Dilip Panthee

The main goal of this proposal is to improve the resilience and sustainability of U.S. tomato farms through the identification and utilization of novel genetic determinants that confer resistance to Verticillium Wilt incited by non-race 1 isolates of Verticillium dahlia (Vdn). The pathogen can live for 20 years or more in the soil and rotation is not feasible for control of the disease because other crops are also hosts. We propose that the critical solution to mitigate VW damage may be host resistance and the most feasible and economic control is the use of verticillium-tolerant tomato cultivars. There are numerous resistant cultivars effective against race 1; however, no source of resistance to non-race 1 isolates is commercially available. Multiple on-farm trials in Vdn infested grower fields enabled us to successfully identify novel sources of Vdn resistant tomato germplasm. The following objectives express a two-tiered approach to achieve and deliver the proposed outcomes to the stakeholders. a) identify and fine-map Vdn resistant locus (loci) in three NCSU tomato breeding lines. b) Utilize Vdn resistance to develop new tomato hybrids stacked with additional disease resistances The addition of Vdn resistance will broaden the disease-resistant spectrum of the elite NCSU tomato cultivars minimizing economic risk for growers in the U.S. and worldwide. Improved cultivars will be selected in a farmers' participatory selection process and released for commercial use. Findings from this research will be published in relevant journals and may also provide a genetic tool to combat VW in other economically important crops.

Fresh-market tomato is an important crop in North Carolina and is produced in all the different growing regions across the state. The mountains of western North Carolina are ideal for the production of high yields of premium quality fruit because of ideal day and night temperatures. In the piedmont and coastal plains areas of North Carolina, tomato production additionally profits from an extended growing season allowing for the planting of early, mid, and late-season crops. However, the industry struggles to maintain a sustainable profit because of the high temperatures in late summer in the piedmont and coastal plains and multiple disease problems throughout the state affecting the yield of high-quality fresh market tomatoes. Unpredictable market prices resulting from the competition with field and greenhouse tomato production in neighboring countries during the summer production season imposes an additional burden on the industry. Therefore, identification of fresh-market tomato cultivars and breeding efforts to develop new hybrids with improved disease resistances and well adapted to tomato production regions are crucial to maintaining high marketable yields to increase the profitability of tomato production in North Carolina. In this research project, we aim to identify commercial and NCSU fresh market tomato cultivars well adapted to Western North Carolina (WNC), Piedmont, and coastal regions through on-farm variety trials. This project will provide important tools to increase production and profitability by growing improved conventional and heirloom-type cultivars with superior fruit quality and multiple disease resistances.

In order to make tomato production more attractive in the current competitive market, means should be devised to reduce the cost of production. Growing disease resistant and stress tolerant variety is the best way to reduce the cost of production. Superior fruit quality of vine ripe tomato offers better opportunity to bring NC tomato into the market. While several varieties have already been released by NC State University, it is necessary to continue the development of such varieties addressing the potential problems. In the proposed project, we aim to develop improved fresh market tomato varieties for NC tomato growers through conventional and molecular approaches.

Tomato is about $35 million industry in NC, with a majority of the crop grown in the Western mountains (National Agricultural Statistics Service 2015; North Carolina Department of Agriculture and Consumer Services 2013). Bacterial wilt (BW) is one of the most important soil-borne diseases causing a significant crop loss. It was estimated that losses caused by BW ranged from 15 to 55% in Taiwan, 10-100% in India, and 5 to 15% in Australia, and with an average of 70% losses in hotspot regions (Elphinstone, 2005). Realizing the magnitude of the problem, with the partial support from North Carolina Crop Improvement Program (NCCIP), we intensified our effort to investigate the source of resistance and introgress the resistance genes into NC-adapted breeding lines. As a result several lines have shown very promising results. We investigated the molecular mechanism by performing RNA-seq analysis (please see the progress report attached herewith). Its manuscript is in preparation stage. That will provide more insight about the genes involved in BW resistance. Still we need to make a significant improvement on fruit quality comparable to the breeding lines from other programs. We observed that there was a negative correlation between fruit quality and BW resistance in tomato. Improving BW resistance along with fruit quality should be the logical step to the next level. Poor fruit quality includes small size, cracking, poor taste, unattractive color or softness. We will have to analyze friuts for all these traits during this phase of the research. Continuing evaluating lines for BW resistance and these quality traits, and hybrids from their inter-crosses will help to combine the desirable traits into a single genotype. We have decided to release small-fruited BW-resistant genotypes as rootstocks for grafting, we may submit the release proposal soon. This will provide us a separate plateform for utilizing resistant genotypes with relatively poor fruit quality in tomato industry.

