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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #384097

Research Project: Management of Pathogens for Strawberry and Vegetable Production Systems

Location: Crop Improvement and Protection Research

Title: Fusarium oxysporum protein-coding sequence markers for population and community analyses, identification, and improved diagnostics

item LI, NINGXIAO - University Of California
item GEISER, DAVID - Pennsylvania State University
item DEL MAR JIMENEZ-GASC, MARIA - Pennsylvania State University
item PARK, BONGSSO - Pennsylvania State University
item KANG, SEOGCHAN - Pennsylvania State University
item Martin, Frank

Submitted to: American Phytopathological Society Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 4/15/2021
Publication Date: 8/2/2021
Citation: Li, N., Geiser, D.M., Del Mar Jimenez-Gasc, M., Park, B., Kang, S., Martin, F.N. 2021. Fusarium oxysporum protein-coding sequence markers for population and community analyses, identification, and improved diagnostics. American Phytopathological Society Annual Meeting, August 2-6, 2021 (virtual).

Interpretive Summary:

Technical Abstract: The Fusarium oxysporum species complex (FOSC) comprises many economically important soilborne fungal pathogens that cause vascular wilt disease in a broad range of plant species. Putatively non-pathogenic isolates are prevalent in natural and agricultural ecosystems and can be readily isolated from soil and roots of asymptomatic plants as endophytes or saprophytes. Despite this diversity, non-orthologous copies of ribosomal RNA genes combined with low levels of sequence divergence among FOSC isolates has limited the power of sequence-based classification within FOSC. Therefore, the research objective in this study was to develop a multi-locus genotyping approach for an improved identification of FOSC isolates. Using 41 phylogenetic informative single copy nuclear protein coding genes, we retrieved their sequences from 167 clone-corrected F. oxysporum genomes representing 49 formae speciales and 54 isolates non-pathogenic on the host of recovery. In silico analysis of the 41 loci dataset showed that five loci are capable of differentiating 89% of all the isolates while all 41 loci are needed to reach 100%. Multi-locus diagnostic amplicon markers were developed that target polymorphic regions within the five loci. This expandable five-locus system was validated by performing PCR assays followed by Sanger sequencing of DNAs from diverse FOSC taxa. A curated database cataloging F. oxysporum sequence types based on the five loci will be made available to the public, providing a more reliable toolkit for diagnosing Fusarium wilt.