Location: Horticultural Crops Disease and Pest Management Research Unit
2024 Annual Report
Objectives
Objective 1: Improve and expand knowledge of the prevalence of genotypic and phenotypic diversity in existing and emerging plant pathogens of small fruits and nursery crops.
Sub-objective 1.A: Evaluate boxwood blight in Oregon nurseries.
Sub-objective 1.B: Develop molecular diagnostics and tools to facilitate research on a nematode/virus disease complex.
Sub-objective 1.C : Identify factors that cause blueberry shock virus recurrence in commercial fields and blueberry breeding lines.
Objective 2: Understand how pathogen biology and diversity interacts with environmental factors to cause disease of small fruits and nursery crops.
Sub-objective 2.A: Influence of plant spacing and irrigation frequency on the spread of boxwood blight from infected plants to healthy plants.
Sub-objective 2.B: Cellular level response of Meloidogyne spp. to nematicides.
Objective 3: Develop chemical and host resistance disease management strategies for nursery crops and small fruits.
Sub-objective 3.A: Evaluate newer fungicide chemistries for control of Phytophthora root rot of rhododendron by sensitivity assays.
Sub-objective 3.B: Novel nematicide discovery: Solanum sisymbriifolium as a source of nematicidal compounds.
Sub-objective 3.C: Screen selected Rubus idaeus (red raspberry) accessions for resistance to raspberry bushy dwarf virus
Objective 4: Develop robust and reliable diagnostic assays for plant virus detection in small fruits.
Sub-objective 4.A: Compare graft indexing, RT-PCR, and high-throughput sequencing methods for virus detection in strawberry.
Sub-objective 4.B: Compare graft indexing, RT-PCR, and high-throughput sequencing methods for virus detection in Rubus.
Approach
The long-term goal of this project is to develop sustainable disease management strategies that are based on a knowledge of the identity and biology of the causal agent(s) and on knowledge of pathogen co-infections and interactions with the environment. This will be accomplished by: (1) determining the prevalence of key
pathogens and nematodes constraining production of nursery and small fruit crops; (2) understanding how environment and management practices influence disease; (3) identifying new pesticides and disease resistant crop genotypes for the management of nursery and small fruit diseases; and (4) developing pathogen detection protocols for nursery certification and quarantine plant material.
Knowledge about the prevalence of fungal pathogens, nematodes, and viruses in agricultural systems is key for establishing effective disease control methods. Surveys will be conducted to assess the incidence of fungal pathogens in nurseries, and viruses and nematodes in small fruit research and production fields. Molecular diagnostic tools will be developed to evaluate the ability of nematodes to vector plant viruses and to assess for virus coinfections in small fruit crops. Pathogen and nematode prevalence is influenced by their response to multiple environmental factors. Therefore, studies will be established to assess the influence of irrigation and plant spacing on the spread of fungal plant pathogens in outdoor container trials, and on the effect of nematicides on nematode fitness in laboratory trials. New pesticide chemistries are needed because multiple oomycete pathogens have developed resistance to fungicides and many traditional nematicides have been phased out because of harmful environmental and human health effects. New pesticide chemistries will be evaluated for their efficacy against oomycete plant pathogens and nematodes in laboratory, greenhouse and field experiments. In addition, host resistance plays a crucial role in successful disease management and diagnostic assays are needed to allow growers, regulatory agencies, and diagnosticians to quickly and accurately identify the pathogens causing disease. Small fruit genotypes from grower fields, breeding programs, and national germplasm collections will be screened for resistance or tolerance to key viruses and both traditional bioassays and modern DNA- or RNA-based technologies will be compared for their ability to detect a wide range of viral pathogens for the small fruit industry.
Together, results from this research will identify chemical and nonchemical practices to reduce plant disease, and that can be deployed in horticultural systems in the future.
Progress Report
This report documents FY 2024 progress for project 2072-22000-046-000D, “Disease Management in Small Fruit and Nursery Crops Based on Knowledge of Pathogen Diversity, Biology, and Environmental Effects”, which began in May 2022.
Progress towards Sub-objective 1.A has been made by sampling for boxwood blight at four additional boxwood nurseries in Oregon. Single-spore cultures of the boxwood blight pathogen have been shared with collaborators.
For Sub-objective 1.B, locations with both virus and vector nematodes were identified in the Pacific Northwest. Plant material was collected, and high throughput sequencing was used to generate genomes of tomato ringspot virus (ToRSV). The genomes were then used to develop inclusive primers that will amplify diverse isolates of ToRSV. A system is under development to allow nematodes to feed on ToRSV-infected plants in order to have viruliferous nematodes to work with to continue to develop a quantitative polymerase chain reaction (qPCR) diagnostic assay.
For Sub-objective 1.C, ARS researchers in Corvallis, Oregon, surveyed and collected over 2,700 blueberry samples from Washington and Oregon. The researchers have collected phenotypic data on all samples and run PCR analysis from blueberry shock virus and blueberry virus L (Luteovirus).
