122123116012%
2121129116047%
Goals / Objectives
Objective 1: Describe the pathogen biology of exotic and emerging plant pathogens affecting horticultural crops. Objective 2: Apply knowledge of biology, ecology, and epidemiology of economically important plant pathogens to the development of improved integrated disease management approaches.
Project Methods
The biology of exotic, emerging, and re-emerging plant pathogens is either poorly understood or inadequate to enable economic and environmentally sustainable management. Objective 1: We will develop and test methods for monitoring pathogen dispersion and describe the evolutionary history, population structure, genetics, epidemiology, and ecology of these pathogens. Objective 2: This knowledge will then be used to develop decision support tools for producers of horticultural crops. Once an increased understanding of a pathogen¿s biology has been developed, this knowledge needs to be translated into disease management strategies that are continually optimized and/or improved based on new knowledge. We will develop and improve disease management strategies for select pathogens affecting horticultural crops. While this objective cannot be achieved directly for quarantine pathogens (e.g. P. ramorum), concepts and approaches can be tested by using proxy pathosystems that are similar in the event of an exotic pathogen introduction or quarantines are lifted. In addition, development and improvement of integrated disease management strategies for endemic pathogens will improve our ability to respond to changing climatic conditions while enhancing the economic and sustainable production of horticultural crops.

Progress 05/14/12 to 05/07/17

Outputs
Progress Report Objectives (from AD-416): Objective 1: Describe the pathogen biology of exotic and emerging plant pathogens affecting horticultural crops. Objective 2: Apply knowledge of biology, ecology, and epidemiology of economically important plant pathogens to the development of improved integrated disease management approaches. Approach (from AD-416): The biology of exotic, emerging, and re-emerging plant pathogens is either poorly understood or inadequate to enable economic and environmentally sustainable management. Objective 1: We will develop and test methods for monitoring pathogen dispersion and describe the evolutionary history, population structure, genetics, epidemiology, and ecology of these pathogens. Objective 2: This knowledge will then be used to develop decision support tools for producers of horticultural crops. Once an increased understanding of a pathogen�s biology has been developed, this knowledge needs to be translated into disease management strategies that are continually optimized and/or improved based on new knowledge. We will develop and improve disease management strategies for select pathogens affecting horticultural crops. While this objective cannot be achieved directly for quarantine pathogens (e.g. P. ramorum), concepts and approaches can be tested by using proxy pathosystems that are similar in the event of an exotic pathogen introduction or quarantines are lifted. In addition, development and improvement of integrated disease management strategies for endemic pathogens will improve our ability to respond to changing climatic conditions while enhancing the economic and sustainable production of horticultural crops. This is a final report for project 2072-22000-039-00D, which was replaced by project 2072-22000-041-00D, "Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops" in May 2017. Under Objective 1, we developed an improved understanding of pathogen biology and genetic evolution in order to develop improved understanding of pathogen emergence and help guide research on disease management. Sub- objective 1.A, examines the evolution and population structure of exotic or re-emerging Phytophthora pathogens such as Phytophthora ramorum. Specifically, we documented that P. ramorum was introduced at least three times into Oregon forests and that a second clonal lineage with opposite mating type emerged in 2015. 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 to manage outbreaks in forests along the west coast of the United States and to manage quarantine in nurseries growing host plants susceptible to this pathogen. Identification of specific pathways of migration of the pathogen has aided in a more rational design of federal and state quarantine programs. In Sub-objective 1.B, we described the small RNA effectors of Phytophthora. We cloned and sequenced silencing effectors in Phytophthora including Argonaute, Dicer and RNA dependent RNA polymerases and conducted evolutionary analyses. This work provides novel insights into the silencing machinery of the genus Phytophthora that has potential applications for implementing RNA interference (RNAi) for plant disease control. This genetic information was augmented under Sub-objective 1.C with an improved understanding of how Phytophthora species are adapted to their environment and their fitness to cause disease. This work is being used by the United States nursery industry and the federal government to identify critical control points in production systems and to implement systems approaches for the management of the Phytophthora diseases. With Sub-objective 1.D, we began extensive investigations into developing a biophysical model for simulating the development of grape powdery mildew. We demonstrated that currently available models for E. necator ascospore release are not accurate in the maritime western climates and lack parameters affecting ascocarp maturation. An improved prediction model was developed and validated but its utility is still limited because of limited understanding of factors influencing ascocarp development. We developed an improved understanding of factors influencing canopy microclimate and its impact on pathogen development and dispersion. This information was incorporated into a vineyard simulation model for grape and powdery mildew development. For Objective 2 we implemented knowledge gained from Objective 1 as well as developed practical approaches to disease management. Under Sub-objective 2.A, we conducted studies to improve management of Phytophthora species in nursery environments. We developed makers for rapid identification of Phytophthora pathogens prevalent in ornamental nurseries and characterized Phytophthora diversity. These data coupled with results from sub-objective 1C can be used to guide management decisions. Research on Sub-objective 2.B led to improved disease control by improving our understanding of fungicide mobility and when particular fungicides are most active in relation to crop phenology. We demonstrated that mobility traits of different fungicides could be used to guide fungicide selection to specific grape phenological growth stages to enhance disease management. Under Sub-objective 2.C, we conducted 3 years of field trials in commercial vineyards that demonstrated that pulling leaves at flowering results in significant benefits to disease management of both grape powdery mildew and Botrytis bunch rot and improves fruit quality compared to leaf pulling around v�raison. This research has been widely implemented by vineyard managers in western and southern Oregon. We also developed methods for using terrestrial Light Detection and Ranging (LiDAR) to assess canopy density and leaf geometry that aid in assessing and developing plant growth models. For Sub-objective 2.D, we continued research on inoculum detection by examining how data on inoculum concentration could be used to further optimize fungicide application timing. We demonstrated that using inoculum monitoring to time fungicide applications could save approximately 4 fungicide applications a season. We also developed a loop- mediated isothermal amplification (LAMP) assay that could be implemented by growers to monitor grape powdery mildew disease pressure and aid management decisions. These technologies were transferred to several commercial entities. This research is being further extended in our new project by developing molecular tools to detect presence of alleles associated with fungicide resistance in E. necator. Sub-objective 2.E proved to be rather difficult as most of the new algorithms developed had little or marginal improvements in predicting grape powdery mildew risk using traditional weather data from stations randomly placed for convenience. We are now developing methods to optimally place weather stations and interpolate data across vineyards based on local topology and canopy architecture and how these impact pathogen development and dispersion. Accomplishments 01 Methodology and software developed to characterize plant canopy 3-D architecture from terrestrial LiDAR data. A new method was developed and tested by scientists in Corvallis, Oregon that uses terrestrial Light Detection and Ranging (LiDAR) scanning data to rapidly measure the three-dimensional distribution of leaf orientation and size. The method was validated by comparing LiDAR-measurements to 1) `synthetic' or computer-generated LiDAR data where the exact orientation and area are known, and 2) direct measurements of leaf parameters in the field using destructive sampling. Overall, agreement between the LiDAR and reference measurements was very good, showing an error of about 15% for the synthetic tests, and 13% in the field. This research will significantly enhance understanding of how canopy architecture influences pest and disease development and dispersion, and the ability to model plant growth, photosynthesis, evapotranspiration, and other transport processes that are dependent on understanding leaf orientation in relation to light or wind interception. Overall, this method will be of great benefit to grape growers, who can use it to improve their crop growing practices. 02 Computational tools for characterizing microbiomes were developed. Community-level sequence data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa, which are limited in conveying the hierarchical structure of taxonomic classifications. As an alternative, scientists in Corvallis, Oregon developed metacoder, an R package for easily parsing, manipulating, and graphing publication- ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. The package complements currently available tools for community analysis and provides an open source with an extensive online user manual for scientists in academia, government, and the private sectors who are interested in conducting population genomic analysis and manipulating this data.

