Source: PURDUE UNIVERSITY submitted to NRP
TOMI3: BRINGING OUR INSIGHTS TO THE FARM TO CO-CREATE MORE EFFECTIVE METHODS OF DISEASE CONTROL IN ORGANIC TOMATO CROPS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1032767
Grant No.
2024-51300-43372
Cumulative Award Amt.
$3,500,000.00
Proposal No.
2024-03325
Multistate No.
(N/A)
Project Start Date
Sep 1, 2024
Project End Date
Aug 31, 2028
Grant Year
2024
Program Code
[113.A]- Organic Agriculture Research & Extension Initiative
Recipient Organization
PURDUE UNIVERSITY
(N/A)
WEST LAFAYETTE,IN 47907
Performing Department
(N/A)
Non Technical Summary
Demand for organic tomatoes continues to grow, yet farmers struggle to keep up due to foliar diseases that can move quickly through farm fields and decimate entire crops. The tomato organic management and improvement project (TOMI) has spent the past 10 years working with organic farmers to overcome this challenge through breeding and investigating how to promote beneficial plant-soil-microbial relationships. Now we propose to build on the knowledge and resources we have developed and create practical tools organic farmers can use to prevent foliar disease outbreaks and deliver tomatoes with end-use quality traits demanded by consumers in local marketplaces. Specifically, we will: 1) identify critical factors needed to promote the efficacy of biocontrol agents and adapt disease forecasting models to account for these practices; 2) use new molecular markers developed in our breeding program for promoting plant associations with microbes that have biocontrol capabilities and disease resistance traits, establish regional participatory breeding programs to select new germplasm from these pools, and develop a new decision-support tool that will help farmers select varieties best-adapted to their farms; 3) create new support networks that will help organic farmers, Extension educators, researchers, students and local food system actors (ie. chefs) connect, overcome production challenges through participatory research, and foster new marketing relationships; and 4) deliver novel and inclusive educational programs that support these efforts. These programs will be disseminated broadly through our website hosted by eOrganic, in webinars, on-farm workshops, print-based materials, variety showcases and TomatoFests. Results will be applicable to other crops.
Animal Health Component
80%
Research Effort Categories
Basic
10%
Applied
80%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2121460116060%
2121460108120%
2121460107020%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants;

Subject Of Investigation
1460 - Tomato;

Field Of Science
1160 - Pathology; 1070 - Ecology; 1081 - Breeding;
Goals / Objectives
Organic tomato growers need practical approaches to manage foliar diseases while meetings consumer demand for fruit with desirable end-use quality characteristics and protecting soil and water quality. Our project will address these challenges by 1) identifying and overcoming critical factors influencing the survival and efficacy of biocontrol agents, 2) establishing decentralized tomato breeding efforts based on regional needs, 3) creating new decision-support tools (DSTs) to help farmers better manage foliar diseases though biocontrol and varietal selection; and, 4) establishing new support networks and delivering novel and inclusive training programs that will help Extension educators and organic farmers better manage foliar diseases in vegetable cropping systems and connect with local chefs to increase marketability of their produce
Project Methods
Obj. #1:Identify critical factors influencing the survival and efficacy of biocontrol agents. These studies will focus primarily on SLS and PM due to their growing challenge nationwide and lack of research to develop solutions relative to other foliar diseases. We expect knowledge generated with respect to characterizing the diversity of the pathogens causing these diseases will not only help us in optimizing disease forecasting models, but will also aid in our efforts to breed for resistance to these diseases. We also expect results will be applicable to other critical foliar diseases we regularly encounter like LB, EB, GM, LM, and BS. We will start by screening popular tomato varieties as well as those under consideration in our breeding program in the greenhouse for their capacity to signal, support and respond favorably to soil and foliar applied biocontrol agents. Next, we will conduct on-farm trials in HT and OF systems in three distinct ecoregions (SE, MW, WC) using responsive genotypes and a commercial product containing a broadly adapted B. subtilis strain in years 1&2. Soil health, leaf microbiomes, climatic conditions, and pathogen timing & diversity will be quantified and compared with disease outbreaks. Local B. subtilis strains with biocontrol activity will be isolated from each ecoregion, and tested against the commercial strain in years 3&4. The data will be used to develop new disease forecasting models (see Obj. 3). These studies will be co-led by Hoagland, Luis & Davis.Obj. #2: Establish decentralized tomato breeding efforts based on regional needs. The goal of these studies is to provide organic growers with new OP varieties that produce abundant yields of markable fruits under high disease pressure. The major diseases of concern vary across the U.S. Standard management practices for organic market farmers also vary; for example, growing