Source: NORTH CAROLINA STATE UNIV submitted to
INTEGRATED DISEASE MANAGEMENT STRATEGIES FOR KEY DISEASE(S) IN ORGANIC TOMATO PRODUCTION SYSTEM
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1027175
Grant No.
2021-51106-35493
Cumulative Award Amt.
$600,000.00
Proposal No.
2021-04809
Multistate No.
(N/A)
Project Start Date
Sep 1, 2021
Project End Date
Aug 31, 2025
Grant Year
2021
Program Code
[112.E]- Organic Transitions
Project Director
Panthee, D.
Recipient Organization
NORTH CAROLINA STATE UNIV
(N/A)
RALEIGH,NC 27695
Performing Department
Horticultural Science
Non Technical Summary
The demand for organic tomatoes in the Southeast is high, but production is limited due to the lack of regionally adapted high-yielding varieties. Organic growers have requested research on disease management practices including improved varieties with superior fruit quality so that they can take advantage of the ever-increasing market demand. Our long-term goal is to develop sustainable approaches in disease management for organic production by integrating resistance breeding and grafting methods well-adapted to organic growing conditions in the Southeast. The proposed project will benefit farmers in the U.S. in general, and in the Southeast in particular, who need high-value crops that can be grown on small acreages. This proposal was developed through direct interaction with the organic growers. The objectives of this proposal are:(1) Determine genotypic differences for foliar and soilborne fungal disease resistance, and fruit quality in heirloom tomato varieties grown under organic conditions. (2) Identification of suitable tomato varieties and rootstocks for organic production through participatory variety selection for high yield, disease resistance, and fruit quality. (3a) Genetic analysis of host resistance to early blight (EB), Septoria leaf spot (SLS), and Southern stem blight (SSB). (3b) Assessment of resistance to pathotypes of Altenaria linariae and Septoria lycopersici using molecular markers complemented by virulence testing. (4) Disseminate knowledge gained on tomato varieties and production systems grown in organic conditions to farmers, extension agents, industry, and the general public. The proposed research is relevant to the ORG program and will facilitate the development of organic agriculture production (especially transitioning systems), biodiversity, management of priority diseases, and integrating novel technology into organic systems.
Animal Health Component
75%
Research Effort Categories
Basic
25%
Applied
75%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20114601081100%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1460 - Tomato;

