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

2020 Annual Report

Objectives
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.

Approach
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
Progress towards Sub-objective 1A identifies common pathogens causing severe damage in the nursery industry and evaluates their risk to rhododendron production and risk for movement among nurseries. Research was completed and a manuscript was published that established losses due to root rot as well as identified the most common soilborne pathogens responsible for the disease. Production practices that increase disease severity were also identified. Results showed that the highest risk for root rot occurs in plants grown in containers and fields rather than in propagation greenhouses. Results also showed that Phytophthora plurivora has become more prevalent than Phytophthora cinnamomi as the most common, aggressive pathogen causing severe root rot in rhododendron. Based on results from previously published research from this Sub-objective, an experiment evaluating the ability of Phytophthora cinnamomi, Phytophthora plurivora, Phytophthora pini, Phytophthora cryptogea, and Phytophthora cambivora to cause disease was completed. Results show that all species except Phytophthora cambivora caused severe disease. A manuscript is being prepared. Towards Sub-objective 1B, over 10 populations of Xiphinema americanum are being characterized morphologically and molecularly. 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, single nematode genomes will be sequenced using HiSeq (a powerful high-throughput sequencing system that enables large-scale genomics). From this data, informative regions will be extracted and phylogenies constructed. Preliminary results indicate that there are at least five species from this complex present in the Pacific Northwest. Also under Sub-objective 1B, the development of a real-time polymerase chain reaction (qPCR) assay for virus detection in nematodes was initiated. It was discovered that qPCR is not sensitive enough to detect this virus in nematodes; therefore, a droplet digital polymerase chain reaction (ddPCR) approach is now being pursued. Based on a previously published manuscript from Sub-objective 2A, ARS scientists, in collaboration with Washington State University, implemented a field study to test different fumigant rates, tarping, and injection depths to improve control against soilborne pathogens and different crop termination dates to improve nematode control. Preliminary results show that tarping improves efficacy of the industry standard fumigant in controlling soilborne fungal pathogens. A second study was conducted to determine the effects of directed energy as an alternative to fumigants for controlling soilborne pathogens. Published results showed that directed energy was effective at controlling soilborne fungal pathogens and plant parasitic nematodes. Field trials continue towards achieving Sub-objective 2B. The field trial in Washington evaluating rootstocks for nematode management is in its fifth year. In this trial, four rootstocks and own-rooted Chardonnay are being evaluated in areas of a vineyard initially with and without nematodes. A manuscript on the establishment years of this vineyard was prepared. Data showed the cumulative response of own-rooted vines to nematode parasitism with a negative relationship between nematode population densities and pruning weights. All of the rootstocks (Harmony, 101-14, 1103P, 5C) were hosts for X. americanum, while they were poor hosts for M. hapla. A second trial was established in another commercial vineyard in Washington where additional rootstocks and own-rooted vines are being evaluated in areas with and without nematodes. The upkeep of this trial is in collaboration with stakeholder viticulturists and colleagues at Washington State University. Progress was made towards Sub-objective 2C to determine the effects of soil moisture on the severity of Phytophthora root rot caused by Phytophthora cinnamomi and Phytophthora plurivora. Preliminary results show that irrigation frequency and volume influence disease progression, but that the results are variable depending on year. A second study is in progress that compares two research methods for inducing root rot, to try and simulate soil moisture conditions that are more reflective of those occurring in the nursery. Preliminary results show that both methods cause similar amounts of disease.

Accomplishments
1. A shift in the Phytophthora species causing root rot in rhododendron may explain why disease control fails. Despite 90 years of research, Phytophthora root rot remains a serious problem for the $42 million rhododendron industry. There are no recent damage estimates to determine the extent of the problem, disease control tactics often fail, and little is known about which pathogen species are currently causing the disease. ARS researchers at Corvallis, Oregon, determined that root rot causes an estimated $6 million in losses (15% of crop value) and identified weak points in the production cycle where Phytophthora pathogens become established. In addition, a new pathogen, P. plurivora, is now more common than P. cinnamomi, which was previously thought to be the main pathogen based on research from 40 years ago. These results may explain why disease control often fails, as the tactics designed to control P. cinnamomi may not be effective for P. plurivora.

2. Boxwood blight range has expanded in Oregon nurseries. Boxwood blight is a serious disease affecting the $126 million boxwood industry in the United States. Oregon produces the most boxwood plants in the nation (20%, $23 million) and the disease was first discovered in two nurseries in 2011. ARS researchers at Corvallis, Oregon, determined that boxwood blight is still present in Oregon nurseries and has spread to new locations. The varieties that are most commonly affected by the disease was also documented. These results are important for documenting the spread of the disease in the nursery industry and help growers make decisions about which varieties to grow.

