Location: Vegetable Research
2025 Annual Report
Objectives
1. Phenotype genetic populations and germplasm and utilize genetic and genomic methodologies to identify gene loci associated with biotic and abiotic stresses, or with horticultural traits in watermelon, broccoli, and leafy Brassicas.
1.A. Evaluate and identify germplasm sources and gene loci useful for improving watermelon cultivars for resistance to the emerging virulent race 3 of Fusarium wilt.
1.B. Optimize light-emitting diode (LED) illumination spectrum for growth and development of collard plants and select genotypes rich in phytonutrients and suitable for cultivation in controlled environment agriculture (CEA) production systems.
2. Use marker assisted selection (MAS) and/or genomic selection (GS) approaches to develop and release watermelon, broccoli, and leafy Brassica germplasm with improved biotic and abiotic stress tolerance, combined with desirable horticultural traits.
2.A. Breed and release small-seeded watermelon lines with desirable fruit qualities and improved resistance to Fusarium oxysporum sp. niveum (Fon) Fon race 1 and to the common aphid-transmitted potyviruses papaya ringspot virus (PRSV) and zucchini yellow mosaic virus (ZYMV).
2.B. Use GS approach to improve Fon race 2-resistance in watermelon cultivars.
2.C. Use GS approach to improve powdery mildew-resistance in watermelon cultivars.
2.D. Use GS approach to improve heat tolerance in broccoli germplasm.
Approach
Germplasm collections will be evaluated for resistance to the emerging virulent race 3 of Fusarium wilt. Marker assisted selection (MAS) will be employed to pyramid qualitative traits of resistance to Fusarium wilt race 1 and potyviruses, while “genomic selection (GS)” approaches will be used to improve watermelon cultivars with complex traits of resistance to Fusarium wilt race 2 and powdery mildew. This project has devoted efforts to elucidate gene loci and to breed for broccoli lines with improved tolerance to high-temperature stress. As with watermelon, GS methods will be employed to uncover all or most gene loci, including those with minor or major effects in conferring heat tolerance and production of high-quality mature broccoli heads. A different objective of this project focuses on evaluating and selecting for collard genotypes suitable for cultivation in controlled environment agriculture (CEA) production systems, used as an alternative to meet the increased demand for local growing food crops. Here, collard genotypes rich in phytochemicals will be selected and bred for cultivation in CEA. Successful completion of this project objectives will contribute to the long-term improvement of disease resistance and abiotic tolerance in cucurbit and brassica crops. It will also greatly benefit seed company breeders, growers, and consumers of these important vegetable crops.
Progress Report
This project has been focusing on genetic research and breeding of watermelon, broccoli, and leafy green Brassicas for resistance to major diseases, tolerance to environmental stress, and enhanced quality or nutritional attributes to help stakeholders, including seed companies, growers, producers, and consumers. Significant progress has been made in identifying and developing new resources of resistance and incorporating disease resistance gene loci into watermelon cultivars. In addition, significant progress has been made in identifying and utilizing gene loci conferring heat tolerance and in developing and releasing heat tolerant broccoli lines. The CRIS project with 1 SY (2021-2025) successfully published 28 peer reviewed journal manuscripts related to watermelon or cucurbit crops, 2 peer reviewed journal manuscripts related to broccoli, and released two heat tolerant broccoli breeding lines (USVL156 and USVL160 inbred lines) adapted to hot summer environments of the eastern United States. ARS researchers at Charleston, North Carolina released a plant variety protection (PVP)- rootstock line “Carolina Strongback” having resistance to fusarium wilt and root-knot nematodes. The “Carolina Strongback” rootstock is highly useful for grafting watermelon cultivars and for planting in fields infested with Fusarium wilt. There has been a significant increase in demand for this rootstock in the US and throughout the world. Disease resistant watermelon and heat tolerant broccoli lines were provided to several national and international seed companies and universities through material transfer agreements (MTA). Through the Cucurbits Coordinated Agricultural Project (CucCAP2): “Harnessing Genomic Resources to Improve Disease Resistance and Disease Management in Cucurbit Crops” we have been collaborating with teams at Michigan State University, Cornell, Univ. of Wisconsin, NCSU, UGA, Univ. of Florida and UC Davis. We have conducted genomic and genetic analyses studies, and in