The long-term goal of this research was to utilize natural genetic variation in tomato to enhance the sustainability of crop management systems by developing breeding tools for resistance to key pests and diseases. Septoria leaf spot (SLS) of tomato has become an increasingly significant fungal disease in the Northeast and neighboring states along the eastern seaboard, where hot and humid conditions prevail during the growing season. This aggressive foliar disease has devastated tomato crops, and no commercial varieties with effective resistance were available. A recently released variety (‘Iron Lady’) was reported to be tolerant to SLS. Still, our trials demonstrated that it did not provide sufficient protection against the predominant pathogen strain in mid-Appalachia.
This project addressed the urgent need to understand the genetic basis of SLS resistance and to develop resistant varieties through the introgression of robust resistance from wild tomato species into cultivated varieties. The specific objectives of this research were: (1) to introgress SLS resistance from wild accessions into a cultivated tomato variety (e.g., ‘Cherokee’ and ‘WV-63’) by creating interspecific hybrids through embryo rescue; (2) to identify the genetic loci responsible for SLS resistance; and (3) to develop reliable CAPS markers for use in breeding programs.
Backcrossing was conducted under controlled greenhouse conditions, with selection occurring in greenhouse and annual field trials at the WVU Organic Farm. Throughout the project, significant progress was made in identifying genetic sources of resistance, developing hybrid lines, and advancing backcross generations. The research team successfully mapped resistance loci and identified candidate genes associated with resistance to SLS. An advisory panel consisting of crop specialists and farmers guided the project, and farmers in West Virginia and neighboring Appalachian regions participated in evaluating advanced breeding lines.
Over four years, this project successfully developed advanced tomato lines with strong resistance to SLS, validated under both controlled and field conditions. Key resistance loci were identified on chromosomes 2, 8, and 11, with a potential novel locus on chromosome 5. The integration of traditional breeding and genomic tools, including CAPS markers and GBS, enabled the refinement of resistance loci and the identification of candidate genes. Field trials confirmed the stability of resistance traits under natural disease pressure, while backcrossing efforts advanced resistant lines to the BC5 generation. Future work will focus on fine mapping, functional validation of candidate genes, and final field evaluations to deliver SLS-resistant tomato varieties to growers. These efforts provide valuable genetic resources and molecular markers for improving tomato disease resistance, contributing to sustainable tomato production.
Throughout the project, outreach activities engaged farmers, educators, and researchers in the development of Septoria leaf spot (SLS)-resistant tomato varieties. Field trials at the WVU Organic Farm allowed farmers to observe resistant line varieties alongside susceptible varieties, with demonstrations at the annual WVU Organic Farm Field Day in 2021, 2022, and 2023. Findings were presented at regional and national conferences, including the National Association of Plant Breeders (NAPB) Meeting and the Student Organic Seed Symposium (SOSS). The research contributed to a Master’s thesis at WVU and was featured in community events like the Food System Panel Discussion & Seed Swap. Results were also disseminated through a press article and newsletter. Two manuscripts are in preparation for peer-reviewed journals, focusing on genetic resistance and variety release. These efforts fostered collaboration and supported the adoption of disease-resistant tomato varieties.
The project’s outcomes contributed to a long-term, science-based solution for managing SLS. The plant materials and molecular markers developed will be made available to farmers, breeders, and researchers to facilitate the development of resistant tomato varieties. Additionally, outreach efforts included field demonstrations, presentations at conferences, and engagement with stakeholders, ensuring that the findings were effectively communicated to the broader agricultural community.
Project Objective:
As a direct response to farmers’ needs, the research objective is to develop a tomato cultivar that is resistant to Septoria Leaf Spot (SLS) by introgressing a novel natural resistance source we identified in wild tomatoes. No effective resistance against SLS is available in any tomato cultivar. We produced several F1 hybrids via embryo rescue. We will also map the resistance locus, identify the gene, and develop molecular markers for breeding. Our research will deliver a breeding toolkit to tomato breeders interested in incorporating SLS resistance in their cultivars, and the resistant materials will be available to farmers and breeders.
Introduction:
This project aims to address the threat the disease Septoria leaf spot (SLS) caused by the fungus Septoria lycopersici poses to tomato cultivation in the Eastern U.S., especially to organic farmers and home gardeners who cannot or are unwilling to spray fungicides on their tomato plants. A genetic solution by discovering genetic resistance to the disease and generating resistant plants that can be used by plant breeders is the most viable approach at the sustainability and economic standpoints. We have identified natural sources of genetic resistance to SLS in wild tomato accessions and generated hybrids through embryo rescue. This project aims at advancing the introgression work through recurrent backcrossing and selection for resistance until we obtain a useful variety with SLS resistance that can be directly used for tomato breeding. Moreover, we aim to develop molecular markers to facilitate breeding by identifying the locus (or loci) involved in this resistance.
