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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Research Project #432677

Research Project: Development of Knowledge-based Approaches for Disease Management in Small Fruit and Nursery Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

2019 Annual Report

Objective 1: Identify species, populations, and genotypes of key pathogens constraining production of small fruit and woody nursery plant species in the Pacific Northwest region of the United States. Subobjective 1.A: Evaluation of soilborne Phytophthora and Pythium communities and populations affecting rhododendron production. Subobjective 1.B: Characterization of X. americanum-group nematodes and ability to vector viruses. Objective 2: Identify and evaluate tools for management of economically-important diseases of small fruit and nursery crops. Subobjective 2.A: Developing effective methods for soilborne pathogen management through removal of root Inoculum in continuous red raspberry production systems. Subobjective 2.B: Identification and implementation of Vitis spp. rootstocks for the management of plant-parasitic nematodes of wine grapes. Subobjective 2.C: Improved management of Phytophthora and Pythium of rhododendron through reduced irrigation regimes.

Determine the prevalence and characterize the population diversity of important soilborne pathogens affecting horticultural crops. Results from this research will identify specific pathogen populations that constrain production of horticultural crops. These populations can be targeted in the future to develop more effective, economical, and environmentally-acceptable disease management systems. Evaluate plant debris removal and irrigation practices for their ability to reduce disease in horticultural crops. Results of this research will identify specific cultural practices that reduce or suppress pathogen populations, thereby resulting in less disease. Evaluate germplasm of grape (Vitis species) rootstocks for resistance to dagger nematodes (Xiphinema americanum) and root knot nematodes (Meloidogyne hapla). Our research will identify grape genotypes that are resistant to these plant-parasitic nematodes, and can be deployed in horticultural systems in the future.

Progress Report
Towards identifying species, populations, and genotypes of key pathogens constraining production of small fruit and woody nursery plant species in the Pacific Northwest region of the U.S., common pathogens were identified and their risk to rhododendron production and movement among nurseries was evaluated. ARS scientists in Corvallis, Oregon, completed this research and a manuscript is being prepared that identifies 31 soilborne pathogen species as causes of root rot in the rhododendron nursery industry. Phytophthora cinnamomi, Phytophthora plurivora, and Pythium cryptoirregulare were the most common pathogens identified from the study. Results also show that the biggest risk for root rot is in container and field systems where Phytophthora species are more frequently isolated, rather than in propagation systems where Pythium species predominate. Research was completed and a manuscript was submitted showing that P. plurivora has limited genetic diversity and has been moved frequently in the nursery industry. Based on results of previously published research from Sub-objective 1A, showing that P. cinnamomi and P. plurivora are aggressive root rot pathogens, an additional experiment is being conducted to evaluate the ability of other common soilborne Phytophthora species to cause root rot in rhododendron. To characterize plant-parasitic nematode diversity, over 10 populations of Xiphinema americanum were collected from small fruit production fields in the Pacific Northwest. The populations are being characterized morphologically and molecularly by ARS scientists in Corvallis, Oregon. From each population, single nematodes were imaged for future measurement and then DNA was extracted from the nematode; 10 individuals from each population were analyzed. For morphological identification, the measurements of diagnostic characters were determined and a preliminary character phylogeny has been constructed. For molecular characterization, DNA was extracted and genus-specific primers targeting a 2,800 base pair (bp) mitochondrial DNA region were designed from accessions deposited in GenBank which included the entire mitochondrial genome, portions of the cytochrome oxidase 1 (CO1) gene, partial sequences from the 3’ end of the ribosomal small subunit (mtSSU), and the cytochrome b (CYTB) gene. Polymerase chain reaction (PCR) amplicons from individual isolates were cloned and sequenced in multiple reactions. Preliminary results indicate that there are at least five species from this complex present in the Pacific Northwest. For Sub-objective 1B, the development of a quantitative PCR assay for virus detection in nematodes was initiated. Starting with tomato ringspot virus, a primer-probe was developed and is currently being validated. As part of identifying and evaluating tools for management of economically-important diseases of small fruit and nursery crops, ARS scientists, in collaboration with Washington State University, published a manuscript showing that root removal was not effective in reducing either soilborne pathogens or plant-parasitic nematodes. Results also showed that the industry standard fumigation treatment was not very effective for reducing soilborne pathogen populations, but is still effective at reducing nematode populations. Based on these results, additional field studies were implemented to test different fumigant rates, tarping, and injection depths to improve control against soilborne pathogens and different crop termination dates to improve nematode control. Greenhouse and field trials were also conducted to identify the utility of rootstocks for the management of plant-parasitic nematodes in wine grapes. Ten rootstocks and an own-rooted Chardonnay control are being screened against Meloidogyne hapla in a greenhouse experiment; this is a repeat of a trial conducted in the first year of the study. The field trial in Washington evaluating rootstocks for nematode management was fumigated in the fall and planted in the spring. Data on initial population densities of plant-parasitic nematodes has been collected. The upkeep of this trial will be in collaboration with a stakeholder viticulturist and colleagues at Washington State University. The role of irrigation as a pathogen management tool was also evaluated by determining whether reduced water availability minimizes rhododendron root damage by Phytophthora and Pythium species. ARS researchers in Corvallis, Oregon, have completed two trials assessing how different irrigation treatments influence disease development. Preliminary results from the first trial show that irrigation frequency and volume can dramatically influence disease progression. A manuscript is in preparation. Based on our results from these trials, further studies are assessing whether the common research method of flooding plants after inoculation to induce pathogenicity is similar to disease progression in the nursery environment.