Impacts
(N/A)

Publications

  • Bailey, B.N., Mahaffee, W.F. 2017. Rapid measurement of the three- dimensional distribution of leaf orientation and the leaf angle probability density function using terrestrial LiDAR scanning. Remote Sensing of Environment. 194(2017):63-76. doi: 10.1016/j.rse.2017.03.011.
  • Hansen, Z.R., Everts, K.L., Fry, W.E., Gevens, A.J., Grunwald, N.J., Gugino, B.K., Johnson, D.A., Johnson, S.B., Judelson, H.S., Knaus, B.J., McGrath, M.T., Myers, K.L., Ristaino, P.D., Roberts, P.D., Secor, G.A., Smart, C.D. 2016. Genetic variation within clonal lineages of Phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology. PLoS One. 11(11):e0165690. doi:10.1371/journal. pone.0165690.
  • Wang, J., Fernandez-Pavia, S.P., Larsen, M.M., Garay-Serrano, E., Gregorio- Cipriano, R., Rodriguez-Alvarado, G., Grunwald, N.J., Goss, E.M. 2017. High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin. Molecular Ecology. 26(4) :1091-1107. doi: 10.1111/mec.14000.
  • Paradis, E., Gosselin, T., Grunwald, N.J., Jombart, T., Manel, S., Lapp, H. 2016. Towards an integrated ecosystem of R packages for the analysis of population genetic data. Molecular Ecology Resources. 17(1):1-4. doi:10. 1111/1755-0998.12636.
  • Foster, Z.S., Sharpton, T.J., Grunwald, N.J. 2017. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Computational Biology. 13(2):e1005404. doi:10.1371/journal.pcbi. 1005404.
  • D'Angeli, M., Baker, J., Call, D., Davis, M., Kauber, K., Malhotra, U., Matsuura, G., Moore, D., Porter, C., Pottinger, P., Stockwell, V.O., Wagner, C., Wohrle, R., Yoder, J., Yoke, L., Rabinowitz, P. 2016. Antimicrobial stewardship through a one health lens: Observations from Washington State. International Journal of Health Governance Information. 21(3):114-130. doi: 10.1108/IJHG-02-2016-0009.
  • Thiessen, L.D., Neill, T.M., Mahaffee, W.F. 2017. Timing fungicide application intervals based on airborne Erysiphe necator concentrations. Phytopathology. 101(7):1246-1252. doi: 10.1094/PDIS-12-16-1727-RE.
  • Thiessen, L.D., Keune, J.A., Neill, T.M., Turechek, W., Grove, G., Mahaffee, W.F. 2015. Development of a grower performed inoculum detection assay for management of grape powdery mildew. Plant Pathology. 65:238�249. doi: 10.1111/ppa.12421
  • Mahaffee, W.F. 2014. Use of airborne inoculum detection for disease management decisions. In: Gullino, M.L., Bonants, P.J.M., editors. Detection and Diagnostics of Plant Pathogens. New York, NY: Springer. p. 39-54.
  • Grunwald, N.J., McDonald, B.A., Milgroom, M.G. 2016. Population genomics of fungal and oomycete pathogens. Annual Review of Phytopathology. 54:323- 346. doi:10.1146/annurev-phyto-080614-115913.
  • Knaus, B.J., Grunwald, N.J. 2016. VCFR: A package to manipulate and visualize variant call format data in R. Molecular Ecology Resources. 17(1) :44-53. doi: 10.1111/1755-0998.12549.
  • Biasi, A., Martin, F.N., Cacciola, S.O., Magnano Di San Lio, G., Grunwald, N.J., Schena, L. 2016. Genetic analysis of Phytophthora nicotianae populations from different hosts using microsatellite markers. Phytopathology. 106(9):1006-1014. doi: 10.1094/PHYTO-11-15-0299-R.
  • Tabima, J.F., Everhart, S.E., Larsen, M.M., Weisberg, A.J., Kamvar, Z.N., Tancos, M.A., Smart, C.D., Chang, J.H., Grunwald, N.J. 2016. Microbe-ID: An open source toolbox for microbial genotyping and species identification. PeerJ. 4:e2279. doi: 10.7717/peerj.2279.
  • Kunjeti, S.G., Anchieta, A.G., Martin, F.N., Choi, Y.-J., Thines, M., Michelmore, R.W., Koike, S.T., Tsuchida, C., Mahaffee, W.F., Subbarao, K.V. , Klosterman, S.J. 2016. Detection and quantification of Bremia lactucae by spore trapping and quantitative PCR. Phytopathology. 106:1426-1437.
  • Villari, C., Mahaffee, W.F., Mitchell, T.K., Pedley, K.F., Pieck, M.L., Peduto Hand, F. 2017. Early detection of airborne inoculum of Magnaporthe oryzae in turfgrass fields using a quantitative LAMP assay. Plant Disease. 101(1):170-177. doi: 10.1094/PDIS-06-16-0834-RE.
  • Knaus, B.J., Tabima, J.F., Davis, C.E., Judelson, H.S., Grunwald, N.J. 2016. Genomic analyses of dominant U.S. clonal lineages of Phytophthora infestans reveals a shared common ancestry for clonal lineages US11 and US18 and a lack of recently shared ancestry among all other U.S. lineages. Phytopathology. 106(11):1393-1403. doi: 10.1094/PHYTO-10-15-0279-R.
  • Gagnon, M., Feau, N., Dale, A.L., Dhillon, B., Hamelin, R.C., Brasier, C.M. , Grunwald, N.J., Briere, S.C., Bilodeau, G.J. 2017. Development and validation of polymorphic microsatellite loci for the NA2 lineage of Phytophthora ramorum from whole genome sequence data. Plant Disease. 101(5) :666-673. doi: 10.1094/PDIS-11-16-1586-RE.
  • Davis, E.W., Weisberg, A.J., Tabima, J., Grunwald, N.J., Chang, J.H. 2016. Gall-ID: Tools for genotyping gall-causing phytopathogenic bacteria. PeerJ. 4:e2222. doi: 10.7717/peerj.2222.
  • Kamvar, Z.N., Lopez-Uribe, M.M., Coughlan, S., Grunwald, N.J., Lapp, H., Manel, S. 2016. Developing educational resources for population genetics in R: An open and collaborative approach. Molecular Ecology Resources. 17(1):120-128. doi: 10.1111/1755-0998.12558.
  • Eyre, C.A., Hayden, K.J., Kozanitas, M., Grunwald, N.J., Garbelotto, M. 2014. Lineage, temperature, and host species have interacting effects on lesion development in Phytophthora ramorum. Plant Disease. 98(12):1717- 1727.


