Project Overview

Reports

Commodities

Target Pests

Practices

Plant diseases, along with pests and weeds, present significant impediments to agricultural economic prosperity and food biosecurity. Global movement of plant materials has dramatically increased risks of introducing and spreading diseases, which has been exacerbated by the recognition of cryptic species of pathogens that are morphologically identical to known pathogens yet are epidemiologically important. We have developed whole genome sequencing (WGS) protocols and demonstrated the power of WGS in genomic epidemiology to track transmission patterns of plant pathogens and model their evolution. Our approach will accelerate diagnoses, shorten response time to outbreaks, prove essential to more accurate and sustainable management strategies, and enable earlier disruption of transmission chains to help stakeholders better mitigate risks of disease and reduce economic losses. We have a long-term goal of building a network of disease diagnostic clinics that use WGS to transform the rate, scale, and manner in which production-limiting microbes and pests are managed. Our short-term goal is to help key laboratories within the National Plant Diagnostic Network (NPDN) implement use of WGS. To this end, we have begun implementing WGS at three University plant clinics. However, the success of genomic epidemiology relies on the availability of rich genome sequence databases, as deeply sampled taxa of pathogens relevant to US agriculture are essential for determining at high resolution the identities of organisms in disease samples, inferring the evolution of pathogens, e.g., extant or emerging, and developing management strategies.  

The work proposed hereafter is an important early step in achieving both short- and long-term goals. Research members identified within are currently funded to develop standards, workflows, and pipelines to enable use of WGS in plant clinics to diagnose three genera of bacterial pathogens. This proposal builds on that effort, and on the mission of the NPDN, by developing a public archive of genomic data of significant bacterial pathogens while extracting actionable information from the genomes to mitigate disease risk for stakeholders.  Specifically, the objectives are to:

1. Solicit samples of problematic bacterial diseases from growers throughout the western region, particularly Oregon, Washington, and California, for isolation and whole genome sequencing.
2. Develop high-quality bacterial pathogen genomes to be archived in local and public databases; characterize genome sequences and mine for information relevant to tracking of specific genotypes, monitoring of novel pathogen lineage development, and exploitation for best management practices.
3. Use insights gained to develop better management practices through specific interventions.

We already have in hand three resources that are critical to the success of the proposed work. First, we have developed a standardized computational pipeline to process and assemble sequencing reads, annotate bacterial genomes, infer the taxonomic identities of samples to sub-species levels, and quantify genetic differences among bacteria to infer their evolutionary relationships and transmission patterns. Second, we have developed gene databases that can be used to infer whether a strain of Agrobacterium is pathogenic and susceptible to currently available biocontrol products. Third, we have a genome sequencing instrument and have developed the necessary infrastructure to use it in a diagnostic setting. While we have amassed over 200 genome sequences from agrobacteria, we lack sufficient representation of lineages that infect grapevine and other small fruits important to agriculture in the Pacific states. Hence, our overarching objective is to compile a comprehensive database of genome sequences from agrobacteria that are agriculturally important to the Pacific western states. This is a crucial step for improving surveillance, early detection and rapid response for crop diseases and translating WGS to address stakeholder needs.

Objectives:

1. Solicit from growers throughout the western region samples of plants with crown gall disease for isolation and whole genome sequencing. We will focus on grapes, blueberries, blackberries, and other small fruits.

Timeline: This will be ongoing throughout the funding period.

2. Develop high-quality genomic information from the bacterial isolates by sequencing using an Illumina MiniSeq instrument. Archive genomes in local and publicly accessible databases such as the National Center for Biotechnology Information. Specifics regarding exact location of sample origin will be held in confidentiality and will not be made public. The genome sequences will be explored for insights to determine things such as transmission routes, a pathogen’s ability to survive in a specific environment, and to monitor and determine the impact of agricultural practices on development of novel pathogen lineages

Timeline: Ongoing throughout the funding period; genome mining will occur toward the end of the funding period as more genomes become available.

3. Use insights gained to develop better management practices through specific interventions. Updated management information will be conveyed through outlets such as the annually revised PNW Plant Disease Management Handbook (https://pnwhandbooks.org/plantdisease), scientific meetings, and trade journal publications.

Timeline: Toward the end of the funding period and beyond.