FACT-CIN: DEVELOPING GENOME AND METAGENOME SEQUENCING AND COMPUTATIONAL TOOLS FOR DISEASE DETECTION IN PLANT CLINICS

The overarching goal of this project is to integrate use of whole genome sequencing information with traditional diagnostics to increase the capacity of plant disease diagnostic clinics to help stakeholders in US agriculture mitigate risks of disease. The project aims to address immediate needs in developing tools useable by diagnosticians and scalable for a nationwide network of adopters. This consortium leverages collaborations between diagnosticians in plant clinics and geneticists/genomicists/population geneticists in three different institutions. This consortium will also interact with the established national network of plant clinics to inform, educate, and initiate adoption of whole genome-based methods. The four goals and their objectives are as follows:Goal I. Implement and integrate tools to apply WGS for disease diagnostics.Obj. 1. Develop standards and optimize preparatory workflow for use in plant clinics.Obj. 2. Integrate currently used WGS analysis tools into a workflow for use in plant clinics.Obj. 3. Develop visuals to effectively interpret and communicate WGS results.Goal II. Implement and integrate tools to apply Meta-WGS for disease diagnostics.Obj. 1. Develop standards and optimize preparatory workflow for use in plant clinics.Obj. 2. Integrate available Meta-WGS analysis tools into a workflow for use in plant clinics. Obj. 3. Develop and optimize novel machine learning algorithms.Goal III. Plant disease clinics validate the developed protocols and tools. Obj. 1. Validation using inoculated samples.Obj. 2. Validation using field collected samples.Goal IV. Engage and inform plant clinics nationally.