Progress 10/01/15 to 09/30/16

Outputs
Progress Report Objectives (from AD-416): Objective 1: Describe the pathogen biology of exotic and emerging plant pathogens affecting horticultural crops. Objective 2: Apply knowledge of biology, ecology, and epidemiology of economically important plant pathogens to the development of improved integrated disease management approaches. Approach (from AD-416): The biology of exotic, emerging, and re-emerging plant pathogens is either poorly understood or inadequate to enable economic and environmentally sustainable management. Objective 1: We will develop and test methods for monitoring pathogen dispersion and describe the evolutionary history, population structure, genetics, epidemiology, and ecology of these pathogens. Objective 2: This knowledge will then be used to develop decision support tools for producers of horticultural crops. Once an increased understanding of a pathogen�s biology has been developed, this knowledge needs to be translated into disease management strategies that are continually optimized and/or improved based on new knowledge. We will develop and improve disease management strategies for select pathogens affecting horticultural crops. While this objective cannot be achieved directly for quarantine pathogens (e.g. P. ramorum), concepts and approaches can be tested by using proxy pathosystems that are similar in the event of an exotic pathogen introduction or quarantines are lifted. In addition, development and improvement of integrated disease management strategies for endemic pathogens will improve our ability to respond to changing climatic conditions while enhancing the economic and sustainable production of horticultural crops. Objective 1A: We developed and applied computational tools for characterizing plant pathogen populations. This work directly relates to characterizing the pathogen biology of exotic and emerging plant pathogens affecting horticultural crops. Objecitve 1B: We finalized cloning, sequencing, and gene expression analysis of silencing effectors in Phytophthora including Argonaute, Dicer, and RNA dependent RNA polymerases and conducted evolutionary analyses. This work directly relates to characterizing the pathogen biology of Phytophthora pathogens affecting horticultural crops. Objective 1C: We finalized statistical analysis and are writing manuscripts to characterize fitness of Phytophthora pathogens on ornamentals. This work has direct implications for managing Phytophthora pathogens in nursery production systems. Objective 1D: We developed and tested five different models for predicting ascospore release and tested four different models from literature. A simple expert rule model performed the best and was an improvement on the New York model that is currently used in the western grape production regions. However, we are still not able to accurately predict how long into the growing season ascospores will be released. Studies using different cleistothecia cohorts in time determined that time of cleistothecia development is not related when ascospores are released. This result indicates that ascospore release is likely a function of the physiological development of individual cleistothecia. Our artificial trunk and spore trapping system again allowed for examination of cleistothecia dehiscence. Further research is needed where different age classes of cleistothecia are monitored for ascospore release. Objective 2A: We identified species of Phytophthora pathogens prevalent in nursery environments and published a manuscript. This work has direct implications for managing Phytophthora pathogens in nursery production systems. Objective 2B: This objective was not pursued in order to pursue a new finding related to Objective 2E. Models indicated that spore deposition was more likely in the region of a grape canopy where the inflorescence and fruit clusters develop, which is in agreement with field observations. Disease is often observed on flowers before it is found on leaves. Thus, a project to specifically target the inflorescence and cluster zone with chemistries that can redistribute was initiated. The first field season is currently being conducted. Objective 2C: Objective was completed in 2015. Objective 2D: Objective was completed in 2015. Objective 2E: We demonstrated that the interactions of air turbulence and canopy architecture are important to accurately predict disease dispersion and development. We developed novel methods for using terrestrial Light Detection and Ranging (LiDAR) to measure canopy architecture components that are then used to inform particle dispersion models. These models are being coupled with host and pathogen development to develop a spatialized disease risk model. A triangulation analysis system of terrestrial LiDAR data was developed that allows for leaf angle, azimuth and leaf area density to be extracted at unprecedented resolution. A software package that leverages the processing power of graphics processors is being developed to rapidly convert LiDAR data to canopy architecture parameters. The analysis technique and software will enable a wide variety of applications. Accomplishments 01 Development of computational tools for characterizing genetics of populations. Many microbial, fungal, or oomycete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. ARS researchers in Corvallis, Oregon, developed a package of computational tools in the programming language R that is open source for rapid and convenient analysis and graphing of population genetic data. This toolset allows more rapid characterization of emerging pathogens and pests threatening U.S. agriculture to assess if they are newly introduced, and has been applied to many organisms including insects, corals, cancer cells, and microbes. 02 Development and implementation of a decision aid to adjust fungicide applications based on airborne inoculum thresholds. There is continuing need to reduce the use fungicides in grape production. A detection and trapping system was developed that allowed vineyard managers to use inoculum thresholds to shorten or extend fungicide application intervals. Field tests in 14 commercial vineyards showed that disease control was better than the current calendar program while reducing the number of fungicide applications by 1 to 4 (average 1.6) applications preseason. This represents a cost saving of over $75 per acre on average. The system is now being commercially implemented in Oregon and California vineyards. Current research will soon add the ability to monitor for fungicide resistance, further adding to the utility of this assay.