Field Of Science
1081 - Breeding;
Goals / Objectives
The overarching goal of this research is to develop and recommend, through extension programming, high-yielding, disease-resistant, flavorful, nutritious tomato varieties for sustainable organic production systems. This project the following objectives: Objective 1: Determine genotypic differences for foliar and soilborne fungal disease resistance, and fruit quality in heirloom tomato varieties grown under organic conditions. Objective 2: Identification of suitable tomato varieties and rootstocks for organic production through participatory variety selection for high yield, disease resistance, and fruit quality. Objective 3a: Genetic analysis of the host resistance to early blight (EB), Septoria leaf spot (SLS), and Southern stem blight (SSB). Late blight (data sets are mature) along with these three diseases are important for organic production. Objective 3b: Assessment of resistance to pathotypes of Altenaria linariae (EB) and other pathogens including Septoria lycopersici (SLS) using molecular markers complemented by virulence testing. Objective 4: Disseminate knowledge gained on tomato varieties and production systems grown in organic conditions to farmers, extension agents, industry, and the public.
Project Methods
To achieve the first objective, in Year 1 and Year 2, we will take our most advanced lines and screen about 30 to 35 tomato genotypes including breeding lines and varieties plus resistant and susceptible controls. In years 1 and 2 each, four trials will be established to evaluate disease resistance for early blight (caused by Alternaria linariae), late blight (caused by Phytophthora infestans), and Septoria leaf spot (caused by Septoria lycopersici). Southern stem blight work will be confined to lab and greenhouse work initially since datasets are not as mature as those for the other pathosystems. Breeding lines, known susceptible controls, and known resistant controls will be established in a randomized complete block design with three replications as mentioned above. Plants will be grown under organic conditions.For fruit quality, separate from the disease evaluation, the genotypes will be evaluated and characterized at vegetative and reproductive growth stages for various plant and fruit traits. A subjective rating of each genotype for flavor will be made by untrained personnel when fruits are at the fully ripe stage, as described by (Sinesio et al., 2010). Fruits will be analyzed for lycopene, TSS, fruit color, and firmness. Total yield per plot will be recorded on physiologically mature or ripe fruits by harvesting at least three times.To achieve the second objective, we will engage with at least three cooperating certified organic farmers in NC. The growers will also be engaged in evaluations throughout the growing season. In Years 3 and 4, the 8-10 most promising varieties identified in Objective 1 will be grown on the cooperating farms. The team will work with each grower to identify the best combination of scions and rootstocks based on known disease pressure in each region of the state, the history of the farm, and grower priorities. Comparisons will be made with the results of the research station studies. On each farm, there will be at least 5 plants of each combination and two to three replications per site. Fruit yield and disease scoring data will be measured as in the first objective.To achieve the third objective, we have already developed a mapping population segregating for EB, LB, and SLS. Briefly, our experimental approach is to grow the F3 population consisting of 250 individuals and resistant and susceptible controls at Mountain Research Station, Waynesville, NC in the summer of 2022. DNA will be extracted from healthy, young seedlings and submitted to the Genome Science Lab at NC State University for GBS. Plants will be inoculated with SLS inoculum when they are six to eight weeks old. Plants will be scored for SLS two weeks after inoculation and will continue scoring every week for four to six weeks. The area under the disease progress curve (AUDPC) will be developed based on this disease score and will be used as a single phenotypic variable for QTL mapping. Single nucleotide polymorphism (SNP) molecular markers will be converted into more useful Kompetitive Allele-Specific PCR (KASP) markers. These are bi-allelic markers and easy to use like SCAR or CAPS. We will design and obtain primers from LGC Genomics (http://info.biosearchtech.com/) to convert the SNPs into KASP markers. The use of reliable molecular markers will facilitate combining the genes conferring resistance to multiple diseases including EB, LB, and SLS. Marker-assisted selection (MAS) also helps to eliminate unwanted genetic backgrounds in an early generation and identifies the most desirable gene combinations or individuals in segregating populations. We will also characterize the isolates of Alternaria linariae and Septoria lycopersicii pathogens by the whole-genome sequencing method. We are interested to identify the potential effectors that can be used to enhance the resistance. Unique 'haplotypes' of Alternaria linariae and Septoria lycopersicii with distinct effector genes revealed in this objective will be selected and their virulence (the ability of an isolate to induce disease by overcoming resistance) will be assessed on selected tomato genotypes. Ten to 12 tomato genotypes identified from the Activity related to the first objective and (NC EBR-1 to NC EBR-8) originating from our tomato breeding programs will be selected and used in this experiment. Cultivar 'Bonny Best' will be included as a susceptible check. Virulence assays will be conducted under controlled conditions in the greenhouse. The primary goals of the fourth objective of this project are to keep the public informed of the progress and impact of the study, keep public and private breeders informed of the relevant information and materials that arise from the project, engage farmers, and train extension agents. For that, we will have workshops and field days, development of electronic resources, giving presentations at conferences, and training undergraduate and graduate students.

