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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: 2038-22000-016-047-R
Project Type: Reimbursable Cooperative Agreement

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

Objective:
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.

Approach:
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.