Location: Horticultural Crops Research2008 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 $59,4000 Program Increase (memo #139). Formerly 5358-22000-030-00D (2/07).
3. Progress Report
Substantial progress has been made on several project plan objectives. Within Objective 1A, we have developed qPCR primers that are specific to E. necator and allow for quantification of airborne inoculum under most conditions. However, at times inhibitors interfere with quantification and detection. We are developing a new method to quantify the impact of inhibitors in each sample and develop corrections to accurately account of the presence of inhibitors to improve accuracy of quantification. Under objective 1B we described the evolution and population structure of Phytophthora ramorum documenting migration of novel clones in the US and demonstrating that the three known clonal lineages of P. ramorum evolved in geographic isolation over long evolutionary times predating the emergence of agriculture before they emerged as significant pathogens in the US. An interactive, searchable database documents emergence of new P. ramorum outbreaks and reports genotype and placement into clonal lineage. AFLP and SAMPL procedures were adapted to describe the population structure of Phragmidium violaceum, however, repeatability of profiles in independent DNA extracts of non standard isolates was problematic. Thus, in order to expedite population description an SSR approach was initiated and 14 primer sets have been identified. Under objective 1C progress has been made in terms of documenting the existence of two distinct small RNA classes describing previously unknown genetic mechanisms in the genus Phytophthora. Under objective 1D, we continue to determine leaf wetness and temperature conditions under which P. ramorum can infect viburnum and lilac and P. violaceum infects blackberry and E. necator infects grape. Disease Forecasting models for P. violaceum and E. necator have been developed and/or modified and are currently being tested in the field. Environmental conditions favorable for infection P. violaceum are extremely rare, making validation of model very difficult (e.g. no infection for two years at test location). Under objective 2, variation in resistance in viburnum and lilac to P. ramorum has been characterized and scientist continue to study the diversity of Phytophthora spp. in nursery environments as a function of plant genotype, season, and cultural practice. Ninety five different cultivars or species of Rubus were tested for susceptibility with two new species identified and susceptible (R. insularis and R. hawaiianense). Objective 3 is currently being validated at 5 vineyards locations across the Willamette valley Oregon as well as at 9 other locations in Oregon and Washington by cooperators. All milestones for FY 2008 are in progress and have been substantially met. NP303, Component 1b
1. Ancient isolation and independent evolution of the emerging sudden oak death pathogen Phytophthora ramorum. This research was performed to understand the evolution of the exotic pathogen Phytophthora ramorum that is responsible for extensive mortality of oaks and tanoaks as well as economic losses to U.S. nurseries due to its infection of common ornamental plants. P. ramorum exists as three distinct clonal lineages and it is not clear if they originate from the same, possibly sexually reproducing population of unknown origin. All research was performed by ARS scientists in the Horticultural Crops Research Unit in Corvallis, OR. We inferred the evolutionary history of P. ramorum from nuclear sequence data. We found that the lineages have been diverged for at least 11% of their history, an evolutionarily significant amount of time estimated to be on the order of 165,000 to 500,000 years. The divergence of the three clonal lineages of P. ramorum supports a scenario in which the three lineages originated from different geographic locations that were sufficiently isolated from each other to allow independent evolution prior to introduction to North America and Europe. This work addresses National Program 303 component Characterization of Plant Pathogens, Problem Statement 1b.
5. Significant Activities that Support Special Target Populations
Park, J., Park, B., Veeraraghavan, N., Jung, K., Lee, Y., Blair, J.E., Geiser, D., Isard, S., Mansfield, M.A., Nikolaeva, E., Park, S., Kim, S.H., Greene, M., Ivors, K.L., Balci, Y., Peiman, M., Erwin, D.C., Coffey, M.D., Rossman, A.Y., Farr, D.F., Cline, E., Grunwald, N.J., Luster, D.G., Schrandt, J.K., Martin, F.N., Ribeiro, O.K., Makalowska, I., Kang, S. 2008. Phytophthora Database: A forensic database supporting the identification and monitoring of Phytophthora. Plant Disease. 92:966-972.