Cooperators
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1194 Evansdale Dr 3425 Agricultural Sciences Blg Morgantown, WV 26506-6108 United States
(304) 293-5434 (office)
Research
Hypothesis:
Our major research question is: What is the genetic component that confers resistance to SLS in tomato? This question will guide us to create a novel, long-lasting SLS resistance for tomato farmers, and a breeding toolkit. Based on our preliminary data, we hypothesize that SLS resistance is monogenic, which are conferred by wild allelic variants from particular accessions.
We also hypothesize that the novel resistance found in multiple wild species are allelic and will be mapped on the same locus of the genome. Following, we will develop reliable molecular markers and deliver a resistant variety for use in breeding programs.
Materials and methods:
The primary objectives of this study were to identify and introgress genetic resistance to Septoria leaf spot (SLS) from wild tomato accessions into cultivated varieties, develop a genotype available for growers and seed companies, map the genetic basis of resistance, and develop molecular markers for breeding applications.
To achieve these goals, we conducted backcrossing of F1 hybrids with the cultivated tomato variety ‘WV-63’ to eliminate non-domesticated alleles and introgress the resistance trait into Solanum lycopersicum. In later introgression stages, we used the ‘Cherokee Purple’ cultivar, based on farmer recommendations, and selected for resistance to multiple pathogens, including Phytophthora infestans, Fusarium oxysporum, and Verticillium albo-atrum, in addition to SLS.
Development of Genetic Populations and Selection for SLS Resistance
We generated segregating F2 populations to characterize the inheritance pattern of resistance, determining whether it was monogenic or polygenic, dominant or recessive, and enabling genetic mapping. Some F1 hybrids were self-incompatible, requiring us to generate pseudo-F2 populations by crossing different hybrids derived from the same parental accessions. However, one hybrid (H4: ‘WV-17B’ × LA1984) was self-fertile, highly resistant, and produced abundant seeds. Due to its superior characteristics, we prioritized this line for further genetic analysis.
We conducted backcrossing and selection under both greenhouse and field conditions. Field trials were established at the WVU Organic Farm, where plants were grown without fungicide applications to evaluate natural disease resistance under high disease pressure. In greenhouse screenings, we maintained a high-humidity chamber (nearly 100% relative humidity for over a week) and used a highly aggressive SLS strain from Long Island at an inoculation level of 500,000 spores/mL. This stringent setup ensured that only plants with strong resistance under controlled conditions were advanced to field testing.
To overcome genetic incompatibility bottlenecks in backcrossing, we employed Micro-Tom as a bridging cultivar. This approach improved the success rate of BC1 production, allowing us to advance resistant lines more efficiently. Over time, we successfully reached BC4 and BC5 generations, with H4-derived populations displaying the highest resistance levels.
Genetic Mapping and Molecular Marker Development
To map the resistance loci, we developed 24 CAPS markers, strategically positioned across the genome, with one marker per chromosome arm. These markers distinguished domesticated tomato chromosomes from wild donor alleles based on available genome sequence data. We used these markers to confirm hybrid status, eliminating escape lines that lacked wild alleles.
In Year 3, we conducted Quantitative Trait Locus (QTL) analysis using Composite Interval Mapping (CIM). The analysis of 347 F2 plants and 24 CAPS markers suggested a complex resistance mechanism, possibly controlled by multiple loci. Further marker refinement in backcross populations (BC1, BC2, and BC3) indicated that resistance mapped to chromosomes 2, 8, and 11, with the chromosome 8 locus playing a dominant role. Additional CAPS markers were designed to narrow down candidate gene regions, and a mapping-by-sequencing approach was planned for BC5 populations to refine the recombination breakpoints.
During the fourth year of the project, genotyping-by-sequencing (GBS) was conducted on key parental and introgressed lines, including Cherokee Purple, WV63, WV17B, and advanced lines with H4 (S. arcanum) and H6xH2 (S. peruvianum) backgrounds. To analyze the GBS data and evaluate SNP density, a standardized bioinformatics pipeline was implemented. Raw sequencing reads were initially processed to remove low-quality bases and adapter sequences. The cleaned reads were then aligned to version 4 of the tomato reference genome. SNP calling was performed using the variant detection tool GATK, which identified and filtered SNPs based on quality scores, depth of coverage, and other quality parameters. The results were visualized using R to generate SNP density plots across chromosomes. This approach allowed for the identification of genomic regions with high SNP density, which were further investigated for potential associations with traits of interest, such as disease resistance.