under HTs is more common in the MW, while OF production is more common in the WC. For that reason, the breeding program will tailor breeding and trialing efforts by region, while operating under a shared set of protocols and centralized winter advancement and marker testing. We will make crosses using genotypes identified in Obj. 1 with germplasm from our on-going program as well as others with known resistance genes and desirable end-use quality traits. Crosses for each ecoregion will be selected based on the most problematic foliar diseases in that region. Segregating populations will be evaluated in on-station trials in 5 states, and we will predict performance of new crosses based on traditional and genomic prediction methods. The relative stability and specificity of varieties, populations and traits including ISR, will be analyzed via changes in the genomes of divergently selected populations. Advanced lines will be evaluated in on-farm trials in 7 states in years 3&4. Data from the field trials will be used to support DSTs (see Obj. 3). These studies will be co-led by Dawson, Myers and Zystro.Obj. #3: Create new DSTs to help farmers better manage foliar diseases. Our goal with this objective is to develop new DSTs that will allow organic growers to implement new insights and germplasm generated in Objectives 1&2, effectively reduce foliar disease outbreaks, and increase the yield and quality of their tomato fruit. We will combine data collected over the past 10 years of the TOMI project with new, more specialized data collected during TOMI3 to create two DSTs. One will help growers better manage diseases by using disease forecasting models that have been adapted by our team to account for biocontrol agents and HT production systems. The second will help growers select best-adapted varieties for their farm using on-line data management and forecasting tools. These activities will be led by Raturi.Obj. #4: Establish new support networks and deliver novel and inclusive training programs. We know that there are currently many barriers limiting the effective transfer of new knowledge generated from academic research to stakeholders, and organic farmers often gain the greatest benefits by interacting and learning from each other. Consequently, we will establish regional networks fostering communications between TOMI personnel, organic farmers, Extension educators, chefs and consumers using CBNs developed by Selman as a model. Subgroups will focus on on-farm research activities, and larger events such as our variety showcases and tomato festivals will engage larger groups with regional foodsheds. We will critically review the impacts of previous TOMI outreach programs as well as other relevant projects to design a suite of training programs and products that can best engage and support a diverse audience of organic food system stakeholders. These activities will be led by Gu, Formiga and Selman.ors influencing the survival and efficacy of biocontrol agents.

Progress 09/01/24 to 08/31/25

Outputs
Target Audience:The target audience for this project included organic and conventional vegetable growers, marketers, and consumers; personnel at vegetable seed companies and organic biopesticide companies; scientists and students in horticulture, plant breeding, plant pathology, and soil science; as well as Extension educators and others involved in outreach to vegetable growers such as personnel at the NRCS and SWCD. In all cases, efforts were made to reach underrepresented audiences in agriculture, such as racial and ethnic minorities, by including faculty and staff from an 1890's land grant institutions and students/staff from many countries and backgrounds worldwide in our research and outreach activities. Changes/Problems:A windstorm destroyed a high tunnel in Wisconsin that was running one of our on-farm biocontrol trials, but the high tunnel is being rebuilt for the future years of our study. Because of a short funding lapse, we were unable to establish research trials in Virginia during summer 2025, but we expect to be able to make up for this during summer 2026. We had some challenges with getting the weather stations up and running in our biocontrol trials, but we were still able to gain valuable data from the first year of these trials, and are still on track with getting the data needed to build our models and DSTs to optimize biocontrol practices. What opportunities for training and professional development has the project provided?Our project has provided multiple opportunities for post-doctoral research associates, graduate and undergraduate students, and visiting undergraduate student scholars to gain valuable experience conducting research and engagement programs. Specifically, they have gained experience conducting studies focused on pathogen biocontrol, organic plant breeding, using molecular tools to quantify mechanisms mediating beneficial plant-microbial relationships and different types of disease resistance, identifying genetic markers to better integrate these traits into breeding programs, and conducting on-farm participatory research trials. They have also gained experience presenting and publishing their results at both scientific and grower-oriented meetings. As a result of this training, many have now gone on to new positions. For example, former post-doc Marian Luis is now a tenure-track faculty member at the University of Hawaii, former graduate student Ambar Carvallo-Lopez