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United States Department of Agriculture

Agricultural Research Service


Location: Horticultural Crops Research

2010 Annual Report

1a.Objectives (from AD-416)
1.Describe the pathogen biology of exotic, emerging, re-emerging, and invasive plant pathogens affecting horticultural crops. 2.Characterize host ranges and levels of resistance of hosts to exotic, emerging, reemerging,and invasive plant pathogens affecting horticultural crops. 3.Apply knowledge of biology, ecology, and epidemiology to the development of improved integrated disease management approaches.

1b.Approach (from AD-416)
This research will be accomplished through a multifaceted approach integrating the disciplines molecular biology, genomics, population ecology, epidemiology, meteorology, climatology, and microbiology. Initially the project will deal with two recently introduced pathogens, Phytophthora ramorum and Phragmidium violaceum, as well as other Phytophthora, powdery mildew and Botrytis diseases of various horticultural crops. This research project will utilize: novel techniques for rapid and accurate assessment of pathogen presence and abundance in the field; quantitative information on distribution of clones, migration of new strains, degree and rates of out-crossing, and sources of resistance to the introduced pathogens P. ramorum and P. violaceum; elucidation of important genetic traits that impact disease development; and increased understanding of factors influencing disease epidemics that will be used to generate improved disease forecasting models. Formerly 5358-22000-024-00D (2/03). FY06 Program Increase (memo #139). Formerly 5358-22000-030-00D (2/07).

3.Progress Report
We completed research on the quantification of airborne propagules of Erysiphe necator (grape powdery mildew) for the initiation of a fungicide management program. A quantitative PCR assay and an inexpensive impaction spore trap were developed and validated in 13 commercial vineyards in Oregon. We demonstrated that 2.3 fungicide applications were saved when growers initiated their management programs based on inoculum detection. In order to extend potential of commercial the use of inoculum detection, we began developing and testing a LAMP-PCR protocol that growers could perform with <$2000 in equipment and no specialized training. Results indicate that grower-preformed LAMP-PCR is as effective as the qPCR procedure we previously validated for inoculum detection in commercial vineyards. We completed assessment of the genetic diversity of Phragmidium violaceum (blackberry rust) with our Australian collaborators. Through the development of microsatellite markers, we were able to determine that the U.S. population was distinct from the Australian and European populations but that the U.S. and European populations appear to be coevolving. It appears that the U.S. population either resulted from a single introduction of a highly diverse population or multiple introductions over numerous years, indicating that the disease observed in 2005 is likely a result of unusual weather in the fall/spring of 2004/2005. We initiated a project on modeling turbulent airflow in perennial crop canopies to help predict pathogen dissemination in collaboration with fluidic engineers (Utah Univ.) specializing in particle dispersion in urban environments. We developed surrogate particles to simulate fungal conidia and collected dispersion, weather, and airflow data from commercial vineyards. These data where used to develop preliminary dispersion models. These models will be useful in directing disease monitoring and management efforts. We continued research on the interpolation of sparse weather data using climatological and orthographic parameters. For the second year, disease management based on site specific weather data was not significantly different from that based on the interpolated data. These results indicate that regional systems for interpolation sparse weather data will be useful for site specific disease management decisions. We described the evolution and population structure of Phytophthora ramorum documenting migration of novel clones in the U.S. and worldwide. Our analysis suggests that there were at least 4 global migrations of P. ramorum. An interactive, searchable database documents emergence of new P. ramorum outbreaks and reports genotype and placement into clonal lineage. We documented the existence of two distinct small RNA classes describing previously unknown genetic mechanisms in the genus Phytophthora. We have characterized biogenesis effectors involved in processing of small rRNAs. The variation in resistance in viburnum and lilac to P. ramorum has been characterized, and scientists continue to study the diversity of Phytophthora spp. in nursery environments as a function of plant genotype, season, and cultural practice.

1. Migration of Phytophthora ramorum. Phytophthora ramorum, the cause of sudden oak death, has been reported in ornamental nurseries on the West Coast of North America from British Columbia to California. Long distance migration of P. ramorum has occurred via the nursery trade. ARS researchers at Corvallis, OR studied migration and genetic diversity of P. ramorum. This analysis provides evidence for four global migration events of which three occurred into North America. This work highlights the repeated global migration of this pathogen and identified pathways of migration into the United States that can be managed.

2. PCR detection in grower fields. Growers use fungicide applications to control grape powdery mildew pathogens. To improve early detection, ARS researchers at Corvallis, OR developed a quantitative PCR assay and inexpensive spore traps shown to be reliable under commercial conditions for the detection of airborne spores of grape powdery mildew. The team demonstrated the commercial feasibility of using PCR detection of airborne spores of this pathogen to initiate fungicide applications to control the disease. Three years of validation in 6-10 commercial vineyards per year saved 2.3 applications per year or >$113/A in application costs without increasing disease development, thus demonstrating that withholding fungicide applications until the pathogen is detected in the air is viable commercially. Commercial application of these procedures has the potential to significantly reduce fungicide use and associated applications costs for managing powdery mildew.

3. Markers to fingerprint exotic blackberry rust pathogen. In 2005, Phragmidium violaceum causing Blackberry rust was discovered in the United States for the first time and caused significant economic loss for Washington and Oregon Blackberry growers. Understanding the population structure would yield insight into the origin and potential sources of the introduction. ARS scientists at Corvallis, OR developed microsatellite markers for assessing the genetic diversity of this pathogen. The U.S. population was distinctly different from both the European and Australian populations, indicating either that a population of isolates were introduced in 2004 and 2005 or that multiple introductions occurred. These data, coupled with data on the distribution of pathogen, indicate that P. violaceum is now endemic to the United States and management practices must be developed to manage the pathogen.

Review Publications
Johnson, K., Mahaffee, W.F. 2010. Factors influencing epidemiology and management of blackberry rust in cultivated Rubus laciniatus. Plant Disease. 94:581-588.

Kang, S., Mansfield, M., Park, B., Geiser, D., Coffey, M., Grunwald, N.J. 2010. The promise and pitfalls of sequence-based identification of plant pathogenic fungi and oomycetes. Phytopathology. 100: 732-737.

Vercauteren, A., De Dobbelaere, I., Grunwald, N.J., Bonants, P., Van Bockstaele, E., Maes, M., Heungens, K. 2009. Clonal expansion of the Belgian Phytophthora ramorum populations based on new microsatellite markers. Molecular Ecology. 19:92-107.

C., Gomez, D., Morin, L., Evans, K., Mahaffee, W.F., Neill, T.M., Grunwald, N.J.,Molecular Ecology Resources Primer Development Consortium. 2010. Permanent genetic resources added to molecular ecology resources database 1 December 2009–31 January 2010. Molecular Ecology Resources. 10:576-579.

Last Modified: 8/2/2014
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