Field Evaluations and Resistance Validation
Field trials were conducted annually at the WVU Organic Farm, where susceptible commercial varieties were grown alongside resistant breeding lines. The 2022 and 2023 field seasons provided critical validation of resistance under natural disease pressure. Although 2023 experienced unusually dry conditions, SLS symptoms developed late in the season, allowing for assessment. The most advanced breeding lines, particularly those derived from H4, showed strong resistance to both SLS and Verticillium wilt, suggesting potential overlapping resistance mechanisms.
The breeding pipeline was nearly complete by the final year, with BC5 generation plants exhibiting 100% resistance to SLS under extreme disease pressure in controlled greenhouse conditions. The project aimed to confirm the stability of resistance, finalize marker development, and prepare resistant lines for seed production and distribution.
Research results and discussion:
Year 1 report
Backcrossing: BC1 has been completed for five F1 hybrids with cv. 'WV'63'. We are conducting a selection for Septoria resistance to identify the best materials (highest resistance levels) to move forward. Once the backcrossing/selection pipeline is well established and the graduate student is well trained since we conduct the backcrossing in the greenhouse, we expect to advance ~2.5 generations per year. We will switch to a more common variety (to be determined upon discussion with farmers in 2022) and select three more disease resistances from the BC3 generation on;
Four F1 hybrids were evaluated in field conditions (WVU Organic Farm) in the summer of 2021. Last year was quite humid and hot, thus creating ideal conditions for the aggressive development of Septoria leaf spot. Indeed, the accessions of cultivated tomato cultivated in our organic plot (intentionally without any disease control) were devastated.
Generation of an F2 segregating population: As expected, some F1 hybrids were self-incompatible and could not be selfed to generate F2 plants. however, we were able to produce pseudo-F2 populations by crossing different hybrids from the same genotypes (e.g., H1 and H3, both derived from crossings between cv. 'WV-63' and LA1984 (Solanum arcanum). We were also lucky to identify a self-fertile hybrid (H4: 'WV-17B' x LA1984). H4 was not only self-fertile but also the line that produced the most seeds and showed the highest resistance level. We have decided to move forward with segregation analyses with H4 for these reasons. Later, the other pseudo-F2 populations will be used to assess whether the genetic resistance behaves similarly when coming from other wild accessions. Characterization of genetic resistance in the H4-F2 population is currently underway.
Development of CAPS markers to map the genetic resistance to Septoria leaf spot: 24 markers were developed (one per chromosome arm of the tomato genome - this is possible due to the high degree of synteny in the genus Solanum). Markers have been designed to distinguish the domesticated chromosome arm and any wild tomato species under study (S. peruvianum, S. corneliomulleri, and S. arcanum) based on the genome sequence information available to us. The markers have been tested and optimized and are ready to be employed on the H4-F2 population to identify in which chromosome arm(s) the resistance is mapped. Later, we will develop markers to zoom in/refine the genetic locus with further development of markers on the identified arm to narrow down the locus further and further. We also used these CAPS markers to successfully confirm the hybrid nature of the lines we are using (and identified hybrid H5 as an escape, which only had the genome from the maternal progenitor, cv. 'WV-63').
Year 2 report:
In year 1 of the project, we focused on producing genetic resources to enable our research. We generated BC1 plants for advancing the backcrossing work to develop an SLS-resistance variety and developed CAPS markers for mapping the genetic resistance. We also evaluated the resistance level of each of the novel germplasm generated (cf. Y1 report above).
Expectedly, Year 2 was of intense work in the greenhouse with backcrosses and analyzing F2 progeny to map the genetic resistance. We faced challenges with the success rate of the backcrossing, but we were able to advance to BC2 with the H6 line, which generated plants with a good level of resistance. Plants showing the highest resistance levels (immunity to SLS) from 3 hybrids (H1, H2, and H3) are still in BC1 but advancing to BC2. One way we learned how to circumvent this genetic recalcitrance and speed up the backcrossing was to use the dwarf variety Micro-Tom as a bridge to advance to BC1. We have made strides on this approach and produced a population that is currently being screened for resistance and will be used to advance to BC2. We expect that at the end of Year 3, we will have reached BC4 with plants screened not only for SLS resistance but also for other fungal diseases (Phytophthora infestans, Fusariumoxysporum, and Verticillium albo-atrum) as well as developmental traits (plant size and architecture, flowering, fruit size, etc.)
