Location: Horticultural Crops Disease and Pest Management Research Unit
Project Number: 2072-22000-045-043-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 31, 2024
End Date: Aug 30, 2028
Objective:
1. Monitor phenotypic and genetic diversity of emerging P. ramorum invasions and spread in the United States.
2. Develop novel disease management strategies such as chemical or biological control.
3. Maintain and sample a network of infested and non-infested sudden oak death plots.
4. Use genomic approaches to characterize pathogen adaptation.
5. Characterize host resistance and develop genomic resources for improving hosts.
6. Sequence and analyze genomes of major Phytophthora pathogens of horticultural, forest, and landscape plants.
Approach:
To meet the objectives a range of molecular, evolutionary, genomic, epidemiological, and plant pathological approaches will be used to characterize the epidemic of the SOD pathogen Phytophthora ramorum in the US and understand their impacts and spillover from forests to agriculture:
Objective 1: Monitor phenotypic and genetic diversity of emerging P. ramorum invasions and spread in the US: A combination of genotyping and growth chamber experiments will be conducted to monitor changes in the genetic diversity of the pathogen population and how they correlate with changes in pathogen aggressiveness. Growth chamber experiments will measure P. ramorum aggressiveness and sporulation potential across a variety of host plants. Genotyping will use a variety of approaches including microsatellite markers and next generation sequencing to characterize the pathogen population. The combination will then be used to correlate changes in genetic diversity with changes in phenotypic diversity.
Objective 2: Develop novel disease management strategies such as chemical or biological control: Test a variety of bacteria and fungi for antagonism against P. ramorum. Experiments will consist of in-vitro and growth chamber experiments. In-vitro experiments will be conducted using fungi and bacteria known to be antagonistic.
Objective 3: Maintain and sample a network of infested and non-infested sudden oak death plots: Annual monitoring of a permanent plot network to quantify ecosystem impacts in southwest Oregon caused by the continued spread of P. ramorum. This plot network consists of infested and uninfested plots, across the ecoregion. In collaboration we will quantify changes to the avian, small mammal, plant, and microbial communities as a result of the SOD outbreaks. Plots will be maintained and sampled yearly as needed.
Objective 4: Use genomic approaches to characterize pathogen adaptation: We will sequence genomes of P. ramorum samples including all clonal lineages and strains from Asia to determine if pathogen is reproducing sexually or is adapting to new hosts and/or is spilling over from forests to agriculture or vice versa.
Objective 5: Characterize host resistance and develop genomic resources for improving hosts: Tanoak is an important host driving the epidemic. We will characterize genetic diversity of tanoak and sequence the genome and transcriptome of tanoak to provide resources for improving resistance in tanoak to the SOD pathogen. Availability of resistant tanoak will slow or stop the epidemic and avoid spillover to agricultural crops such as Rhododendron.
Objective 6: Sequence and analyze genomes of major Phytophthora pathogens of horticultural, forest, and landscape plants: Because pathogens spill over from natural ecosystems to agricultural crops, we will monitor invasive and native pathogens in forests that could threaten horticultural production. We will sequence select genomes of forest and ornamental nursery Phytophthora pathogens. Genomes will be sequenced using Oxford nanopore long-read technology that currently results in near chromosome level assemblies of high quality. Genomes will be characterized.