Impacts
(N/A)

Publications

  • Mahaffee, W.F., Stoll, R. 2016. The ebb and flow of airborne pathogens: Monitoring and use in disease management decisions. Phytopathology. 106(5) :420-431. doi: 10.1094/PHYTO-02-16-0060-RVW.
  • Hansen, Z.R., Knaus, B.J., Tabima, J.F., Press, C.M., Judelson, H.S., Grunwald, N.J., Smart, C.D. 2016. SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high resolution melt analysis. Plant Disease. 100(7):1297-1306. doi: 10.1094/PDIS-11-15-1247-RE.
  • Hansen, Z.R., Knaus, B.J., Tabima, J.F., Judelson, H.S., Grunwald, N.J., Smart, C.D. 2016. Loop-mediated isothermal amplification for detection of the tomato and potato late blight pathogen, Phytophthora infestans. Journal of Applied Microbiology. 120(4):1010�1020. doi: 10.1111/jam.13079.
  • Grunwald, N.J., Larsen, M.M., Kamvar, Z.N., Reeser, P.W., Kanaskie, A., Laine, J., Wiese, R. 2016. First report of the EU1 clonal lineage of Phytophthora ramorum on tanoak in an Oregon forest. Plant Disease. 100(5) :1024. doi: 10.1094/PDIS-10-15-1169-PDN
  • Bollmann, S.R., Fang, Y., Press, C.M., Tyler, B.M., Grunwald, N.J. 2016. Diverse evolutionary trajectories for small RNA biogenesis genes in the oomycete genus Phytophthora. Frontiers in Plant Science. 7:284. doi: 10. 3389/fpls.2016.00284.
  • Kasuga, T., Bui, M.Q., Berhardt, E., Swiecki, T., Aram, K., Cano, L.M., Webber, J., Brasier, C., Press, C.M., Grunwald, N.J., Rizzo, D.M., Garbelotto, M. 2016. Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum. BMC Genomics. 17:385. doi: 10.1186/s12864-016-2717-z.


Progress 10/01/14 to 09/30/15

Outputs
Progress Report Objectives (from AD-416): Objective 1: Describe the pathogen biology of exotic and emerging plant pathogens affecting horticultural crops. Objective 2: Apply knowledge of biology, ecology, and epidemiology of economically important plant pathogens to the development of improved integrated disease management approaches. Approach (from AD-416): The biology of exotic, emerging, and re-emerging plant pathogens is either poorly understood or inadequate to enable economic and environmentally sustainable management. Objective 1: We will develop and test methods for monitoring pathogen dispersion and describe the evolutionary history, population structure, genetics, epidemiology, and ecology of these pathogens. Objective 2: This knowledge will then be used to develop decision support tools for producers of horticultural crops. Once an increased understanding of a pathogen�s biology has been developed, this knowledge needs to be translated into disease management strategies that are continually optimized and/or improved based on new knowledge. We will develop and improve disease management strategies for select pathogens affecting horticultural crops. While this objective cannot be achieved directly for quarantine pathogens (e.g. P. ramorum), concepts and approaches can be tested by using proxy pathosystems that are similar in the event of an exotic pathogen introduction or quarantines are lifted. In addition, development and improvement of integrated disease management strategies for endemic pathogens will improve our ability to respond to changing climatic conditions while enhancing the economic and sustainable production of horticultural crops. Objective 1A: In 2015, we studied populations of the sudden oak death pathogen Phytophthora ramorum in nurseries and forests in the U.S. using microsatellite markers and established that there likely were two introductions into Curry County, Oregon forests between 2001 and 2013. Objective 1B: We cloned and sequenced gene involved in small RNA biogenesis including Argonautes, RNA-dependent RNA polymerases and Dicer- like loci. Objective 1C: We conducted field trials and in vitro and growthchamber experiments to characterize infection by P. ramorum. Objective 1D: We developed an artificial grape trunk that allows for more precise estimates of cleistothecia maturation and dehiscence. This coupled with our novel trapping system allows for very accurate estimates of total ascospores released in relation to the number of cleistothecia present on the artificial grape truck. Two years of data allowed us to develop a preliminary model that was tested this spring. The model was predictive of ascospore release events but did not perform well in predicting how long ascospores would be released. Further research is needed where different age classes of cleistothecia are monitored for ascospore release. A warm winter failed to produce the temperature differentials needed to completely evaluate this objective. However, the lack of increased disease indicates that something other than just response to cold temperatures is impacting disease development. Objective 2A: We sampled Phytophthora species in nurseries and determined diversity of foliar Phytophthora on Rhododendron. We also characterized a new Phytophthora pathogen on Buxus and Ceanothus using molecular, host range testing, and morphological approaches. Objective 2B: This objective was not pursued in order to pursue a new finding related to 2E. Models indicated that spore deposition was more likely in the region of a grape canopy where the inflorescence and fruit clusters develop, which is in agreement with field observations. Disease is often observed on flowers before it is found on leaves. Thus, a project to specifically target the inflorescence and cluster zone with chemistries that can redistribute was initiated. The first field season is currently being conducted. Objective 2C: Three years of study indicates that pulling leaves at flowering results in significant benefits to disease management of both grape powdery mildew and Botrytis bunch rot without reducing fruit quality. In fact fruit quality was improved. The early leaf pulling is now implemented by vineyard managers in Western and Southern Oregon. Objective 2D: Two years of testing of the LAMP (Loop mediated isothermal AMPlification) assay indicates that the assay performed in lab environment is as effective as a PCR (polymerase chain reaction) assay for monitoring the presence of the E. necator inoculum in the air. Unfortunately, the grower performed quantitative LAMP assay is far less accurate than lab performed assay. However, when growers used the data derived from the Grower performed LAMP assay to initiate their fungicide program they were still able to effectively manage grape powdery mildew compared to their standard practice, while saving 3.5 fungicide applications. This technology has been transferred to three commercial entities (Gallo Wines, Diagenetics, Inc, and Revolution, LLC). In place of Objective 2E: We continued research and modeling efforts on the effects of canopy architecture on particle dispersion. This research demonstrated that interactions of the grape canopy with air currents will result in decreased cross row spread as rows spacing gets wider but a greater chance of long distance dispersion. The research is supported by field data on disease spread where disease foci tend to be elongated along rows with little to no spread across rows. Modeling efforts have been able to duplicate the observed dispersion pattern and indicate that leaf area and row spacing will significantly alter pattern of disease spread and may be used to design vineyards that reduce disease development. External funding from the Northwest Small Fruit Research Center was obtained to examine how to best use sulfur for the management of grape powdery mildew. Research conducted to date indicates that about half the current rate of sulfur is needed to manage grape powdery mildew and that longer application intervals can be used once canopy growth slows during fruit development. Two years of field trials and growth chamber studies indicate that sulfur rates can be significantly reduced and application intervals can be extended out 21 days without reducing disease control. Accomplishments 01 Inoculum concentration for grape powdery mildew management. ARS researchers in Corvallis, Oregon, demonstrated that inoculum concentration can be used to alter fungicide application interval for grape powdery mildew management and resulted in 3.5 fewer fungicide applications without affecting disease control. This research extends previous research on using inoculum detection to initiate fungicide applications in the spring. The combination of approaches has been shown to reduce fungicide applications by 50% in western Oregon. This technology has been transferred to several commercial entities and is being commercially implemented in Oregon and California. In addition, the spore trap design is being used by numerous researchers throughout the U.S to extend the concept of using inoculum detection as a decision aid to other crops. 02 Sudden oak death pathogen characterized. ARS researchers in Corvallis, Oregon, characterized populations of the sudden oak death pathogen in Oregon Forests. Populations sampled between 2001-2014 were genotyped using microsatellites and studied to infer the population genetic history. To date, only the NA1 clonal lineage is established in this region, although three lineages exist on the North American west coast. Our data support two distinct introduction events.