is a now a post-doc at the University of British Columbia, and former visiting scholar Maria Fernanda Morena has started a graduate program at Purdue University. We have also engaged farmers and culinary professionals as well, helping them to better understand the breeding process and how to improve the efficacy of biocontrol practices. These efforts have also helped u better understand their needs for regionally adapted tomato varieties and more practical approaches to organic disease management. Finally, we have integrated components of our program in undergraduate and graduate classes, helping a diverse set of students learn more about organic agriculture, pathogen biocontrol, and organic plant breeding. How have the results been disseminated to communities of interest?In the past year, results from our project have been published in four scientific papers. One of these focused on increasing the efficacy of biocontrol practices by integrating essential oils into nanoemulsions. Another focused on identifying the molecular mechanisms mediating responsiveness to induced systemic resistance against foliar pathogens. This paper was selected as the Editor's Choice in the journal Phytopathology, highlighting the novelty of this work and the strong potential of this study to improve plant breeding efforts and develop more sustainable methods of disease control. The third evaluated advanced breeding organic breeding lines, and the final paper evaluated the effectiveness of incorporating new septoria resistance alleles in organic tomato varieties. We have continued to advance breeding lines developed in our program and evaluate their performance, as well as the efficacy of new biocontrol strategies, in on-farm trials across the country. Results have also been shared more broadly in field days, events held at grower-oriented meetings, and in updates to our TOMI website. Finally, we participated in a variety showcase and tomatofest so that the public could learn about new varieties we are developing, the process of plant breeding, and how to optimize biocontrol practices. What do you plan to do during the next reporting period to accomplish the goals?We will continue to refine our disease forecasting model using data collected during the 2025 growing season, and we will repeat all the biocontrol trials on the same 9 organic farmers using the improved model. Efforts to isolate local biocontrol isolates from each of the 9 locations is underway and will continue for the 3rd and 4th growing season of the project. We will continue to advance our breeding populations in field trials, and use both existing molecular markers for disease resistance and new markers developed in our program to screen for ISR responsiveness and Septoria resistance to advance these efforts. We will continue refining our data sets and begin developing DSTs for our breeding and biocontrol projects. We will continue our efforts to interact with growers, chefs and consumer to build support networks, evaluate results of a survey designed to optimize our engagement efforts, and apply the results in field days, extension publications and other outreach tools. Finally, we will continue publishing new results from our project in peer-reviewed scientific journals.

Impacts
What was accomplished under these goals? Goal #1: Identify critical factors influencing the survival and efficacy of biocontrol agents The team advanced two studies aimed at improving the efficacy of biocontrol practices to control foliar diseases in tomato. One involved a large multistate project aimed at developing new forecasting models for biocontrol practices in open fields and high tunnel production systems. In this study, trials were established on 9 working organic farms in North Carolina (2 farms), Indiana (2 farms), Wisconsin (2 farms), Oregon (2 farms), and California (1 farm). The trials were set up in a mix of open-field and high tunnel production systems. There were three treatments. There were three treatments: 1) weekly spray of inoculant starting at transplanting, weekly spray of inoculant when existing disease forecasting models predicted disease pressure, a sterile water control. Weather stations were established at each trial, which collected data on air temperature and humidity, rainfall, and leaf moisture at intervals of every 60 seconds. Spore traps were used to collect pathogen spores, and disease ratings were conducted weekly. Leaves were collected at four time points and assessments of the phyllosphere microbiome are underway. Plant roots, stems and leaves were also collected at harvest, and isolation of local native Bacillus species at each location is underway. All of the data collected over the growing season is being used to develop improved disease forecasting models. This trial will be repeated on the same farms in 2-26. In a second study, we investigated how feedstocks can influence the biocontrol efficacy of bokashi amendments in a greenhouse and laboratory trial. Goal #2: Establish decentralized breeding efforts based on regional needs During winter 2024-25, advanced lines from our breeding program were advanced and new crosses were made to develop breeding populations with improved resistance to Septoria leaf spot, early blight, late blight, and powdery mildew. The crosses were made using parents that are relevant to each region in our breeding program (west coast, Midwest, and southeast), vs. trying to develop populations expected