A considerable amount of effort was placed into mapping the genetic resistance on the tomato genome. CAPS markers developed in the previous year were used to map a Ψ-F2 population generated from a crossing between H6 x H2 plants (due to self-incompatibility). The parental hybrids are both derived from S. peruvianum (accession LA2744). The analysis of 347 Ψ-F2 plants and 24 CAPS markers (2 per chromosome, one per arm) indicates that the resistance may be more complex than monogenic, especially because we observe segregation of the resistance level (perhaps a quantitative trait). We want to verify these results by conducting this analysis using a mapping-by-sequencing approach either on an F2 population from a different hybrid with the highest level of resistance observed (H4, which is the only self-compatible F1 hybrid from S. arcanum LA1984, and we now have enough F2 seeds available for the analysis) or on a more advanced backcrossing population (BC2 or BC3) derived from H4.
2022 Field Trial at the Organic Farm. Left: F1 hybrids; Right: tomato varieties showing susceptibility to Septoria leaf spot. The photo was taken in August 2022.
Given its hot and humid summer, 2022 was quite a challenging year in Morgantown, WV (and the whole East of the U.S.) for tomato plants cultivated without fungicide interventions. Our annual field trial at the WVU Organic Farm, which is cultivated without any spraying, demonstrated how devastating SLS is when left uncontrolled. Our disease resistance screening setup in the greenhouse is stringent as we utilize a more aggressive strain (from Long Island) than that occurring in Morgantown, WV, the inoculation level (50,000 spores/mL) and constant high humidity (almost 100% RH for more than a week). This setup aims to ensure that when a plant is scored highly resistant in the greenhouse, it will perform well in the field when the infection pressure is lower. In 2023, we plan to send BC1 and BC2 plants for performance evaluation in field conditions.
Year 3 Report:
As a recap, in Year 2, we conducted intensive greenhouse work, focusing on backcrossing and analyzing the F2 progeny for genetic resistance against Septoria leaf spot (SLS). Despite facing some challenges in achieving successful backcrosses, we progressed to BC2 with the H6 line, resulting in plants displaying robust resistance. The utilization of the dwarf variety Micro-Tom facilitated the backcrossing process as a bridge. Genetic resistance mapping of the tomato genome uncovered complexities potentially linked to quantitative traits.
In the past year (year 3), we overcame the challenges of crossings and advanced to the BC3 generation using the Hybrid-4 (which shows the highest Septoria-resistant level) in both 'WV-63' and 'Cherokee Purple' tomatoes as recurrent parents. Additionally, we advanced to the BC3 population with the remainder hybrids (H1, H2, H3, and H6). Our efforts for subsequent generations are now focusing on the H4, given its clear superiority regarding SLS resistance. In order to stack the resistance level as high as possible, we also conducted crossings between a genotype showing a high level of resistance in BC2derived from S. peruvianum (LA2744) (Ψ-F2 H6xH2) and a BC3 population from S. arcanum (LA1984) (H4) as a source of resistance. The plants from these crossings are being screened for Septoria resistance, and they will provide excellent insights into stacking or even increasing our current resistance level. We reached BC4 fruits using H4, which will be screened soon for SLS resistance, fungal diseases, and the developmental traits mentioned in the previous report.
The summer of 2023 in Morgantown, WV was unexpectedly dry, causing an effect of late disease symptoms in tomatoes cultivated following non-chemical practices. However, in late summer, when the conditions were more humid, we identified intense infestations of Septoria leaf spot and Verticillium wilt in our trials. This year, BC1 and BC2 plants were selected for performance evaluation under field conditions. Because of the stringent conditions of spore concentration, strain, and humidity under greenhouse conditions, the selected plants showed high resistance against SLS on the organic farm. Interestingly, a high level of resistance to Verticilium wilt was also observed in most of the plants, potentially pointing to a common strategy of genetic resistance. In 2024, we anticipate using BC4 and BC5 plants for field-based performance evaluation.