Impacts
(N/A)

Publications

  • Mahaffee, W.F., Glawe, D. 2014. Powdery mildew. In: Linderman, R.G., Benson, D.M., editors. Compendium of Rhododendron and Azalea Diseases and Pests. 2nd edition. St. Paul, MN: The American Phytopathological Society Press. p. 41-44.
  • Mahaffee, W.F., Schwebs, S., Hand, F., Gubler, D., Baily, B., Stoll, R. 2014. Improving management of grape powdery mildew with new tools and knowledge. Practical Winery and Vineyards. April:59-67.
  • Miller, N., Stoll, R., Mahaffee, W.F., Neill, T.M., Pardyjak, E.R. 2015. An experimental study of momentum and heavy particle transport in a trellised agricultural canopy. Agriculture and Forest Meterology. 211- 212:100-114.
  • Gent, D.H., Nelson, M., Grove, G., Mahaffee, W.F., Turechek, W., Woods, J. 2012. Association of spring pruning practices with severity of powdery mildew and downy mildew on hop. Plant Disease. 96:1343-1351.
  • Bailey, B.N., Stoll, R., Pardyjak, E.R., Mahaffee, W.F. 2014. Effect of vegetative canopy architecture on vertical transport of massless particles. Atmospheric Environment. 95:480-489.
  • Bailey, B., Overby, M., Willemsen, P., Pardyjak, E.R., Mahaffee, W.F., Stoll, R. 2014. A scalable plant-resolving radiative transfer model based on optimized GPU ray tracing. Agriculture and Forest Meterology. 198- 199:192-208. doi.org/10.1016/j.agrformet.2014.08.012.
  • Grunwald, N.J., Goss, E.M. 2011. Evolution and population genetics of exotic and re-emerging pathogens: Novel tools and approaches. Annual Review of Phytopathology. 49:249-267.
  • Grunwald, N.J. 2012. Genome sequences of Phytophthora enable translational plant disease management and accelerate research. Canadian Journal of Plant Pathology. 34:13-19.
  • Grunwald, N.J. 2012. Novel insights into the emergence of pathogens: the case of chestnut blight. Molecular Ecology. 21:3896-3897.
  • Flier, W.G., Grunwald, N.J. 2013. Phytophthora ipomoeae Flier & Gr�nwald, sp. nov.. Fungal Planet. 197:264-265.
  • Everhart, S.E., Tabima, J.F., Grunwald, N.J. 2014. Phytophthora ramorum. In: Dean, R.A. et al. In genomics of plant-associated fungi and oomycetes: Dicot pathogens. Berlin, Germany: Springer Berlin Heidelberg. p. 159-174.
  • Goss, E.M., Press, C.M., Grunwald, N.J. 2013. Evolution of RXLR-class effectors in the Oomycete plant pathogen Phytophthora ramorum. PLoS One. 8(11):e79347. doi: 10.1371/journal.pone.0079347.
  • Dunn, A.R., Bruening, S.R., Grunwald, N.J., Smart, C.D. 2014. Evolution of an experimental population of Phytophthora capsici in the field. Phytopathology. 104(10):1107-1117.
  • Saville, A., Graham, K., Grunwald, N.J., Myers, K., Fry, W.E., Ristaino, J. B. 2015. Fungicide sensitivity of US genotypes of Phytophthora infestans (Mont.) de Bary to six oomycete-targeted compounds. Plant Disease. 99:659- 666.
  • Kamvar, Z.N., Brooks, J.C., Grunwald, N.J. 2015. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Frontiers in Genetics. 6:208. doi: 10.3389/fgene.2015.00208.
  • Gagnon, M.C., Bergeron, M.J., Hamelin, R.C., Grunwald, N.J., Bilodeau, G.J. 2014. Real-time PCR assay to distinguish the four Phytophthora ramorum lineages using cellulose binding elicitor lectin (CBEL) locus. Canadian Journal of Plant Pathology. 36(3):367-376.
  • Restrepo, S., Tabima, J.F., Mideros, M.F., Grunwald, N.J., Matute, D.R. 2014. Speciation in fungal and oomycete plant pathogens. Annual Review of Phytopathology. 52:289-316.
