Location: Crop Improvement and Protection Research
Project Number: 2038-22000-016-028-A
Project Type: Cooperative Agreement
Start Date: Nov 1, 2018
End Date: Jun 30, 2021
The objective is to validate molecular quantification assays of soil by comparison with soil plating assays to determine the relationship between colony counts and results from real time PCR assays. When appropriate genomic sequencing of important isolates will be done to confirm results and support diagnostic assay validation. The initial focus will be with quantification assays for F. oxysporum f. sp. lactucae and then expand to additional taxa as the need arises.
Field soils will be plated on selective medium by our cooperator to determine population densities of the soilborne strawberry pathogen Fusarium oxysporum f. sp. lactucae. The ARS lab will do DNA extractions from the same soils and use the TaqMan real time polymerase chain reaction (PCR) assay that is specific for the pathogen to evaluate the amount of DNA that is present. Regression analysis will be used to look at the correlation between the two. Important isolates will be cultured and DNA extracted for sending to a genomic sequencing facility for Illumina sequencing.