Our further exploration into mapping the genetic resistance in the Ψ-F2 population generated from a crossing between H6 x H2 plants, both derived from S. peruvianum (accession LA2744), included the QTL analysis using the Composite Internal Mapping (CIM) method. This approach allowed us to identify two markers among the initial 24 CAPS markers used (2 per chromosome). The position of the markers belongs to chromosomes 2 and 11. Additionally, 190 plants from backcrossing populations (BC1, BC2, and BC3) derived from H4 were also analyzed for QTL analysis via the CIM method. The results reveal strong evidence that the position responsible for the genetic resistance of SLS lies on chromosome 8, in addition to chromosome 11. Our efforts in mapping the regions responsible for SLS resistance allowed us to narrow down and identify a genomic region containing 34 genes within chromosome 8 after the design and evaluation of an additional set of 11 CAPS markers between the initial markers. The same strategy of narrowing down regions on chromosomes 2 and 11 is being applied with the design of new CAPS markers. Meanwhile, a fast advance in crossings is expected, and we expect to use a mapping-by-sequencing approach in a BC5 population derived from H4 to identify the limits of recombination and define a smaller set of genes potentially responsible for the resistance trait.
This is the report for year 3. We requested and have been granted a one-year no-cost extension of this project. The PhD student responsible for this project was recruited after about 6 months into year 1, and there was a learning curve, along with technical difficulties with genetic compatibility in advancing to BC1 and BC2. Now that all the technical issues have been resolved and the graduate student is sharp with plant care, phytopathology, and quantitative genetics, we anticipate that at the end of the next period we will have a tomato line with a strong level of resistance to Septoria (as well as other fungal diseases) and excellent growing and organoleptic properties. We also expect to provide markers and candidate gene lists within defined regions of the tomato genome potentially responsible for the genetic resistance to SLS.
Year 4 Report:
The fourth year of this project has marked substantial progress in developing Septoria leaf spot (SLS)- resistant tomato lines, building on the foundational work of previous years. Through a combination of advanced backcrossing, field trials, and genomic analysis, we have deepened our understanding of the genetic mechanisms underlying SLS resistance and advanced the development of robust, resistant tomato lines. Our overarching goal remains to identify key genomic regions associated with resistance and integrate these traits into elite tomato germplasm for future cultivar development. Over the past year, significant strides were made in backcrossing and line development. The Hybrid-4 (H4) line, which has consistently demonstrated the highest level of SLS resistance, was advanced to the BC5 generation. This line served as a cornerstone for further breeding efforts. Additionally, targeted crosses were performed between an advanced BC3 population derived from Solanum arcanum (LA1984) and a highly resistant BC2 population from Solanum peruvianum (LA2744). These crosses were designed to combine resistance factors from both wild relatives, resulting in offspring with enhanced disease resistance. Screening of these offspring revealed a major improvement in resistance compared to previous lines. This new line was subsequently advanced to the BC4 generation, with ongoing efforts to refine the selection process and stack resistance traits.
Field trials were conducted to evaluate the disease resistance and agronomic performance of BC4 and BC5 plants. The trials were carried out under variable environmental conditions, including an unusually dry early summer followed by a period of high humidity that favored disease development. Despite these challenges, the selected lines exhibited high levels of SLS resistance, confirming the robustness of the resistance traits. These results not only validate the effectiveness of the breeding strategy but also provide critical insights for optimizing future field evaluations and breeding protocols.
To further elucidate the genetic basis of SLS resistance, genome-by-sequencing (GBS) was performed on key parental and introgressed lines, including Cherokee Purple, WV63 and WV17B (as a parental control), and advanced lines with H4 (S. arcanum) and H6xH2 (S. peruvianum) backgrounds. Bioinformatics analysis of SNP density confirmed previously identified resistance-associated regions on chromosomes 2, 8, and 11. Notably, an unexpected SNP density peak was observed on chromosome 5, suggesting the presence of a novel resistance locus. This finding opens new avenues for investigation, and further studies are planned to validate the role of this region in SLS resistance.
Fine mapping efforts have continued to refine the resistance loci associated with SLS. Using additional CAPS markers, the resistance-associated region on chromosome 8 was narrowed down, and similar approaches are being applied to chromosomes 2 and 11. The newly identified region on chromosome 5 will be subjected to detailed analysis to determine its significance in resistance. A mapping-by-sequencing approach is currently underway in the BC5 population to identify recombination limits and define candidate genes within the resistance loci. These candidate genes are being prioritized for functional validation, with future steps potentially including transcriptomic analysis and gene editing to confirm their roles in SLS resistance.
