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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Research Project #441968

Research Project: Disease Management and Improved Detection Systems for Control of Pathogens of Vegetables and Strawberries

Location: Crop Improvement and Protection Research

Project Number: 2038-22000-019-000-D
Project Type: In-House Appropriated

Start Date: Mar 30, 2022
End Date: Mar 29, 2027

This project will create new ways to manage plant diseases of strawberries and vegetables. New approaches to disease management and resistance breeding are needed to protect crops from diseases, including increased knowledge of pathogen detection, disease cycles, and pathogen and plant genomes, as well as the potential for soil microbes that can be utilized for disease suppression. This project will lead to disease control with reduced fungicides and fumigants and will use both agricultural automation and traditional approaches. We will focus on the following major objectives and subobjectives during the next five years. Objective 1: Integrate understanding of pathogen genomes into new tools for pathogen diagnostics. Sub-objective 1.A: Develop molecular markers for diagnostic assay development for formae speciales of Fusarium oxysporum by analysis of genomic sequence data. Sub-objective 1.B: Develop diagnostic markers and tools for rapid identification of oomycetes using comparative analysis of mitochondrial genomes. Sub-objective 1.C: Determine if strawberry-pathogenic isolates of Macrophomina phaseolina are polyphyletic within the context of the broad diversity of this species. Objective 2: Gain a better understanding of strawberry and vegetable pathogen life cycles and how microbial communities can be used for new management strategies. Sub-objective 2.A: Identify genes required for microsclerotia formation in Verticillium dahliae. Sub-objective 2.B: Functionally characterize the role of a predicted pathogenicity chromosome in F. oxysporum f. sp. fragariae on the strawberry host-specific pathogenicity phenotype. Sub-objective 2.C: Investigate the role of oospores in the life cycle of Peronospora effusa. Sub-objective 2.D: Determine if genetically diverse Macrophomina phaseolina isolates from strawberry exhibit differential virulence on tolerant strawberry varieties. Sub-objective 2.E: Identify the role of the strawberry root microbiome in Verticillium wilt of strawberry. Objective 3: Integrate management strategies for improved control of strawberry and vegetable pathogens. Sub-objective 3.A: Determine if an avirulence gene identified in race 1 strains of F.o. fragariae is the avirulence gene specific for FW1-mediated resistance (called AvrFW1). Sub-objective 3.B: Characterize gene expression in spinach-downy mildew interactions in response to two races of Peronospora effusa. Sub-objective 3.C.1: Identify the effect of biofumigant green manure soil amendment type and application rate on soil microbiome function and soilborne pathogen inoculum survival. Sub-objective 3.C.2: Identify the effect of pre-plant application of antimicrobial producing Streptomyces bacteria on Fusarium wilt diseases of vegetables. Sub-objective 3.D.1: Evaluate nitrogen dioxide (NO2) as a seed treatment for two pathogens carried on spinach seeds. Sub-objective 3.D.2: Investigate applications of automation technology for use in strawberry production systems toward improving production practices and control of pests and diseases. Sub-objective 3.D.3: Identify alternative soil fumigants to control soilborne pathogens and nematodes in carrot and other crops.

Sub-objective 1.A: Unique sequences suitable as targets for developing taxon specific markers will be identified in genomic sequence data. Sub-objective 1.B: Mitochondrial genomes will be used for selection of loci for development of diagnostic markers. Sub-objective 1.C: Phylogenies will reveal if strawberry-pathogenic strains of M. phaseolina are polyphyletic within the broader diversity of this species. Sub-objective 2.A: Comparative analyses of genomes of Verticillium species will reveal sequences required for microsclerotia formation. Sub-objective 2.B: The loss of the chromosome will be induced and/or transferred to a non-pathogenic strain, and disease examined. Sub-objective 2.C: Oospores of P. effusa will be examined for their ability to infect roots or leaves in growth chambers and humidity tents. Sub-objective 2.D: A broad diversity of isolates will be tested for pathogenicity on 4 tolerant and 2 susceptible varieties. Sub-objective 2.E: We will assess if microbial taxa in the root microbiome that correlates with pathogen biomass in the roots or disease severity significantly affects Verticillium wilt of strawberry. Sub-objective 3.A: Quantitative trait loci (QTL) and genome-wide association studies(GWAS) to map genomic regions associated with resistance. Sub-objective 3.B: RNASeq analysis of gene expression will be performed. Sub-objective 3.C.1: Five weed or crop species will be tested against Verticillium dahliae as biofumigants. Sub-objective 3.C.2: Biological control will be tested by applying Streptomyces spores to field soil as pre-plant treatments for control of Fusarium wilt. Sub-objective 3.D.1: Varying percent of NO2 will be applied in chambers with seeds harboring two pathogens. Sub-objective 3.D.2: Approaches using automation technology will be assessed for use in strawberry production systems to improve disease control. Sub-objective 3.D.3: Assess anaerobic soil disinfestation and incorporation of green manures to control soilborne pathogens and nematodes in California carrot and other cropping systems.