Progress 09/01/23 to 08/31/24

Outputs
Target Audience:Our target audiences are tomato stakeholders, particularly organic tomato growers in NC, organic researchers in academic institutions, and the seed industry. We reached out to these stakeholders by making presentations at the Winter Vegetable Conference held in Asheville in February 2024 and Tomato Field Day held in August 2024. Presentations were also made at the American Phytopathological Society in July 2024, which were received very well. These presentations have helped us expand our connections with the stakeholders, which will benefit the organic industry in the US. Changes/Problems:We anticipate that the last year will remain the same. This project was implemented successfully. Next year is the last year of the project. We will focus on implementing the planned activities in the fourth year. We hope that it will go as smoothly as in other years. What opportunities for training and professional development has the project provided?Two graduate students and one post-doctoral research associate are being mentored in this project. The graduate students are graduating in the Spring or summer of 2025, whereas the post-doc is wrapping up his research by the end of this project. This will be a massive resource for the country's organic tomato program. We leveraged all available resources to train these people in our program. We are optimistic that they will play a pivotal role in the country's organic research program. How have the results been disseminated to communities of interest?We presented the results on Tomato Field Day, attended by as many as 600 stakeholders. Presentations were made on a range of diseases, including early blight, late blight, Septoria leaf spot, and southern blight. Similar presentations were made at the Winter Vegetable Conference and theAmerican Phytopathological Society. This captures the diversity of stakeholders, including tomato growers, researchers, and seed industry representatives. All of them may benefit from the information presented in these meetings. What do you plan to do during the next reporting period to accomplish the goals?Weare approaching the end of this project cycle. Next year, we will repeat the grafting experiment under on-farm conditions. We will focus on writing the final reports, including manuscripts, and working towards the second phase of this project. We will submit the second phase of the proposal and advance our research.

Impacts
What was accomplished under these goals? We started by screening more than 240 tomato accessions in the greenhouse for resistance to early blight and Septoria leaf spot. The experiment was replicated two timesand repeated twice. Based on this experiment, we evaluated 40 tomato lines under field conditions in theorganic unit at Mountain Research Station, Waynesville, NC. (1). In 2024, the top 14 lines were assessed in four organic production environments, including two on-farm conditions with three replications. These lines are being scored for disease resistance and yield potentials. While final data is yet to be collected, the performance of multiple lines is impressive. (2). A grafting experiment is in progress to identify a suitable rootstock to address the problem of soil-borne disease, including Sothern blight. Preliminary data indicates that NC RST-01 is more effective in managing soil-borne diseases than other rootstocks. We will present the detailed results with the complete data set by the end of this season. (3). Isolates of Alternaria, Sclerotium, and Septoria were collected from various tomato growing locations in NC. Diversity analysis and pathogenicity evaluation are underway. We are optimistic that we will get some sensible results from these experiments. (4). Various extension activitieshave been made, including presentations on Tomato Field Day, Regional and National professional meetings, and local growers' meetings. We also tweet the important information. We will continue making such presentations in the future.