1. Soilborne pathogens causing production losses in rhododendron industry. Rhododendron root rot is a serious disease, causing significant plant mortality in the $42 million U.S. rhododendron industry. Research on rhododendron root rot has focused almost exclusively on a single pathogen (Phytophthora cinnamomi); however, there are numerous other root rot pathogens that have not yet been evaluated for their potential to cause disease. ARS researchers in Corvallis, Oregon, evaluated Phytophthora plurivora and Pythium cryptoirregulare for their ability to cause root rot in comparison to P. cinnamomi on two rhododendron varieties. Phytophthora plurivora caused severe root rot on both varieties, but at a slower rate than P. cinnamomi, while Py. cryptoirregulare only caused mild damage. In addition, disease caused by both pathogens was slower to develop on the rhododendron variety 'Yaku Princess' than on variety 'Cunningham's White'. Results show growers that they should be more concerned about the presence of both Phytophthora species in rhododendron production facilities than Py. cryptoirregulare.

2. Genomic resources for potato cyst nematodes expanded. Potato cyst nematodes, Globodera pallida and G. rostochiensis, are globally important nematode parasites of potato, with the potential to cause up to 80 percent reduction in potato yield. Recently, a new potato cyst nematode, G. ellingtonae, was described, with this nematode being genetically intermediate between the other potato cyst nematodes. ARS researchers at Corvallis, Oregon, conducted research to characterize the genome (the nematode's complete set of DNA) and transcriptome (the nematode's gene expression). These results are significant because they provide a framework for further understanding the genetic relationships among the potato cyst nematodes and ultimately how they interact with their host. This research will be used by scientists to continue to explore the genetics of potato cyst nematodes and may lead to the development of novel management for these production-limiting pests.

3. Life cycle model developed for the northern root-knot nematode in Washington vineyards. Wine grape growers in Washington do not have adequate methods to manage plant parasitic nematodes. ARS scientists in Corvallis, Oregon, and researchers from Washington State University, characterized the development dynamics of the most numerous nematode parasite in Washington vineyards, the northern root-knot nematode, over two years at multiple sites. This nematode produced only one generation per year in Washington wine grape vineyards. By gaining insight into the biology of this pest in production vineyards, it is now possible to improve time management strategies, such as the application of pesticides. For example, it is now known that the susceptible stage of this nematode is most abundant in soil in the spring and fall. These findings will be used by wine grape growers to better time control strategies to reduce the impact of this damaging pest.

4. Root removal does not improve fumigant efficacy against soilborne pathogens and plant-parasitic nematodes. At the end of the raspberry field production cycle, raspberry plants are killed and the aboveground canes are removed from the field. Roots are left in the soil and may serve as a continued food source for plant-parasitic nematodes, as a reservoir of pathogen inoculum for the next crop of raspberry, and may interfere with soil fumigation for disease control. ARS researchers in Corvallis, Oregon, collaborated with farmers and Washington State University, to determine if removing roots from field soil prior to fumigation could improve disease control efficacy and further reduce nematode and soilborne pathogen populations. Fumigation alone was effective at reducing the root-lesion nematode, but not fungal pathogens. This research is important because it helps explain why growers sometimes experience poor fungal disease control in some fields. Further research is needed to determine whether other fumigant chemistries, rates, and the addition of tarping to hold the fumigant in the soil can be used to improve disease control against soilborne plant pathogens.

