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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Research Project #442102

Research Project: Harnessing Genomic Technologies Toward Improving Vegetable Health in Field and Controlled Environments

Location: Vegetable Research

Project Number: 6080-22000-032-000-D
Project Type: In-House Appropriated

Start Date: May 1, 2022
End Date: Apr 30, 2027

Objective:
Objective 1: Characterize biological and molecular properties of emerging and important plant pathogens to develop sensitive detection systems and accurate disease diagnostic protocols. Sub-objective 1.1: Develop a multiplex real-time PCR useful for seed health testing of tobamoviruses on tomato and engineer an infectious clone of tomato brown rugose fruit virus and its recombinants for functional characterization. Sub-Objective 1.2: Develop a bioassay for Fusarium oxysporum f. sp. niveum (Fon) race 1 and race 2 differentiation using genetically fixed Citrullus amarus differentials. Sub-Objective 1.3. Develop a PCR-based race determination assay to differentiate race 1 from race 2 of the watermelon Fusarium wilt pathogen Fusarium oxysporum f. sp. niveum (Fon). Objective 2: Identify and develop new germplasm or cultivars with resistance to emerging or important diseases or pathogen-vectors using molecular-based tools or biotechnology. Sub-objective 2.1: Develop plant genetic materials with resistance to emerging tobamoviruses, ToBRFV in tomato and CGMMV in watermelon. Sub-objective 2.2: Applying biotechnology to develop novel genetic materials with resistance to viruses or whitefly. Sub-Objective 2.3. Develop bacterial blight resistant collard greens (Brassica oleracea var. viridis). Sub-Objective 2.4. Develop bacterial blight resistant brassica leafy greens (Brassica rapa). Objective 3: Design and implement integrated pest management to manage emerging and important diseases on vegetable crops under field and controlled environments. Sub-objective 3.1: Develop effective disinfectants and far UV light treatment for plant diseases and greenhouse whitefly on vegetable crops in controlled environment. Sub-Objective 3.2. Develop Bacterial Leaf Blight resistant mustard and/or turnip-green lines suitable for controlled environment agriculture (CEA).

Approach:
Relative to Objective 1, a multiplex real-time polymerase chain reqaction (PCR) useful for seed health testing and specific detection of three tomato infecting tobamoviruses: tomato brown rugose fruit virus (ToBRFV), tomato mottle mosaic virus (ToMMV) and tomato mosaic virus (ToMV) will be developed. We will engineer infectious clones of ToBRFV, ToMMV and ToMV and their respective recombinants for functional characterization, particularly on the resistance breaking by ToBRFV to the Tm-2^2 resistance gene. We will also conduct experiments to identify host tomato factors or receptors that resulted in the susceptibility by ToBRFV and characterize the gene-silencing suppressor and its interaction with host receptors. In separate experiments, we will develop a bioassay for Fusarium oxysporum f. sp. niveum (Fon) race 1 and race 2 differentiation using genetically fixed Citrullus amarus differentials. A PCR-based race determination assay will also be developed to differentiate race 1 from race 2 of the watermelon Fusarium wilt pathogen Fon. For Objective 2, we will identify and develop new germplasm or cultivars with resistance to emerging or important diseases or pathogen-vectors using molecular-based tools or biotechnology. First, on developing plant genetic materials with resistance to emerging tobamoviruses, ToBRFV in tomato and cucumber green mottle mosaic virus (CGMMV) in watermelon, segregating populations (F1, F2) of tomato to ToBRFV and watermelon to CGMMV have been developed using previously identified resistance germplasm. We will conduct phenotyping on the breeding populations for their resistance properties to the respective viruses and bulk segregant analysis (QTL-seq) on these tomato or watermelon genetic materials. Single nucleotide polymorphisms (SNPs) in association with the resistance traits will be identified and molecular markers developed. In a separate experiment, we will apply biotechnology to develop novel genetic materials with resistance to viruses or whitefly. Several candidate genes that are useful for genome editing to the target viruses and whitefly have been identified. Gene constructs will be used for transformation of appropriate plant materials. Transgenic plant materials with gene edited mutations will be used to evaluate for resistance to the target viruses. Once it is confirmed for their resistance, we will apply permit for large-scale field trials and deregulation of the gene-edited materials. In another experiment, we will develop bacterial blight resistant collard greens and brassica leafy greens through breeding, marker-assisted selection and field trial evaluations. Under Objective 3, we will design and implement integrated pest management to manage emerging and important diseases on vegetable crops under field and controlled environments. Developing effective disinfectants and far ultra violet (UV) light treatment that are useful to manage plant diseases and greenhouse whitefly on vegetable crops in controlled environment. In a seperate experiment, we will develop bacterial leaf blight resistant mustard and/or turnip-green lines suitable for controlled environment agriculture.