  • Fry, W.E., Birch, P.R., Judelson, H.S., Grunwald, N.J., Danies, G., Everts, K.L., Gevens, A.J., Gugino, B.K., Johnson, D.A., Johnson, S.B., Mcgrath, M.T., Myers, K.L., Ristaino, J.B., Roberts, P.D., Secor, G., Smart, C.D. 2015. Five reasons to consider Phytophthora infestans a reemerging pathogen. Phytopathology. 105:966-981.
  • Kamvar, Z.N., Larsen, M.M., Kanaskie, A.M., Hansen, E.M., Grunwald, N.J. 2015. Spatial and temporal analysis of populations of the Sudden Oak Death pathogen in Oregon forests. Phytopathology. 105:982-989.
  • Rauscher, G., Simko, I., Mayton, H., Bonierbale, M., Smart, C.D., Grunwald, N.J., Greenland, A., Fry, W.E. 2010. Quantitative resistance to late blight from Solanum berthaultii cosegregates with RPi-ber: insights in stability through isolates and environment. Theoretical and Applied Genetics. 121:1553-1567.
  • Huai, W., Tian, G., Hansen, E.M., Zhao, W., Goheen, E.M., Grunwald, N.J., Cheng, C. 2013. Identification of Phytophthora species baited and isolated from forest soil and streams in northwestern Yunnan province, China. Forest Pathology. 43(2):87�103.
  • Goss, E.M., Cardenas, M.E., Myers, K., Forbes, G.A., Fry, W.E., Restrepo, S.O., Grunwald, N.J. 2011. The plant pathogen Phytophthora andina emerged via hybridization of an unknown Phytophthora species and the Irish famine pathogen, P. infestans. PLoS One. 6(9):e24543. doi: 10.1371/journal.pone. 0024543.
  • Fahlgren, N., Bollmann, S.R., Kasschau, K.D., Cuperus, J.T., Press, C.M., Sullivan, C.M., Chapman, E.J., Hoyer, J.S., Gilbert, K.B., Grunwald, N.J., Carrington, J.C. 2013. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs. PLoS One. 8(10) :e77181.
  • Goss, E.M., Tabima, J.F., Cooke, D., Restrepo, S., Fry, W.E., Forbes, G.A., Fieland, V.J., Cardenas, M., Myers, K.L., Grunwald, N.J. 2014. The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes. Proceedings of the National Academy of Sciences. 111(24):8791-8796.
  • Danies, G., Myers, K., Mideros, M.F., Restrepo, S., Martin, F.N., Cooke, D. E., Smart, C.D., Ristaino, J.B., Seaman, A.J., Gugino, B.K., Grunwald, N.J. , Fry, W.E. 2014. An ephemeral sexual population of Phytophthora infestans in the northeastern United States and Canada. PLoS One. 9(12):e116354. doi: 10.1371/journal.pone.0116354.
  • Fry, W., Mcgrath, M.T., Seaman, A., Zitter, T.A., Mcleod, A., Danies, G., Small, I.M., Myers, K., Everts, K., Gevens, A.J., Gugino, B.K., Johnson, S. B., Judelson, H., Ristaino, J., Roberts, P., Secor, G., Seebold, K., Snover-Clift, K., Wyenandt, A., Grunwald, N.J., Smart, C.D. 2012. The 2009 late blight pandemic in eastern USA. Plant Disease. 97(3):296-306.
  • Kamoun, S., Furzer, O., Jones, J.D., Judelson, H.S., Ali, G., Dalio, R.J., Roy, S., Schena, L., Zampounis, A., Panabieres, F., Cahill, D., Ruocco, M., Figueirdo, A., Chen, X., Hulvey, J., Stam, R., Lamour, K., Gizen, M., Tyler, B.M., Grunwald, N.J., Tor, M., Mukhtar, S.M., Tome, D., Ackerveken, G., Mcdowell, J., Daayf, F., Fry, W.E., Lindqvist-Kreuze, H., Meijer, H.J., Petre, B., Ristaino, J., Yoshida, K., Birch, P., Govers, F. 2015. The top 10 oomycete pathogens in molecular plant pathology. Molecular Plant Pathology. 16:413:434.
  • Parke, J.L., Fieland, V.J., Lewis, C., Knaus, B.J., Grunwald, N.J. 2014. Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management. Phytopathology. 104(10):1052- 1062.
  • Dunn, A.R., Bruening, S.R., Grunwald, N.J., Smart, C.D. 2014. Evolution of an experimental population of Phytophthora capsici in the field. Phytopathology. 104(10):1052-1062.


