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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Research Project #441431

Research Project: A Metagenomics Marker System for Identification of All Fusarium oxysporum Taxa in Field Soils

Location: Crop Improvement and Protection Research

Project Number: 2038-22000-019-027-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Nov 1, 2021
End Date: Jun 30, 2024

To validate the use of a Fusarium oxysporum specific amplicon for characterization of pathogens in California specialty crop production systems and predict risk for the growers.

Potential targets in F. oxysporum that will be useful as a barcode for identification of isolates have been bioinformatically identified and will be evaluated as metagenomic markers for investigating population structure of the pathogen in field soil. Conserved primers will amplify the target sequence and Illumina MiSeq 300 bp PE sequencing will be done to generate the data for analysis. A sequence database representing a range of F. oxysporum taxa has been developed to support development and validation of metagenomic markers. In this project the work will be expanded to include additional taxa in the database and do a broader scale validation of the locus for characterizing pathogen communities.