The phasing out of methyl-bromide has left many agricultural systems vulnerable to soil-borne plant pests. Bacterial wilt and Verticillium wilt are existential threats to many crop systems. Addressing these threats requires a multifaceted approach. Understanding how to restore tired soils will involve researching how plant genetics, microbiomes, and grower inputs are interconnected. NC State has a large number of proprietary sequenced tomato lines and access to commercial lines with diverse genetic backgrounds known to improve soil health. To better understand how to utilize this rich source of genetics, we propose to study the impacts of these tomato lines on soil health in disease infested fields. Several locations with bacterial wilt and Verticillium wilt infested soils are available to us. In cooperation with growers, we propose to study the impact of this diverse tomato collection on soil health under various conditions [fumigated, non-fumigated, and anaerobic soil disinfestation (ASD)]. The utilization of these tomato lines will also be studied in grafted and non-grafted systems to allow growers the usage of cultivars with their preferred characteristics. Soil health will be assessed by measuring plant-available nutrient content, microbiome diversity, disease severity, and subsequent increases in yields.

The demand for organic tomatoes in the Southeast is high, but production is limited due to lack of regionally adapted high yielding varieties. Organic growers have requested research 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 approach of disease management for organic production by integrating organic disease management system and resistance breeding well-adapted to organically 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 soil-borne fungal disease resistance, and fruit quality in heirloom tomato varieties grown under organic conditions 2: Production system: grafting for the management of major diseases and enhancing fruit quality under organic transition conditions 3: Identification of suitable tomato varieties for organic production through participatory variety selection for high yield, disease resistance, and fruit quality 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 Organic Transition program and will facilitate the development of organic agriculture production, biodiversity, and soil health by minimizing the pressure of soil-borne pathogens, and integrating novel technology into organic system.

North Carolina (NC) ranks among the top ten states in the US for tomato production and has a farm-gate value of over $45 million (USDA NASS 2017). However, there are many leaf spot diseases which greatly impact the production of tomatoes in NC. Tomato gray leaf spot (GLS), caused by three fungal species in the genus Stemphylium: S. botryosum, S. lycopersici, and S. solani, causes necrotic lesions on leaves which leads to defoliation, yield loss, and fruit scald (Jones et al. 2014). Most conventional hybrid tomato varieties have resistance to GLS; however, heirloom varieties as well as grape and cherry tomato cultivars are very susceptible to this disease. These tomato types are highly sought after in local markets (P. Shoemaker, personal communication) and, therefore, many small farmers have an interest in growing these varieties. Small acreage farms (<5 acres) make up 94% (192/204) tomato production in NC, therefore, this disease is likely to impact many of these growers.To keep small farms in NC viable, it is important to continue to update our management of diseases of tomato as horticultural practices change with shifting consumer preferences. This project aims to address these gaps by: (1) understanding the prevalence and severity of gray leaf spot (GLS) (Stemphylium species) on tomato in heirloom tomato production in NC, (2) evaluating effective spray schedules for control of gray leaf spot on tomato through field trials, and (3) identifying heirloom type experimental cultivars currently under development for resistance to GLS.

Our goal is to establish a novel microspore culture system to generate homozygous Double Haploid (DH) inbred lines for tomato breeding and genomic community. We expect the knowledge and technology generated in the proposed research will put NC in a technical competitive position for tomato breeding, the technology will be translational to other economically important crops that are currently not amenable to double haploid production.

The North Carolina State University will incorporate polygenic host resistance into NCSU fresh market tomato hybrids, for large scale commercial production and specialty types of different sizes, shapes, and colors with multiple disease resistance and outstanding flavor, in order to mitigate the damage caused by tomato spotted wilt virus (TSWV). Tomato spotted wilt, spread by thrips, is a widespread, destructive disease in North Carolina, especially in the piedmont and coastal plain regions. It is controlled in commercial production by the use of determinate hybrids with the Sw-5b resistance gene. However, indeterminate varieties, especially heirloom and other specialty types that are becoming more popular lack TSWV resistance. In addition, new strains of the virus not controlled by the Sw-5b gene will create additional challenges. In this research, we aim to (1) develop TSWV resistant tomato cultivars by incorporating the SW-5b gene into the parental lines for all types of fresh market tomato hybrids through traditional and molecular breeding, (2) utilize molecular breeding to stack the SW-5b gene with other TSWV resistance genes, SW-1 and SW-7, and (3) identify additional sources of TSWV resistance. Resistance will be confirmed in grower fields with high TSW incidence, selected in a farmers' participatory selection process, and released for commercial use. This project will provide important tools to prevent TSW and increase production and profitability by growing improved conventional and heirloom-type cultivars with superior fruit quality and multiple disease resistances. This proposal integrates research and extension by acquiring direct input from growers and extension agents.

Borlaug Fellowship Program for Kazakhstan fellow to spend 12 weeks at NC State conducting research to identify new genes associated with grain quality, productivity and disease resistance using new genomic technologies.