The next phase of this project will focus on completing the fine mapping of resistance loci and conducting final field evaluations of BC5F2 lines. These evaluations will assess performance under natural infection conditions and across different geographic locations to ensure broad adaptability and agronomic suitability. Additionally, findings on SLS resistance genetics and marker development will be prepared for publication, providing valuable resources for the broader scientific and breeding communities. Selected BC5-derived lines will be proposed as pre-breeding material for further cultivar development, to deliver SLS-resistant tomato varieties to growers.
The fourth year of this project has yielded significant advancements in the development of SLS-resistant tomato lines. By integrating traditional breeding approaches with cutting-edge genomic tools, we have identified key resistance loci, developed advanced breeding lines, and laid the groundwork for future functional validation of candidate genes. These efforts are expected to provide breeders with the genetic resources and molecular markers needed to improve tomato disease resistance, ultimately contributing to more sustainable and productive tomato production systems.
Research conclusions:
Over the past four years, our work has advanced toward the ultimate goal of developing a tomato line with robust resistance to Septoria leaf spot (SLS) and desirable horticultural traits. In Year 1, our primary focus was on establishing the breeding pipeline, generating backcross (BC1) lines, and designing CAPS markers to begin mapping the genetic basis of SLS resistance. We also identified promising hybrid lines in field trials under organic conditions, although the hot and humid summer underscored the severity of SLS without fungicidal intervention.
In Year 2, we intensified our greenhouse work to refine the backcross strategy and analyze F2 progenies for resistance. Despite challenges in achieving successful backcrosses due to genetic incompatibility, we progressed to BC2 in key lines and employed Micro-Tom as a bridging cultivar to accelerate breeding. Our greenhouse screening system—using an aggressive SLS strain and high humidity—helped ensure that lines showing strong resistance under these stringent conditions would also perform well in the field.
Year 3 built on these efforts by advancing multiple lines (including H4, which exhibits the highest SLS resistance) to the BC3 and BC4 generations, while also validating and fine-tuning genetic resistance mapping. QTL analysis revealed multiple loci associated with SLS resistance on chromosomes 2, 8, and 11. The design and use of additional CAPS markers helped us narrow down the key resistance regions, bringing us closer to identifying a definitive set of candidate genes. Field trials in 2023, although initially affected by a dry summer, ultimately confirmed high levels of resistance to both SLS and Verticillium wilt in many of our advanced lines when disease pressure intensified later in the season.
Having secured a one-year no-cost extension, we leverage our refined methodologies and the graduate student’s now well-honed skills to finalize this research with two main outcomes: first, a tomato line with strong multi-fungal resistance and desirable agronomic and organoleptic properties; and second, a robust set of markers and candidate genes that will serve as practical tools for the broader research community. By focusing on both the breeding pipeline and high-resolution genetic mapping, we are delivering valuable germplasm and scientific insights that can be applied to tomato-improvement efforts.
The breeding work is almost concluded (currently in BC5Fn). The tomato plants with a high level of resistance to Septoria leaf spot under unreasonably high disease pressure (aggressive strain of fungus, inoculation with high spore count, high temperatures, and high-humidity chamber) still show no signs of infection. We identified 3 loci, 2 of which together provide 100% of protection, and we continue to narrow down their genomic regions and shorten the list of potential candidate genes involved in this resistance mechanism.
In toto, we will be concluding the breeding pipeline by testing the stability of the final genotypes and preparing for seed production for distribution. We have been contacted by several farmers, breeders, and researchers interested in obtaining our genotypes to incorporate them into their breeding and research pipelines. We are currently writing 3 manuscripts as a result of this project: 1 on identifying and introgressing the Septoria leaf spot trait into commercial varieties; 1 on the identification of loci involved with this trait; and 1 about the variety release.
This project allowed for a breakthrough in resolving a worldwide problem in tomato production.
Participation Summary
Education & Outreach Activities and Participation Summary
Educational activities:
3 On-farm demonstrations
1 Published press articles, newsletters
Participation Summary:
60 Farmers participated
35 Number of agricultural educator or service providers reached through education and outreach activities
Outreach description:
The current pandemic certainly creates hurdles for in-person interactions and outreach activities. Nevertheless, we made efforts to have a presence with the farmers through participating in the WVU Organic Farm Field Day (a yearly event at WVU, which occurred on August 28, 2021 and August 27, 2022) by displaying a plot with our hybrids alongside other tomato cultivars. This year, the Septoria leaf spot disease was very aggressive on tomato cultivars (see picture 1), but impressively the five H1 hybrids we tested were mostly unharmed by them (see picture 2 - commercial varieties on the left and our F1 hybrids on the right). The plot was visited by around 30 local organic farmer families each year and counted with 10 agricultural educators and extension specialists.
