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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Research Project #433652

Research Project: Enumeration of Fusarium oxysporum f sp. Fragariae in Soil

Location: Crop Improvement and Protection Research

Project Number: 2038-22000-016-19-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2017
End Date: Aug 31, 2021

Objective:
1. 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 polymerase chain reaction (PCR) assays. When appropriate genomic sequencing of important isolates will be conducted to confirm results and support diagnostic assay validation. 2. The objective of this work is to analyze genomic and transcriptomic data from Fusarium oxysporum f. sp. fragariae and Macrophomina phaseolina infecting strawberry roots. This work will provide insight into the signaling and metabolic pathways that are trigged in the plant during infection by these pathogens. Results can be used to inform methods that will block host colonization by interfering with the disrupted signaling networks. In addition to analyzing host response, we will identify genes that are up-regulated during infection by the fungus. Transcriptomic data was collected for multiple isolates of Fusarium oxysporum f. sp. fragariae and it will be possible to identify homologs that are consistently up-expressed between isolates. Furthermore, genes unique to each genotype of this pathogen that are expressed during infection will be identified. Genomic comparison will focus on identifying evolutionary mechanisms resulting in host specificity. The outcome of this work will be a foundational understanding of the interaction between this host and pathogen at the transcriptional level.

Approach:
1. Field soils will be plated on selective medium by our cooperator to determine population densities of the soilborne strawberry pathogen Fusarium oxysporum f. sp. fragariae. The USDA, Agricultural Research Service (ARS) lab will do DNA extractions from the same soils and use the TaqMan real time 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. 2. The personnel will analyze transcriptomic data by pre-processing reads for quality, identifying unique molecular indices, mapping reads to reference genomes, and identifying differentially expressed genes. This work will include writing custom python and bash scripts to achieve the stated goals. We will also identify homologs between pathogen genomes. This work will include identifying uniquely present genes in each fungal genome as well as synteny between genomes. Visualization of results in R will be conducted after previous analyses are conducted.