Progress 10/01/13 to 09/30/14

Outputs
Progress Report Objectives (from AD-416): Objective 1: Describe the pathogen biology of exotic and emerging plant pathogens affecting horticultural crops. Objective 2: Apply knowledge of biology, ecology, and epidemiology of economically important plant pathogens to the development of improved integrated disease management approaches. Approach (from AD-416): The biology of exotic, emerging, and re-emerging plant pathogens is either poorly understood or inadequate to enable economic and environmentally sustainable management. Objective 1: We will develop and test methods for monitoring pathogen dispersion and describe the evolutionary history, population structure, genetics, epidemiology, and ecology of these pathogens. Objective 2: This knowledge will then be used to develop decision support tools for producers of horticultural crops. Once an increased understanding of a pathogen�s biology has been developed, this knowledge needs to be translated into disease management strategies that are continually optimized and/or improved based on new knowledge. We will develop and improve disease management strategies for select pathogens affecting horticultural crops. While this objective cannot be achieved directly for quarantine pathogens (e.g. P. ramorum), concepts and approaches can be tested by using proxy pathosystems that are similar in the event of an exotic pathogen introduction or quarantines are lifted. In addition, development and improvement of integrated disease management strategies for endemic pathogens will improve our ability to respond to changing climatic conditions while enhancing the economic and sustainable production of horticultural crops. Under Objective 1A, we genotyped 266 strains of the sudden oak death pathogen Phytophthora ramorum in nurseries and forests in the U.S. using microsatellite markers. In regard to Objective 1B, we cloned and sequenced genes involved in small RNA biogenesis including AGO, RDR and DCL. For Objective 1C, we conducted field trails and in vitro and growth chamber experiments to characterize infection by P. ramorum. To take care of Objective 1D, we developed an artificial grape trunk that allows for more precise estimates of cleistothecia maturation and dehiscence. This coupled with our novel trapping system allows for very accurate estimates of total ascospores released in relation number of cleistothecia present on the artificial grape truck. These data will allow us to develop models to estimate the time and quantity of ascospore release from the overwinter cleistothecia. Two years of field data indicate that cleistothecia are mature enough for release soon after leaf drop and maturation is most likely a function of temperature and not the number of wetting events. However, there are also indications that individual cohorts of the cleistothecia have broad distribution of maturation that needs to be accounted for. Under Objective 1D, a preliminary experiment on impact of cold events was supported by small scale studies. Temperature fluctuation prior to inoculation does appear to impact the success of E. necator infection. In regards to Objective 2A, we sampled Phytophthora species in nurseries and determined diversity of foliar Phytophthora on Rhododendron. We also characterized a new Phytophthora pathogen on Buxus and Ceanothus using molecular, host range testing, and morphological approaches. Progress was made on Objective 2C for the third year of study that indicates pulling leaves at flowering results in significant benefits to disease management of both grape powdery mildew and Botrytis bunch rot without reducing fruit quality. In fact, fruit quality seems to be improved. Under Objective 2D, the second year of testing of the LAMP assay indicates that the assay performed in a laboratory environment is as effective as a quantitative PCR assay for monitoring the presence of the E. necator inoculum in the air. Unfortunately, a grower performed LAMP assay is far less accurate then a lab performed assay. However, when growers used the data derived from their LAMP assay to initiate their fungicide program, they were still able to effectively manage grape powdery mildew compared to their standard practice while saving 3.5 fungicide applications. In place of Objective 2E, we conducted research on the effects of canopy architecture on particle dispersion. This research demonstrated that interactions of the grape canopy with air currents will result in decreased cross row spread as row spacing gets wider but has greater chance of long distance dispersion. The research supports field observations of disease spread where disease foci tend to be elongated along rows with little to no cross spread. To further explore this phenomenon, we develop a novel spore trap to assess the effect of wind speed on the escape of pathogen spores from the plant canopy. External funding was received from the Northwest Small Fruit Research Center for examination of how to best use sulfur for the management of grape powdery mildew. Research conducted to date indicates that about half the current rate of sulfur is needed to manage grape powdery mildew and that longer application intervals can be used once canopy growth slows during fruit development. Accomplishments 01 Identification of Mexico as the center or origin of the Irish potato famine pathogen. The potato late blight pathogen was introduced to Europe in the 1840s and caused devastating loss of a staple crop, resulting in the Irish potato famine and subsequent diaspora. Research on this disease has engendered much debate, which, in recent years, has focused on whether the geographic origin of the pathogen is South America or central Mexico. Different lines of evidence support each hypothesis. ARS researchers at Corvallis, Oregon, sequenced four nuclear genes in representative samples from Mexico and the South American Andes. An Andean origin of P. infestans does not receive support from detailed analyses of Andean and Mexican populations. This is one of a few examples of a pathogen with a known origin that is secondary to its current major host. This research has implications for breeding potato and tomato for resistance to late blight as well as guarding against emergence of new clones of this pathogen. 02 Development of computational tools for characterizing genetics of populations. Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. ARS researchers at Corvallis, Oregon, developed a package of computational tools in the programming language R that is open source for rapid and convenient analysis and graphing of population genetic data. This toolset allows more rapid characterization of emerging pathogens and pests threatening U.S. Agriculture to assess if they are newly introduced. 03 Characterizing Phytophthora pathogen communities in ornamentals nurseries. Nursery plants are important vectors for plant pathogens. Understanding what pathogens occur in nurseries in different production stages can be useful to development of integrated systems approaches. ARS scientists in Corvallis, Oregon, in collaboration with colleagues at Oregon State University, sampled four horticultural nurseries in Oregon every two months for four years to determine the identity and community structure of Phytophthora species associated with different sources and stages in the nursery production cycle. Nurseries differed in composition of Phytophthora communities across years, seasons, and source within the nursery. These findings suggest likely contamination hazards and critical control target points for management of Phytophthora disease using a systems approach. 04 Radiative transport model based leaf canopy developed. Understanding radiation interception and scattering in complex canopies is needed to better predict water and energy use, plant growth and yield, and pathogen and pest development in natural, urban and agriculture ecosystems. In collaboration with the University of Utah and University of Minnesota Duluth, ARS researchers at Corvallis, Oregon, developed a radiative transfer model for complex plant canopies that realistically represents light interception and scattering at a leaf scale. The efficiency of the graphics processing code allows for approximately 100, 000 trees or more for smaller plant canopies to be modeled at the leaf scale on a desktop workstation. The speed and reduced computational costs of this model will be useful in developing improved models for photosynthesis/plant growth, evapotranspiration, water usage, plant growth and potentially assessing approaches to mitigating global climate change. 05 Plant canopy architecture effects on air turbulence and disease development modeled. An improved understanding of pathogen and pest spread in natural, urban, and agriculture environments with complex plant canopy heterogeneity is needed to accurately assess disease risk. There is also a need to be able to accurately predict numerous ecosystem functions (e.g. water use, microclimate) and the effects of global climate change. Using massively parallel computer simulation, researchers at the University of Utah and ARS, Corvallis, Oregon, have develop and validated new models for how row structure of perennial crops impacts air turbulence and subsequent pathogen or pest dispersion. These models will be useful in developing improved ability to more accurately predict the risk of disease spread, particularly in perennial plant canopies.

Impacts
(N/A)

Publications

  • Kamvar, Z.N., Tabima, J.F., Grunwald, N.J. 2014. Poppr: an R package for genetic analysis of populations with mixed (clonal/sexual) reproduction. PeerJ. 2:e281.
  • Morin, L., Gomez, D., Evans, K., Neill, T.M., Mahaffee, W.F., Linde, C. 2013. Invaded range of the blackberry pathogen Phragmidium violaceum in the Pacific Northwest of the USA and the search for its provenance. Biological Invasions. 15(8):1847-1861.