In future years, after the pandemic is over, we aim to attend local and national in-person conferences, but for now, we will limit our participation in open-field and online to guarantee the safety of our researchers.
A Masters thesis by Estefania Tavares Flores (WVU Genetics and Developmental Biology Program, title: "Traditional and modern breeding strategies towards developing resilient crops: Two case studies in tomato"; advisor: Prof. Vagner Benedito) was defended in July 2021. Chapter II (Introgressing Septoria leaf spot resistance from wild tomato accessions into West Virginia cultivars using in vitro techniques and genetic markers: Developing alternatives for organic farmers) is a product of this research.
Year 3 Updates
We will present the results of this project at the 2024 Meeting of the National Association of Plant Breeders (NAPB) in Saint Louis, MO, and the Plant Health 2024 conference in Memphis, TN, both in July 2024.
End of Project period: In 2024, we presented the results of this project to participants in the meetings specified above in the previous report, with excellent support and feedback. We are finalizing the SLS-resistant line and preparing manuscripts for submission for publication in top, peer-reviewed journals specialized in plant pathology.
Learning Outcomes
60 Farmers reported changes in knowledge, attitudes, skills and/or awareness as a result of their participation
35 Service providers reported changes in knowledge, attitudes, skills and/or awareness as a result of project outreach
35 Educators or agricultural service providers reported changes in knowledge, skills, and/or attitudes as a result of their project outreach
Key areas in which farmers reported changes in knowledge, attitude, skills and/or awareness:
In our WVU Organic Farm Field Day, which occurred on Aug 28, 2021, and Aug 27, 2022 (each with some 30 farmer attendants) we were able to interact with 30 farmer families and 10 agricultural specialists, who were educated about Septoria leaf spot and other tomato diseases and could witness the strong disease resistance in our hybrid. Since this is year 1 of our project, we have not actively employed farmer participation but intend to do so for testing variety performance in later stages, when we have more advanced introgressions.
In 2022, we were also able to present our work to the Student Organic Seed Symposium (SOSS: https://organicseedsociety.org/meetings-events/student-organic-seed-symposium/) in July 29th (around 25 students attended the event).
We have also marked presence in the Food System Panel Discussion & Seed Swap: Sowing Sustainable Local Food Systems promoted by WVU (Eberly College, led by Dr. Mehmet Oztan).
60 Farmers reported changes in knowledge, attitudes, skills, and/or awareness as a result of their participation.
35 Service providers reported changes in knowledge, attitudes, skills, and/or awareness as a result of project outreach.
35 Educators or agricultural service providers reported changes in knowledge, skills, and/or attitudes as a result of their project outreach.
Key areas in which farmers and educators reported changes in knowledge, attitudes, skills, and/or awareness:
Awareness of Septoria leaf spot (SLS) symptoms and impact: Farmers and educators gained a better understanding of how to identify SLS symptoms and the significant damage it can cause to tomato crops.
Importance of selecting disease-resistant varieties: Participants learned about the value of using resistant tomato varieties to reduce crop losses and improve yield stability.
Knowledge of breeding techniques for disease resistance: Farmers and educators were introduced to the process of developing resistant varieties through backcrossing and genetic mapping.
Recognition of sustainable farming practices: Participants became more aware of the role of disease-resistant crops in reducing reliance on chemical fungicides and promoting sustainable agriculture.
Skills in disease management: Farmers gained practical insights into managing SLS and other fungal diseases through integrated approaches, including resistant varieties and cultural practices.
Outreach Activities:
At the WVU Organic Farm Field Day (August 28, 2021, and August 27, 2022), 30 farmer families and 10 agricultural specialists interacted with the research team, observed resistant hybrids, and learned about SLS and other tomato diseases.
In 2022, the project was presented at the Student Organic Seed Symposium (SOSS), attended by 25 students, who gained knowledge about organic seed development and disease resistance breeding.
The research team participated in the Food System Panel Discussion & Seed Swap hosted by WVU, promoting sustainable local food systems and sharing project findings with the community.
These outreach efforts successfully increased awareness and understanding of SLS resistance, sustainable farming practices, and the importance of disease-resistant varieties among farmers, educators, and students.
Project Outcomes
1 Grant applied for that built upon this project
10 New working collaborations
Additional Outcomes:
So far, the major outcomes in year 1 are obtaining F2 and BC1 populations and the development of high-quality molecular markers. The work so far is running according to the original plan.