Review Publications
Zasada, I.A., Dandurand, L., Gleason, C., Hagerty, C., Ingham, R. 2018. Plant-parasitic nematodes of Idaho, Oregon, and Washington (Pacific Northwest). In: Subbotin, S.A., Chitambar, J.J., editors. Plant Parasitic Nematodes in Sustainable Agriculture of North America, Vol. 1 – Canada, Mexico and Western USA. Cham, Switzerland: Springer. p. 211-240.
Brown, A.M., Wasala, S.K., Howe, D.K., Peetz, A.B., Zasada, I.A., Denver, D.R. 2018. Comparative genomics of Wolbachia-Cardinium dual endosymbiosis in a plant-parasitic nematode. Frontiers in Microbiology. 9:2482.
Devetter, L., Watkinson, S., Zasada, I.A., Weiland, G.E., Hesse, C.N., Walters, T.W. 2018. Effectiveness of nontarped broadcast fumigation and root removal on root lesion nematode and Fusarium and Pythium species in a red raspberry system. Plant Health Progress. 19(2):168-175.
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.
Phillips, W.S., Howe, D.K., Brown, A.M., Eves-van den Akker, S., Dettwyler, L., Peetz, A.B., Denver, D.R., Zasada, I.A. 2017. The draft genome of Globodera ellingtonae. Journal of Nematology. 49(2):127–128.
Phillips, W.S., Eves-van den Akker, S., Zasada, I.A. 2017. Draft transcriptome of Globodera ellingtonae. Journal of Nematology. 49(2):129–130.
Rudolph, R.E., Zasada, I.A., Hesse, C.N., Devetter, L.W. 2018. Brassicaceous seed meal, root removal, and chemical fumigation vary in their effects on soil quality parameters and Pratylenchus penetrans in a replanted floricane raspberry production system. Applied Soil Ecology. 113:44-51.
Howe, D.K., Smith, M., Tom, D.M., Brown, A.M., Peetz, A.B., Zasada, I.A., Denver, D.R. 2018. Analysis of nematode-endosymbiont coevolution in the Xiphinema americanum species complex using molecular markers of variable evolutionary rates. Nematology. 21(5):533-546.
Whitworth, J.L., Novy, R.G., Zasada, I.A., Dandurand, L., Wang, X., Kuhl, J.C. 2018. Resistance of potato breeding clones and cultivars to three species of potato cyst nematode. Plant Disease. 102(11):2120-2128.
Zhang, H., Miles, C., Ghimire, S., Benedict, C., Zasada, I.A., Devetter, L.W. 2019. Polyethylene and biodegradable plastic mulches improve growth, yield, and weed management in floricane red raspberry. Scientia Horticulturae. 250:371-379.
Rudolph, R., Zasada, I.A., Devetter, L. 2017. Annual and perennial alleyway cover crops vary in their effects on Pratylenchus penetrans in Pacific Northwest red raspberry (Rubus idaeus). Journal of Nematology. 49(4):446-456.
Zasada, I.A., Kitner, M.L., Wram, C., Wade, N., Ingham, R.E., Hafez, S., Mojtahedi, H., Chavoshi, S., Hammack, N. 2019. Trends in occurrence, distribution, and population densities of plant-parasitic nematodes in the Pacific Northwest of the United States from 2012 to 2016. Plant Health Progress. 20(1):20-28.
Wasala, S.K., Brown, A.M., Kang, J., Howe, D.K., Peetz, A.B., Zasada, I.A., Denver, D.R. 2019. Variable abundance and distribution of Wolbachia and Cardinium Endosymbionts in plant-parasitic nematode field populations. Frontiers in Microbiology. 10:964.
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.
Dandurand, L., Morra, M.J., Zasada, I.A., Phillips, W., Popova, I., Harder, C. 2017. Control of Globodera spp. using Brassica juncea seed meal and seed meal extract. Journal of Nematology. 49(4):437–445.
East, K.E., Zasada, I.A., Schreiner, R.P., Moyer, M.M. 2019. Developmental dynamics of Meloidogyne hapla in Washington wine grapes. Plant Disease. 103(5):966-971.