to work in all of these ecoregions. We also continued to advance the five mapping populations developed to identify genes or QTLs associated with microbiome-mediated resistance to foliar pathogens via stimulation of induced systemic disease resistance (ISR). One of these mapping populations has been phenotyped in the greenhouse for ISR and associated traits, and genotyped. Results of this assay indicate that the ISR trait can be mapped to one major QTL. During summer 2025, we evaluated advanced breeding lines, new breeding populations, and four check varieties in North Carolina, Wisconsin, Oregon, and California. At each site, there were at least 8 unreplicated checks of each breeding line, and four replicates of the four check varieties that vary in resistance and susceptibility to our key disease of interest nationally and regionally. The plots were evaluated for germination, vigor, disease resistance, and yield. Populations with promise for each region will be advanced during winter 2025-26. The advanced populations will also be genotyped to generate seed that contains major resistance genes. They will also be evaluated for the presence of molecular markers indicating responsiveness to ISR. Goal #3: Create new decision-support tools (DSTs) to help farmers optimize biocontrol practices and select new varieties In 2025, our team focused on unifying historical TOMI data and laying the groundwork for improved TOMI data management. A data audit was conducted using historical TOMI data (2015-2024). The goal of this process was to evaluate data collection procedures and identify potential areas for improvement to ensure consistent and clean data outputs. During meetings with the project team, we created maps to trace data management practices and uncover data touchpoints and pain areas for improvement. This involved going through each data artifact produced by the team over the decade-long period. Each artifact was assessed for minor errors, data coverage and completeness, provenance, and any transformations performed (i.e. statistical transformation). Minor errors were recorded as GitHub issues and were corrected where reasonably possible. After finalizing these efforts, we will continue to organize data from on-going experiments and move forward in developing DSTs using the unified and supplementary data. To support this effort, data mapping is currently underway. We began the process by mapping metadata and variables to relevant agricultural ontologies. Agricultural ontologies, as symbolic representations of knowledge within domain specialties, allow for the description of data objects with semantic precision. Next, we will automate the data mapping process, where possible. Using BERT-style word embeddings and cosine similarity to create a high-throughput semantic annotation engine, we aim to map the terms to ontologies, which can then be leveraged for data integration across participating institutions, and support automated reasoning in future DST development work. Goal #4: Establish new support networks and deliver novel and inclusive educational programs. In the past year, we have continued to develop new support networks that have provided valuable insights needed to advance our research, disseminate the results, and support the organic vegetable the continued growth and long-term success of the organic vegetable industry. These efforts included a meeting with our advisory board, which includes organic farmers from across the country, as well as scientists and extension educators who are not involved in our project. During this meeting, we gained valuable insights on the evolving needs of organic vegetable growers, especially with respect to the most problematic diseases, and gained critical feedback on how to best meet these concerns in our on-going trials. As described above, we also established biocontrol studies on 9 working organic farms across the country, and we brought these growers together to discuss results and how to improve our studies. We also brought organic farmers, chefs and consumers together though numerous events including a TomatoFest held in Portland, OR, a Farm to Flavor event in Madison, WI, and field days in all of our project locations across the country. In addition, to help farmers better connect with chefs and consumers, we have begun working on a TomatoZine and other informational resources. Finally, a new post-doctoral research associate has started building surveys that will be used to identify engagement activities that have been most impactful for growers over the past 10 years of our project, and generate new ideas to further extend our impacts.

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Luis, M., Johnson, L.D., Vega-Vasquez, P., Ristroph, K., Hoagland, L., 2025. Use of cinnamon essential oil nanoemulsions to manage gray mold in tomato. Plant Disease DOI: 10.1094/PDIS-02-25-0261-RE
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Luis, M., Jaiswal, A., Mengiste, T., Myers, J., Hoagland, L., 2025. Deciphering the mechanisms regulating variability in induced systemic resistance among tomato genotypes. Phytopathology DOI: 10.1094/PHYTO-07-24-0240-R
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Carvallo Lopez, A., M. McCaslin, and J. Dawson. 2025. The sls-1 and sls-2 Genes Confer Significant Resistance to Septoria Leaf Spot (Septoria lycopersici L.) in Organic Field-Grown Tomatoes (Solanum lycopersicum). Plant Breeding 144, no. 5: 705714.