Publications

  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Panthee, D.R. 2023. Improving Heat Stress Tolerance in Tomato. HortScience 58: S81-S82. Panthee, D.R., A. Pandey and R. Paudel. (2024). Multiple Foliar Fungal Disease Management in Tomatoes: A Comprehensive Approach. International Journal of Plant Biology 15: 69-93.
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Siddique, M.I., E. Silverman, F. Louws and D.R. Panthee. (2024). Quantitative Trait Loci Mapping for Bacterial Wilt Resistance and Plant Height in Tomatoes. Plants (Basel) 13. doi:10.3390/plants13060876.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Adhikari, P., M.I. Siddique, F.J. Louws and D.R. Panthee. 2023. Identification of quantitative trait loci associated with bacterial spot race T4 resistance in intra-specific populations of tomato (Solanum lycopersicum L.). PLoS ONE 18: e0295551. doi:10.1371/journal.pone.0295551.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2024 Citation: Paudel, R., Pandey, A., Ingram, T., Panthee, D.R., Louws, F.J., and Adhikari, T.B. (2024). Exploring effector profiles of Alternaria linariae isolates in North Carolina. Phytpathology. XX; xx-xx.
  • Type: Other Status: Published Year Published: 2024 Citation: Paudel, R., Morgan, W., Louws, F.J. and Panthee, D.R. (2024). Evaluation of different rootstocks for grafting to manage southern stem blight of tomato in NC. Department of Horticultural Science. North Carolina State University, Tomato Field Day, Aug 15, 2024, Mills River, NC.
  • Type: Other Status: Published Year Published: 2024 Citation: Zhang, J. and Panthee, D.R. (2024). Bacterial Spot Resistance in Tomato Department of Horticultural Science. North Carolina State University, Tomato Field Day, Aug 15, 2024, Mills River, NC.
  • Type: Other Status: Published Year Published: 2024 Citation: Siddique, M.I. and Panthee, D.R. (2024). Early Blight Resistance in Tomato. Department of Horticultural Science. North Carolina State University, Tomato Field Day, Aug 15, 2024, Mills River, NC.
  • Type: Other Status: Published Year Published: 2024 Citation: Pandey, A., Paudel, R., and Panthee, D.R. (2024). Septoria Leaf Spot Resistance in Tomatoes. Department of Horticultural Science. North Carolina State University, Tomato Field Day, Aug 15, 2024, Mills River, NC.
  • Type: Other Status: Published Year Published: 2024 Citation: Panthee, D.R., Morgan, W., and Cleary, S. (2024). Evaluation of Tomato Hybrids for Fruit Yield, Quality, and Disease Resistance. Department of Horticultural Science, North Carolina State University, Tomato Field Day, Aug 15, 2024, Mills River, NC.
  • Type: Other Status: Published Year Published: 2024 Citation: Morgan, W., Cleary, S., & Panthee, D.R., (2024). Breeding for late blight resistance in tomato breeding program at NC State University. Department of Horticultural Science, North Carolina State University, Tomato Field Day, Aug 15, 2024, Mills River, NC.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2024 Citation: Adhikari, T.B., Olukolu, B.A., Pandey, A., Philbrick, A.N., Panthee,, D.R., Shekasteban,, R., Dean, R.A., and Louws, F.J. (2024). Genome?wide association analysis reveals novel candidate genes associated with resistance to Verticillium dahliae race 3 in tomato. Phytpathology. XX; xx-xx.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2024 Citation: Siddique, M.I., Blume, J., Zhang, J. and Panthee, D.R. (2024). Genetic mapping of loci conferring resistance to Septoria leaf spot in tomato. Phytpathology. XX; xx-xx.


Progress 09/01/22 to 08/31/23

Outputs
Target Audience:Our target audience are toamto growers in NC, tomato researchers in academia, tomato industry, and overall tomato industry people. We reached out to these stakeholdrs by making presentations on Winter Vegetable conference held at Asheville, NC, tomato field day held at Mills River, NC, professional meetings including APS and ASHS. All presentations were received by very well. Changes/Problems:We will not make any changes to the project. Now project activities are being implemented smoothly. We believe that it will move even more smoothly next year. What opportunities for training and professional development has the project provided?Two graduate students and one post-doctoral research associate are being trained in organic plant breeding. They are doing a fantastic job making wonderful progress. Dr. Siddique published a manuscript and is working in his second manuscript now whereas graduate students are implementing their experiments smoothly as per original plan. How have the results been disseminated to communities of interest?One of the graduate students, Anju Pandy, and Post-Doctoral Research Associate Dr. Irfan Siddique presented their research on Tomato Field Day on August 10, 2023, at Mountain Horticultural Crops Research and Extension Center, Mills River, NC. Dr. Panthee, PI of the project, also gave a talk on the tomato variety development program and the status of variety development. Participants were excited to know the statu of all new tomato varieties. Graduate students and post-docs also gave talks in professional meetings (American Society for Horticultural Science, and Amecian Phytopathological Society) about their research findings. It was received very well by the audience. What do you plan to do during the next reporting period to accomplish the goals?We will be able to submit or even publish one of the manuscripts. Currently, we are analyzing the data. It may not take a long time to finish the data analysis. Once it is done, we should be able to prepare the manuscript and submit it for publication.

