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 Horticultural Crops Disease and Pest Management Research Unit: Corvallis, OR
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ARS Home Pacific West Area Corvallis, Oregon Horticultural Crops Disease and Pest Management Research Unit Research





- Mahaffee, Walter - Walt
- Grunwald, Niklaus - Nik
- Stockwell, Virginia
- 2023
- 2022
- Publications
- Plant Diseases (303)

Research Project: Knowledge Based Tools for Exotic and Emerging Diseases of Small Fruit and Nursery Crops **Location:
                            Horticultural Crops Disease and Pest Management Research Unit** 2022 Annual Report **Objectives**
                                

Objective 1: Describe the pathogen biology and disease epidemiology of exotic and emerging plant pathogens affecting perennial fruit and nursery crops. 
Sub-objective 1.A: Conduct comparative genomic analyses of Phytophthora ramorum. 
Sub-objective 1.B: Investigate genes differentially expressed in the EU1 and NA1 clonal lineages causing sudden oak death in Oregon forests. 
Sub-objective 1.C: Characterize fungicide resistance of Botrytis populations from small fruit and grape. 
Sub-objective 1.D: Assess fitness of sensitive and resistant QoI and DMI E. necator isolates. 
Sub-objective 1.E: Conduct mating studies of sensitive and resistant QoI and DMI E. necator isolates. 
Sub-objective 1.F: Determine relationship between mutation frequency and fungicide tolerance. 
Sub-objective 1.G: Describe the pathogen and epidemiology of the re-emerging disease, dry berry of Rubus. 
Sub-objective 1.H: Insight into the ecology and pathobiology of the aerial gall pathogen of blueberry. 
Sub-objective 1.I: Identify cranberry fruit rot pathogens, their fungicide sensitivity, and estimate yield loss to rots in Oregon and Washington production beds. 
Sub-objective 1.J: Elucidate the disease cycle of Gnomoniopsis idaeicola, an emerging pathogen of blackberry. 

Objective 2: Apply knowledge of biology, ecology, and epidemiology to the development of improved integrated disease management approaches. 
Sub-objective 2.A: Examine the utility of UVC for management of grape diseases. 
Sub-objective 2.B: Develop and improve plant pathogen diagnostics, detection, and identification. **Approach**
                                

The long-term goal of this project is to develop the knowledge and tools needed to respond to plant disease epidemics using approaches that are economically and environmentally sustainable, with emphasis on increasing our ability to respond to exotic, emerging, and re-emerging pathogens. This will be accomplished through trans-disciplinary approaches that: (1) improve methods for pathogen monitoring and conduct pathogen surveys to ascertain changes in diversity and specific genetic traits in critical pathogen populations; (2) increase knowledge of pathogen biology and life cycles; (3) integrate this knowledge into decision aids to enhance the economic and environmental sustainability of horticultural crops while improving disease management. 

The globalization of agricultural markets, increased human, plant, and animal intercontinental travel, and climate change will continue to enhance pathogen spread and introduction of exotic pathogens that threaten natural and agronomic ecosystems. Comparative genomics and transcriptomics will be used to identify new variants and tract population diversity and alleles associated with differences in pathogenesis and fungicide resistance. 

The consequences of pathogen movement will depend on the speed with which we can detect and track their introduction and adjust management practices in response. We will use the latest advances in CRISPR technology to develop inexpensive diagnostic assays suitable for tracking pathogen variants. The fitness costs associated with genetic variation associated with fungicide resistance will be examined using traditional phenotype characterization and by examining allele segregation and prevalence in laboratory experiments and natural environments.

Crop production is also threatened by pathogens currently considered manageable or insignificant but may emerge or re-emerge due to pesticide resistance development, overcoming available host resistance, and/or removal of pesticides from the commercial market. These threats can result in direct and indirect economic impacts, such as reduced yield or quality, loss of foreign or domestic markets, and non-crop impacts. The epidemiology of numerous emerging fungal diseases will be examined using a series of in-field and laboratory studies that elucidate the causal agents, the environmental conditions suitable for disease development, and methods to reduce disease progression. The utility and constraints of germicidal ultraviolet radiation treatments for disease management will be examined in laboratory and field settings. 

Greater knowledge of the factors influencing establishment and spread of pathogens, and subsequent disease development is needed to develop economically and environmentally sustainable management strategies. For these reasons, this project focuses on a multitude of pathosystems that cause major impacts on horticulture crops, including sudden oak death, botrytis blight and grape powdery mildew. **Progress Report**
                                

This report documents progress for project 2072-22000-045-000D, “Knowledge Based Tools for Exotic and Emerging Diseases of Small Fruit and Nursery Crops,” which started in May 2022 and continues research from project 2072-22000-041-000D, “Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops.” For additional information, see the report for the expired project.

In support of Sub-objective 1A, we continue to conduct a comparative genomic analysis of long-read sequenced and fully assembled genomes of major U.S. and Asian variants of the sudden oak death pathogen, Phytophthora ramorum. We initiated a large transcriptomics experiment using tanoak infected with P. ramorum with EU1 and NA1 strains. The transcriptome was sequenced and is currently being analyzed.

To address Sub-objectives 1B and 2B, we used re-sequenced genomes to identify genetic regions that are diagnostic for differentiating species and clonal lineages of P. ramorum.

For Sub-objective 1D, phenotyping efforts of eight isolates of E. necator were initiated by first examining the effects of temperature on germination and infection. Results indicate that there may be a fitness advantage conferred by the A143 mutation under cool growing conditions with some cost at temperatures greater than 33 degrees C.

The mating studies described in Sub-objective 1E have been initiated and fields are being monitored for disease development.

In support of Sub-objective 1G, we sequenced the genomes of the type strain of the fungal pathogen, Monilinia rubi, isolated in the 1950s, and a recent isolate. DNA was submitted for short-read Illumina Hi-Seq and Pac-Bio long-read sequencing.

In support of Sub-objective 1H, the whole genomes of blueberry stem gall isolates were sequenced, using Illumina Hi-Seq.

In support of Sub-objective 1I, we sampled commercial cranberry beds and determined the disease incidence and isolate fruit rot pathogens in Washington and Oregon. About 20% of cranberries had symptoms of fruit rot, and we isolated nine different types of fungal pathogens.

In support of Sub-objective 1J, sampling of blackberry fields with blackberry collapse is scheduled to start in late September.

To address Sub-objective 2A, a delivery unit was designed and built that can deliver 1200 watts of UVC radiation. A small plot field trial was initiated that examines four doses of ultraviolet light spectrum C (UVC) in conjunction with various fungicide application regimes.

To address sub-objective 2B, we assembled the mitochondrial genomes for P. ramorum samples currently available and developed a web-based implementation using Nextstrain. This implementation still requires further work and is not yet final. **Accomplishments**


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