3. Fumigant alternative shows promise in controlling soilborne plant pathogens and plant parasitic nematodes. Disease control of soilborne plant pathogens and plant parasitic nematodes in many agricultural industries often relies on soil fumigation with highly toxic fumigants. ARS researchers in Corvallis, Oregon, in collaboration with industry, tested a new directed energy system which generates pulses of energy to kill Meloidogyne hapla, Globodera ellingtoniae, Verticillium dahliae, and Phytophthora cinnamomi nematodes. Dosages were identified which successfully reduced populations of these organisms by at least 50%. This technology may provide a valuable new tool for controlling soilborne plant pathogens and plant parasitic nematodes in agricultural crops.

4. Who, what, and where of nematodes in the Pacific Northwest. Plant-parasitic nematodes, microscopic worms, cause millions of dollars of crop loss to commodities grown in the Pacific Northwest (Oregon, Washington, and Idaho) including cherry, alfalfa, potato, wheat, and grapes. For growers in the region to properly manage nematodes, they need information on the types and numbers of nematodes that potentially cause damage. An ARS researcher in Corvallis, Oregon, in collaboration with regional nematode diagnostic laboratories, analyzed and summarized five years of historical data to reveal trends in nematodes in the region. This data provides a rich source of information upon which growers can interpret their reports and make management decisions.

Review Publications
Riga, E., Crisp, J.D., McComb, G.J., Zasada, I.A., Weiland, G.E. 2020. Directed energy system technology for the control of soil borne fungal pathogens and plant-parasitic nematodes. Pest Management Science. 76(6):2072-2078. https://doi.org/10.1002/ps.5745.
Zhang, H., Ghimire, S., Benedict, C., Zasada, I.A., Liu, H., Devetter, L., Miles, C. 2020. Plastic mulches improved plant growth and suppressed weeds in late summer-planted floricane raspberrry. HortScience. 55(4):565-572. https://doi.org/10.21273/HORTSCI14734-19.
Sacher, G.O., Weiland, G.E., Putnam, M.L., Crouch, J., Castroaguddin, V.L. 2020. Confirmation of Calonectria pseudonaviculata causing boxwood blight of Buxus sempervirens and Buxus cultivars in Oregon. Plant Disease. 104(6):1862. https://doi.org/10.1094/PDIS-01-20-0078-PDN.
Weiland, G.E., Scagel, C.F., Grunwald, N.J., Davis, E.A., Beck, B.R., Foster, Z.S., Fieland, V.J. 2020. Soilborne Phytophthora and Pythium diversity from rhododendron in propagation, container, and field production systems of the Pacific Northwest. Plant Disease. 104(6):1841-1850. https://doi.org/10.1094/PDIS-08-19-1672-RE.
Sales, B.K., Bryla, D.R., Trippe, K.M., Weiland, G.E., Scagel, C.F., Strik, B.C., Sullivan, D.M. 2020. Amending sandy soil with a softwood biochar promotes plant growth and root colonization by mycorrhizal fungi in highbush blueberry. HortScience. 55(3):353-361. https://doi.org/10.21273/HORTSCI14542-19.
Foster, Z.S., Weiland, G.E., Scagel, C.F., Grunwald, N.J. 2020. The composition of the fungal and oomycete microbiome of Rhododendron roots under varying growth conditions, nurseries, and cultivars. Phytobiomes Journal. 4(2):156-164. https://doi.org/10.1094/PBIOMES-09-19-0052-R.
Dandurand, L.M., Zasada, I.A., Wang, X., Mimee, B., Dejong, W., Novy, R.G., Whitworth, J.L., Kuhl, J. 2019. Current status of potato cyst nematodes in the United States and Canada. Annual Review of Phytopathology. 57:117-133. https://doi.org/10.1146/annurev-phyto-082718-100254.
Dandurand, L.M., Zasada, I.A., Lamondia, J.A. 2019. Effect of the trap crop, Solanum sisymbriifolium, on Globodera pallida, Globodera tabacum, and Globodera ellingtonae. Journal of Nematology. 51:1-11. https://doi.org/10.21307/jofnem-2019-030.
East, K.E., Moyer, M.M., Madden, N.M., Zasada, I.A. 2019. How low can they go? Plant-parasitic nematodes in a Washington vineyard. Catalyst: Discovery into Practice. 3(1):31-36. https://doi.org/10.5344/catalyst.2019.19001.
Peetz, A.B., Baker, H., Zasada, I.A. 2019. Further elucidation of the host range of Globodera ellingtonae. Nematropica. 49(1):12-17.
Wram, C.L., Zasada, I.A. 2019. Difference in toxicity and physiological response of Meloidogyne incognita to sub-lethal doses of post-plant nematicides. Phytopathology. 109(9):1605-1613. https://doi.org/10.1094/PHYTO-11-18-0420-R.
Zasada, I.A., Howland, A.D., Peetz, A.B., East, K., Moyer, M.M. 2019. Vitis spp. rootstocks are poor hosts for Meloidogyne hapla, a nematode commonly found in Washington winegrape vineyards. American Journal of Enology and Viticulture. 70(1):1-8. https://doi.org/10.5344/ajev.2018.18027.