  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Carvallo-Lopez, A., Nix, M., Hickey, T., and Dawson, J. C. 2024. Improved Tomato Breeding Lines Adapted to Organic Farming Systems Have Enhanced Flavor, Yield, and Disease Resistance. HortScience 59(9), 1299-1307.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Hoagland, L., Davis, J., Davis, J., Dawson, J., Denny, A., Dubey, S., Feiler, H., Formiga, A., Garcia, E., Gu, S., Hickey, T., Landgraver, E., Learn, K., Luis, M., Myers, J., Nix, M., Qu, L., Raturi, A., Salinas, C., Smith, B., Selman, L., Zystro. J., 2025. The tomato organic management and improvement (TOMI) project: helping tomato growers better manage foliar diseases. American Society of Horticultural Science Annual Meeting, New Orleans, LA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Farm to Flavor, Madison, WI (October 5th 2025)  300+ participants
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Hoagland, L., Blevins, M., Bloomquist, M., Carvallo, A., Coffey, P., Colley, M., Davis, J., Davis, J., Dawson, J., Dubey, S., Egel, D., Feiler, H., Formiga, A., Gu, S., Hickey, T., Jaiswal, A., Landgraver, E., Learn, K., Luis, M., McCluskey, C., Mengiste, T., Myers, J., Nix, M., Peery, J., Qu, L., Raturi, A., Salinas, C., Selman, L., Zystro, J., 2024. 10 years of TOMI  what weve learned that can help reduce foliar disease in tomato. Crop, Agronomy, Soil, and Environmental Science Societies (CANVAS) International Meeting, San Antonio, TX.
  • Type: Theses/Dissertations Status: Published Year Published: 2025 Citation: Ambar Carvallo Lopez. 2025. From field to genetics: exploring disease resistance and flavor in organic tomato breeding. Plant Breeding and Plant Genetics. University of Wisconsin-Madison Date of final examination: March 21, 2025.
  • Type: Other Status: Accepted Year Published: 2026 Citation: Nicolas Chavez Montana (Universidad ICESI, Colombia) Biochemical quality of anaerobic composts. Undergraduate research thesis (August 2025)
  • Type: Other Status: Accepted Year Published: 2026 Citation: Maria Fernanda Moreno de la Espriella (Universidad EAFIT, Colombia) Pathogen suppressive activity of anaerobic composts. Undergraduate research thesis (August 2025)
  • Type: Other Status: Published Year Published: 2025 Citation: Stephanie Castano (Caldas University, Colombia) How do soil inoculums influence the bokashi process? Undergraduate student thesis (August 2024)
  • Type: Websites Status: Published Year Published: 2025 Citation: Tomato Organic Management and Improvement Project (TOMI) website http://eorganic.info/tomi
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Carvallo, A. 2024. S�lection v�g�tale participative, exp�rience d'am�lioration de la tomate dans le Haut Midwest des �tats-Unis. S�minaires Saint Maurice, GAFL, INRAE
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: OSU  TomatoFest, Portland, OR (Sept. 13, 2025)  700+ participants
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: UW - Hosted a vegetable variety roundtable at the Organic Vegetable Production Conference in Madison, WI on February 1st, 2025. Attendance the conference was about 200.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: UW - Hosted a tomato tasting with Pasture and Plenty, a restaurant and educational center featuring local ingredients on August 14th  Attendance the conference was about 50.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Hoagland, L., Promoting healthy soils and plant microbiomes for crop and human health. Indiana Grown Symposium, Danville, IN (2025). Attendance the event was about 50.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Hoagland, L., Supporting your plants through soil health. Indiana Arborists Association Annual Conference, Indianapolis, IN (2025) Attendance the event was about 150.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Hoagland, L., Managing soil and plant microbiomes for better crop and human health. Indiana Certified Crop Advisors Annual Meeting, Indianapolis, IN (2024) Attendance the event was about 200.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Hoagland, L., Managing soil and plant microbiomes for better crop and human health. Indiana Certified Crop Advisors Annual Meeting, Indianapolis, IN (2024). Attendance the event was about 200.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Hoagland, L., Promoting beneficial microbes with biocontrol capabilities in tomato cropping systems. Great Lakes Vegetable Expo. Grand Rapids, MI (2024). Attendance the event was about 150.