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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Research Project #439503

Research Project: Systematic Identification of Oomycete Plant Pathogens Important to California Specialty Crops

Location: Crop Improvement and Protection Research

Project Number: 2038-22000-019-016-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Nov 1, 2020
End Date: Jun 30, 2023

To validate the use of an oomycete specific amplicon for characterization of oomycete plant pathogens in California specialty crop production systems and predict risk for the growers.

The Martin lab identified a unique gene order in oomycetes that is not present in plants or Eumycotan fungi that enables highly specific amplification of a sequencing template that is useful for species identification. A sequence database representing a range of oomycete taxa was provided to the Grunwald lab and they designed nested primers that were capable of amplifying a smaller template that was suitable for Illumina MiSeq sequencing. They have validated the use of the locus for analysis of oomycete communities and developed a website to share the sequence data and techniques with others. In this project the work will be expanded to include additional oomycete taxa in the database and do a broader scale validation of the locus for characterizing oomycete communities. Sequencing technology developed by Oxford Nanopore will also be evaluated for the ability to generate data from larger amplicons.