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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #393138
Research Project: Management of Pathogens for Strawberry and Vegetable Production Systems

Location: Crop Improvement and Protection Research

Title: A specific TaqMan assay for detection of Fusarium oxysporum f. sp. lactucae race 1 based on unique genomic sequences

Author
item LI, NINGXIAO - University Of California
item GEISER, DAVID - Pennsylvania State University
item KOIKE, STEVE - Trical Inc
item SLINSKI, STEPHANIE - Arizona State University
item Martin, Frank

Submitted to: American Phytopathological Society Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 3/25/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Fusarium oxysporum f. sp. lactucae (FOL) is a soil- and seedborne pathogen and the causal agent of fusarium wilt of lettuce. The pathogen occurs in most countries in which lettuce is grown and causes serious economic losses. Based on the ability to cause disease on differential lettuce cultivars, four races (1, 2, 3, and 4) of the pathogen have been identified so far. Race 1 is the most widespread race and is the only race that has been detected in the US so far. Phylogenetic analysis revealed that FOL race 1 and race 4 are closely related with an almost identical core genome. Therefore, a diagnostic marker that is specific to FOL race 1 is needed. In this study, we deployed a bioinformatic pipeline to identify genomic sequences that only exist in FOL race 1 and screened over 600 F. oxysporum genomes to validate their uniqueness. Based on the in silico analyses, we designed primers for six unique loci and chose one for the development of a TaqMan assay. This final locus showed robust amplification in race 1 isolates and no cross reaction with race 4 and nonpathogenic isolates of lettuce. Specificity of the TaqMan assay was evaluated by screening a panel of 170 F. oxysporum isolates, including 17 FOL race 1 isolates, and 153 nontarget F. oxysporum isolates. The results thus far showed that the assay was specific in detecting FOL race 1 with a detection limit of 2 pg of purified DNA. We are currently surveying symptomatic lettuce plants grown in both CA and AZ to evaluate the assay in diagnosing fusarium wilt of lettuce. Progress on adopting the method for quantifying soil inoculum density of FOL race 1 using a drug marked race 1 isolate will be discussed.