For Sub-objective 2.A, a second potted plant experiment was initiated to test the influence of irrigation and plant spacing on boxwood blight disease progress. Plants in each plot are irrigated once, twice, or three times a day and spaced so that the pots are touching or are six inches apart. Preliminary evidence from last year’s trial shows disease spreads fastest on plants that are irrigated three times a day and are spaced closer together compared to the other treatments.
Under Sub-objective 2.B, M. incognita second-stage juveniles were exposed to four nematicides and a water control for two hours. After exposure, nematodes were collected and processed immediately for RNA extraction. The samples were sequenced and the data is now being analyzed.
In support of Sub-objective 3.A, tests to evaluate Phytophthora isolates against the fungicide phosphorous acid have been completed. Tests to determine sensitivity to the fungicide oxathiapiprolin are in progress.
For Sub-objective 3.B, extracts from S. sisymbriifolium were collected using different solvents to extract compounds with different polarities. The extracts were evaluated against M. hapla in microwell assays as well as greenhouse experiments. Shoot extracts obtained using butanol were the most toxic against the nematode. When M. hapla was exposed to extracts for 24 or 48 hours prior to inoculation onto a susceptible host, all S. sisymbriifolium extracts caused a reduction in nematode reproduction.
Under Sub-objective 3.C, all 50 raspberry accessions were clonally replicated and have been grafted with raspberry bushy dwarf virus (RBDV), taken through dormancy, and then evaluated for virus presence using enzyme linked immunosorbent assay (ELISA).
In support of Sub-objective 4.A, all grafting experiments have concluded, high throughput sequencing (HTS) has been performed, and PCR is ongoing and near completion.
For Sub-objective 4.B, all grafting experiments have concluded, HTS has been performed, and PCR is ongoing and near completion.
Accomplishments
1. Improving fungicide performance against Phytophthora root rot of red raspberry. Washington state is the largest producer of frozen red raspberries in the United States, generating $112 million annually. However, Phytophthora root rot disease threatens production of this valuable crop. Growers typically apply fungicides during cool fall weather to manage this disease. Despite this, the treatments often do not provide adequate control, leading growers to suspect fungicide resistance had developed. ARS researchers in Corvallis, Oregon, and Washington State University researchers investigated this issue and found no evidence for fungicide resistance. Instead, they discovered that the timing of the fungicide applications may be the problem and suggested that applying the fungicides during the summer could improve disease control significantly.
Review Publications
Soule, M.L., Kitner, M.L., Studebaker, G.W., Feldman, M.J., Sathuvalli, V., Zasada, I.A. 2023. A canister assay for evaluating host status of potato to Meloidogyne chitwoodi. American Journal of Potato Research. 100:479-478. https://doi.org/10.1007/s12230-023-09936-0.
Wasala, S., Hesse, C.N., Wram, C.L., Howe, D.K., Zasada, I.A., Denver, D.R. 2023. Unraveling microbial endosymbiosis dynamics in plant-parasitic nematodes with a genome skimming strategy. Journal of Applied Microbiology. 3(4):1229-1248. https://doi.org/10.3390/applmicrobiol3040085.
Nunez-Rodriguez, L., Rivedal, H.M., Peetz, A.B., Ocamb, C.M., Zasada, I.A. 2024. First report of Meloidogyne hapla on hemp (Cannabis sativa) in Oregon. Journal of Nematology. 56(1). Article e2024-1. https://doi.org/10.2478/jofnem-2024-0008.
Ohkura, M., Beck, B.R., Scagel, C.F., Weiland, G.E. 2024. The effect of boxwood leaf volatiles on conidial germination of Calonectria pseudonaviculata, the causal agent of boxwood blight. Phytopathology. https://doi.org/10.1094/PHYTO-12-23-0507-R.
Weiland, G.E., Scagel, C.F., Benedict, C., Wasko DeVetter, L., Beck, B.R. 2024. Fungicide sensitivity of Phytophthora isolates from the Washington red raspberry industry. Plant Disease. 108(7):2104-2110. https://doi.org/10.1094/PDIS-12-23-2641-RE.
Li, X., Weiland, J.E., Ohkura, M., Luster, D.G., Daughtrey, M.L., Gouker, F.E., Chen, G., Kong, P., and Hong, C. 2024. Cultivars and production environments shape shoot endophyte profiles of boxwood with different blight resistance. Phytofrontiers 4: 602-615. https://doi.org/10.1094/PHYTOFR-03-24-0023-R
Benedetti, T., Weiland, G.E., Zasada, I.A. 2024. Host status of ornamental shade trees and shrubs to plant parasitic nematodes. Journal of Nematology. 56(1). Article e2024-1. https://doi.org/10.2478/jofnem-2024-0024.