Impacts
What was accomplished under these goals? We started screening tomato genotypes for early blight, late blight, and Septoria leaf spot resistance in the greenhouse and under field conditions. A total of 202 genotypes were screened for the above foliar disease resistance by inoculating using an appropriate concentrations of Alternaria and Septoria pathogens. We are also evaluating 40 tomato genotypes out of 202 set of tomato genotypes for its performance. and disease response in two location (MHCREC, Mills River and MRS Waynesville NC). As of now, the trials look excellent. Lines are segregating very well for all three disease, and there are multiple lines with good level of disease resistance. We will have to verify the results next year. We are also growing a mapping population for the identification of QTL associated with EB and SLS resistance. We will do it by bulk-segregant analysis (BSA). For that reason, this population was screened in the greenhouse and two extreme lines (resistanct and susceptible) for EB and SLS are being evaluated under the field conditions. Trials are excellent as of now. We are also collecting isolates of Alternaria and Septoria from conventional and organic farm conditions. While we already sequenced 20 isolates, we will sequence more pathogens once we have more collection. This activity will address the third objective.

Publications

  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Adhikari, T.B., Siddique, M.I., Louws, , F.J., Sim, S.C. and Panthee, D.R. (2023). Molecular mapping of quantitative trait loci for resistance to early blight in tomatoes. Frontiers in Plant Science. 14; https://doi.org/10.3389/fpls.2023.1135884.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2023 Citation: Siddique, M.I., Blume, J., Zhang, J., and Panthee, D.R. (2023). Mapping QTL for septoria leaf spot resistance in tomatoes. HortScience, 59: xx-xx.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2023 Citation: Paudel, R., Pandey, A., Panthee, D.R., Halterman, D., Louws, F.J. and Adhikari, T. (2023). Comparative genome analysis of three Alternaria species threatening tomato and potato production in North Carolina and Wisconsin. Phytopathology. Xx: xx-xx.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2023 Citation: Pandey, A., Paudel, R. Adhikari, T. Louws, F. and Panthee, D.R. (2023). Genome-wide association study (GWAS) to discover the novel markers linked to SLS resistance in tomato. Phytopathology. Xx: xx-xx.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2023 Citation: Panthee, D.R. (2023). Improving heat stress tolerance in tomatoes. HortScience, 59: xx-xx.
  • Type: Other Status: Published Year Published: 2023 Citation: Anju Pandey, A., Paudel, R., Adhikari, T., Louws,, F. and Panthee, D.R. (2023). Mapping of resistance genes to Septoria leaf spot in tomato. Tomato Field Day. Aug 11, 2023, Mills River, NC.
  • Type: Other Status: Published Year Published: 2023 Citation: Siddique, I. and Panthee, D.R. (2023). Mapping QTL for Septoria leaf spot resistance in tomato. Tomato Field Day. Aug 11, 2023, Mills River, NC.
  • Type: Other Status: Published Year Published: 2023 Citation: Zhang, J., and Panthee, D.R. (2023). Evaluation of tomato lines for Bacterial diseases. Tomato Field Day. Aug 11, 2023, Mills River, NC.
  • Type: Other Status: Published Year Published: 2023 Citation: Panthee, D.R., Stone, R., Solsbery, H., Zhang, J., and Siddique, I. (2023). Evaluation of tomato hybrids in replicated trials 2023. Tomato Field Day. Aug 11, 2023, Mills River, NC.