Year 3 Update:
At last, it is noteworthy to mention that 101-year-old and WVU Emeritus Professor Mannon Gallegly is the developer of the iconic tomato variety The People's tomato WV'63 (launched in 1963 from an initial crossing with S. peruvianum, which carries a long-lasting genetic resistance to late blight; WV'62 is still used in tomato breeding as the source of this resistance). He launched his fourth (and said to be his last) variety, which has been named 'Mannon’s Majesty WV'23'. This variety builds on the genetic background of WV'63 and has some level of SLS resistance derived from Solanum hybrochaites. You can find the press release here.
'Mannon’s Majesty WV'23' is superior in SLS resistance to the hybrid launched by Cornell some years ago ('Iron Lady'), for which we found it to have a very low resistance level in Appalachia. Given that the sources of resistance were much stronger, the lines generated by this SARE-NE project are expected to show an unprecedented high level of resistance, create breeding tools (germplasm and molecular markers), and define a small set of candidate genes to enable molecular studies of the genetic resistance of fungal diseases, which can potentially have long-term implications for crops afflicted by fungal diseases well beyond tomato and the Solanaceae.
Final report: This project allowed the development of large national and international networks of researchers and farmers interested in a solution for Septoria leaf spot in organic tomato production. An AFRI project proposal was submitted for funding (currently under evaluation) seeking to continue this project by conducting functional analysis of candidate genes within each loci involved in the mechanism of resistance. We are also developing a large OREI project (led by the PI of this grant), in which our Septoria-resistant genotypes will play a central role as key material to solve organic production.
Assessment of Project Approach and Areas of Further Study:
This project was innovative in identifying a source of Septoria resistance in wild accessions of tomatoes and introgressing the trait into cultivated varieties. This was a long-standing goal in Tomato that we could resolve with the funding provided to us by the Northeast SARE program.
Furthermore, we were very effective in identifying narrow regions of the tomato genome (discrete QTLs) to yield a small number of candidate genes that will help us unveil the molecular mechanism of resistance in tomatoes. This knowledge will not only help create markers that are 100% linked to the resistance, thus facilitating tomato breeding efforts but also expand this knowledge to other crops affected by Septoria spp. and create novel ways to curb this disease in other crops, such as wheat, poplar, celery, stevia, hemp, etc.
Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and should not be construed to represent any official USDA or U.S. Government determination or policy.
Backcrossing: BC1 has been completed for five F1 hybrids with cv. 'WV'63'. We are conducting a selection for Septoria resistance to identify the best materials (highest resistance levels) to move forward. Once the backcrossing/selection pipeline is well established and the graduate student is well trained since we conduct the backcrossing in the greenhouse, we expect to advance ~2.5 generations per year. We will switch to a more common variety (to be determined upon discussion with farmers in 2022) and select three more disease resistances from the BC3 generation on;
Expectedly, Year 2 was of intense work in the greenhouse with backcrosses and analyzing F2 progeny to map the genetic resistance. We faced challenges with the success rate of the backcrossing, but we were able to advance to BC2 with the H6 line, which generated plants with a good level of resistance. Plants showing the highest resistance levels (immunity to SLS) from 3 hybrids (H1, H2, and H3) are still in BC1 but advancing to BC2. One way we learned how to circumvent this genetic recalcitrance and speed up the backcrossing was to use the dwarf variety Micro-Tom as a bridge to advance to BC1. We have made strides on this approach and produced a population that is currently being screened for resistance and will be used to advance to BC2. We expect that at the end of Year 3, we will have reached BC4 with plants screened not only for SLS resistance but also for other fungal diseases (Phytophthora infestans, Fusarium oxysporum, and Verticillium albo-atrum) as well as developmental traits (plant size and architecture, flowering, fruit size, etc.)
The current pandemic certainly creates hurdles for in-person interactions and outreach activities. Nevertheless, we made efforts to have a presence with the farmers through participating in the WVU Organic Farm Field Day (a yearly event at WVU, which occurred on August 28, 2021 and August 27, 2022) by displaying a plot with our hybrids alongside other tomato cultivars. This year, the Septoria leaf spot disease was very aggressive on tomato cultivars (see picture 1), but impressively the five H1 hybrids we tested were mostly unharmed by them (see picture 2 - commercial varieties on the left and our F1 hybrids on the right). The plot was visited by around 30 local organic farmer families each year and counted with 10 agricultural educators and extension specialists.