Progress 10/01/12 to 09/30/13

Outputs
Progress Report Objectives (from AD-416): Objective 1: Describe the pathogen biology of exotic and emerging plant pathogens affecting horticultural crops. Objective 2: Apply knowledge of biology, ecology, and epidemiology of economically important plant pathogens to the development of improved integrated disease management approaches. Approach (from AD-416): The biology of exotic, emerging, and re-emerging plant pathogens is either poorly understood or inadequate to enable economic and environmentally sustainable management. Objective 1: We will develop and test methods for monitoring pathogen dispersion and describe the evolutionary history, population structure, genetics, epidemiology, and ecology of these pathogens. Objective 2: This knowledge will then be used to develop decision support tools for producers of horticultural crops. Once an increased understanding of a pathogen�s biology has been developed, this knowledge needs to be translated into disease management strategies that are continually optimized and/or improved based on new knowledge. We will develop and improve disease management strategies for select pathogens affecting horticultural crops. While this objective cannot be achieved directly for quarantine pathogens (e.g. P. ramorum), concepts and approaches can be tested by using proxy pathosystems that are similar in the event of an exotic pathogen introduction or quarantines are lifted. In addition, development and improvement of integrated disease management strategies for endemic pathogens will improve our ability to respond to changing climatic conditions while enhancing the economic and sustainable production of horticultural crops. Objective 1A: We conducted routine analysis to determine population structure and emergence of new strains of Phytophthora ramorum by genotyping isolates received from new findings across the US using microsatellite genotyping. We have also sampled isolates of P. syringae and P. plurivora that are being characterized using genotyping-by- sequencing. Objective 1C: We have compared the ability of different Phytophthora species to infect the host plant Rhododendron. Two pathogens, P. plurivora and P. syringae appear to be the most aggressive under warm and cold temperatures, respectively. Objective 1D: We developed a novel spore trapping system that can be used to capture airborne spores released after specific temperature and wetness periods. We developed techniques to simulate grape bark wetting and drying that will allow for greater experimental control and flexibility than using grape trunks to experimentally manipulate overwintering conditions and test their impact on cleistothecia. These advances will allow us to better determine the exact conditions required for ascospore release and improve disease forecasting. Objective 2A: We sampled foliar infections of Rhododendron to assess which species of Phytophthora are dominant. P. syringae and P. plurivora are the two dominant species causing foliar Phytophthora disease on Rhododendron in the Pacific Northwestern US. Objective 2C: We demonstrated that leaf removal occurring as early as BBCH growth 53 did not reduce yield or grape quality but reduced severity powdery mildew and bunch rot. These results indicate the growers can pull leaves earlier in the season improve disease control without increasing production costs. Objective 2D: We demonstrated that loop mediated isothermal amplification can be used by growers to detect the grape powdery mildew pathogen and time fungicide applications. The significantly lower capital costs and simplicity of the technique indicate that this tool could be commercially viable for disease management. Significant Activities that Support Special Target Populations: ARS scientists from Corvallis, Oregon, hosted two Research Experiences for Undergraduates (REU)interns that conducted a 10-week research internship and presented results at an Howard Hughes Medical Institute (HHMI) symposium on the campus of Oregon State University.

Impacts
(N/A)

Publications

  • Parke, J.L., Grunwald, N.J. 2012. A systems approach for management of pests and pathogens of nursery crops. Plant Disease. 96(9):1236-1244.
  • Utro, F., Haiminen, N., Livingstone Iii, D., Cornejo, O.E., Royaert, S., Schnell, R.J., Motamayor, J.C., Kuhn, D.N., Parida, L. 2013. iXora1: exact haplotype inferencing and trait association. BioMed Central (BMC) Genetics. 14:48.
  • Faukner, J., Rawles, S.D., Proctor, A., Sink, T.D., Chen, R., Philips, H., Lochmann, R.T. 2013. The effects of diets containing standard soybean oil, soybean oil enhanced with conjugated linoleic acids, menhaden fish oil, or an algal docosahexaenoic acid supplement on channel catfish performance, body composition, sensory evaluation, and storage characteristics. North American Journal of Aquaculture. 75:252�265.
  • Fry, W.E., Mcgrath, M.T., Seaman, A., Zitter, T.A., Mcleod, A., Danies, G., Small, I.M., Myers, K., Everts, K., Gevens, A.J., Gugino, B.K., Johnson, S.B., Judelson, H., Ristaino, J., Roberts, P., Secor, G., Seebold, K., Snover-Clift, K., Wyenandt, A., Grunwald, N.J., Smart, C.D. 2013. The 2009 late blight pandemic in eastern USA � causes and results. Plant Disease. 97:296-306.
  • Berbegal, M., Perez-Sierra, A., Armengol, J., Grunwald, N.J. 2013. Evidence for multiple introductions and clonality in Spanish populations of Fusarium circinatum. Phytopathology. 103:851-861.
  • Gent, D.H., Mahaffee, W.F., Mcroberts, N., Pfender, W.F. 2013. The use and role of predictive systems in disease management. Annual Review of Phytopathology. 51:267-89.


Progress 10/01/11 to 09/30/12

Outputs
Progress Report Objectives (from AD-416): Objective 1: Describe the pathogen biology of exotic and emerging plant pathogens affecting horticultural crops. Objective 2: Apply knowledge of biology, ecology, and epidemiology of economically important plant pathogens to the development of improved integrated disease management approaches. Approach (from AD-416): The biology of exotic, emerging, and re-emerging plant pathogens is either poorly understood or inadequate to enable economic and environmentally sustainable management. Objective 1: We will develop and test methods for monitoring pathogen dispersion and describe the evolutionary history, population structure, genetics, epidemiology, and ecology of these pathogens. Objective 2: This knowledge will then be used to develop decision support tools for producers of horticultural crops. Once an increased understanding of a pathogen�s biology has been developed, this knowledge needs to be translated into disease management strategies that are continually optimized and/or improved based on new knowledge. We will develop and improve disease management strategies for select pathogens affecting horticultural crops. While this objective cannot be achieved directly for quarantine pathogens (e.g. P. ramorum), concepts and approaches can be tested by using proxy pathosystems that are similar in the event of an exotic pathogen introduction or quarantines are lifted. In addition, development and improvement of integrated disease management strategies for endemic pathogens will improve our ability to respond to changing climatic conditions while enhancing the economic and sustainable production of horticultural crops. This report documents progress for the project 5358-22000-039-00D Exotic and Emerging Plant Diseases of Horticultural Crops which started 6/18/2012 and continues research from Project 5358-22000-034-00D Exotic, Emerging, Re-Emerging and Invasive Plant Diseases of Horticultural Crops. Due to the short duration of the current project being active, the scientific progress made in relation to the above projects is presented 2012 annual report for Project 5358-22000-034-00D.

Impacts
(N/A)

Publications