Progress 09/01/21 to 08/31/22

Outputs
Target Audience:Our target audience is tomato growers, particularly organic tomato growers in NC. Our audentce is also the seed industry representatives who deliver the technology through seed distribution. We reached out to tomato growers including conventional as well organic growers in North Carolina. We visited growers' fields to monitor the tomato crop, monitor the disease situation, and collect the tomato diseases including early blight (EB) and Septoria leaf spot (SLS)samples. Five talks were delivered on the tomato field day, which was attended by about 300 participants,on various aspects of tomato diseases and breeding programs in the North Carolina tomato breeding program. Changes/Problems:There was not enough certified Organic field to plant the trials consisting of more than 100 lines. We decided to do the seedling screening for both EB as well as SLS instead this year. By doing this, we will have a limited number of lines to evaluate next year under field conditions. What opportunities for training and professional development has the project provided?We hired two graduate students and one post-doc for this project. All of them are doing a very good job. This is a very good opportunity for them as they are learning new professional skills required in the organc toamto industry including resistance breeding, disease management, and interactions with tomato growers. They are enjoying the opportunity. How have the results been disseminated to communities of interest?While the final results of a completed experiment are yet to be published and delivered, preliminary information was presented on tomato field day by making oral presentations. Every speaker was allowed to speak for 10 minutes and describe the project. What do you plan to do during the next reporting period to accomplish the goals?1. Repeat the seedling screening during spring before finalizing the planting list for summer trials. 2. Evaluate tomato lines for fruit quality under organic conditions. This list will come from seedling screening results. 3. Possible launching of grafting studies. 4. Experiment on QTL mapping for EB and SLS resistance. 5. Characterization of isolates of Alternaria, and Septoria. 6. Extension activities including growers' field visits, field days, and talks on field days.

Impacts
What was accomplished under these goals? We started the project and implemented the project activities to achieve the project goals. The following activities were initiated during this reporting period: Objective 1: We started screening more than 100 tomato breeding lines with different genetic backgrounds for early blight (EB), and Septoria leaf spot (SLS) resistance. We optimized the conditions for seedling screening, and these lines were screened at the seedling stage. The main purpose of screening at the seedling stage was to save time. We also tested various concentrations of the pathogens to optimize the screening process. Objective 2: None. Objective 3a: The SLS segregating population was planted in two locations with the objective of determining the inheritance pattern of resistance to the SLS, and mapping the genes/QTL associated with resistance to the SLS. Data recording from these trials is complete now. We still need to analyze the data. Objective 3b: We started collecting isolates of Alternaria, and Septoria from various organic as well as conventional fields of various counties in NC. We have started culturing and purifying the isolates. The process is still ongoing. Objective 4: We made five presentations on Tomato Field Day,three of which were related to organic tomato production or foliar fungal diseases. We also visited organic and conventional tomato growers to monitor the crop status including disease identification, and disease sample collection, and provide any suggestions related to tomato production.

Publications

  • Type: Other Status: Published Year Published: 2022 Citation: Pandey, A., Paudel, R., and Panthee, D.R. (2022). Screening tomato lines for foliar fungal disease resistance. Tomato Field Day. Aug 11, 2022, Mills River, NC.
  • Type: Other Status: Published Year Published: 2022 Citation: Paudel, R., Pandey, A., Panthee, D.R. (2022). Disease identification and management practices for foliar fungal diseases. Tomato Field Day. Aug 11, 2022, Mills River, NC.
  • Type: Other Status: Published Year Published: 2022 Citation: Siddique, M.I., Blume, J., Paudel, R., Pandey, A. and Panthee, D.R. (2022). Breeding tomato for Septoria leaf spot resistance. Tomato Field Day. Aug 11, 2022, Mills River, NC.
  • Type: Other Status: Published Year Published: 2022 Citation: Zhang, J., and Panthee, D.R. (2022). Evaluation of tomato breeding lines for Bacterial speck, and Bacterial spot disease resistance. Tomato Field Day. Aug 11, 2022, Mills River, NC.
  • Type: Other Status: Published Year Published: 2022 Citation: Panthee, D.R., and Zhang, J. (2022). Evaluation of tomato hybrids in replicated trials 2022. Tomato Field Day. Aug 11, 2022, Mills River, NC.