collaboration with the bioinformatics team at the Boyce Thompson Institute (Cornell University) we constructed a super-pangenome for watermelon. This project included the sequencing and assembly of selected germplasm lines with unique qualities developed at the U.S. Vegetable Laboratory. In addition, the re-sequencing of 547 watermelon accessions, including cultivars and United States Plant Introductions (PIs) of the USDA-ARS watermelon (Citrullus spp.) germplasm collection. Using advanced genomic approaches, we were able to identify gene loci associated with soluble solids content, flesh color, fruit shape, and cold tolerance in watermelon. We identified gene loci associated with resistance to root-knot nematodes and to Fusarium wilt races 1, 2, gummy stem blight, downy mildew and powdery mildew of watermelon. We developed DNA markers for gene loci conferring resistance to Fusarium wilt races 1 and 2, and to papaya ringspot virus (PRSV) and Zucchini yellow mosaic virus (ZYMV) of watermelon. We have screened the USDA, ARS Citrullus spp. germplasm collection and identified viable sources of resistance to the emerging virulent Fon race 3 of watermelon. Using ‘genomic selection’ approach have been incorporating the Fon race 3-resistance into the genome background of watermelon cultivars. We have developed and released a self-compatible green sprouting broccoli cultivar ‘HiTest’ that yields seed with high levels of the phytonutrient Glucoraphanin which is known to have health benefits. We have been developing ornamental collard lines rich in phytonutrients and selected broccoli lines suitable for growing in CEA. All these work and new research projects are being continued in the next five-year project plan cycle (2023-2028) to provide stakeholders with genomic and genetic tools and germplasm useful for enhancing biotic and abiotic stress tolerance in vegetable crops.
As part of the CucCAP project objectives, we have completed the construction and development of a large multi-parent advanced intercross generation (MAGIC) population for watermelon and have been collaborating with seed companies in the development of the MAGIC-recombinant inbred lines (RILs). This MAGIC population (developed in collaboration with six seed companies) will be a robust germplasm source with diverse allelic combinations, useful to watermelon breeders and will provide an opportunity for exploring the Citrullus spp. genome interactions, track introgressions and chromosomal recombination as well as performing genetic studies.
In collaboration with ARS scientists at the location and the team at West Virginia State University (WVSU) we conducted a genetic study and identified gene loci associated with resistance to powdery mildew in watermelon. DNA markers are currently developed and will be used in breeding programs aiming to develop powdery mildew-resistant watermelon cultivars.
In collaboration with a team at West Virginia State University (WVSU) we conducted a genetic study and identified gene loci associated with resistance to gummy stem blight (GSB)-a major soilborne disease of watermelon. The DNA markers developed through this study should be useful in breeding programs aiming to develop watermelon cultivars with resistance to GSB.
In collaboration with a team at the Agricultural Research Organization (ARO), Israel, we submitted a grant proposal “Exploiting the hidden half- using wild accession to improve drought tolerance related root traits in cultivated watermelon.” The proposal was funded for three years (2026-2029). In collaboration with the ARO team we have been screening and selecting watermelon germplasm with drought resistance. Using digital technology (WinRhizo) we were able to identify germplasm with an extensive root system. Additionally, we identified gene loci associated with extensive root system trait. The germplasm sources and gene loci identified in this study will be useful for enhancing watermelon cultivars for drought stress conditions.
Accomplishments
1. ‘Genomic selection’ approach for Improving watermelon cultivars with polygenic disease resistance traits (complex traits). ARS researchers at Charleston, North Carolina have introduced and tested a ‘genomic selection’ approach for Improving watermelon cultivars with polygenic disease resistance traits (complex traits) controlled by many small-effect gene loci and are difficult to incorporate them from wild into watermelon cultivars using the conventional approach of marker assisted selection (MAS). Our study (Biswas et al. 2025) received great attention from seed company breeders interested in improving disease resistances in watermelon cultivars using genomic selection approach.
Review Publications
Natarajan, P., Rathnagiri, A., Rivera-Burgos, L., Lopez-Ortiz, C., Nimmakayala, P., Sari, N., Wehner, T.T., Levi, A., Reddy, U. 2024. Exploring the genomic landscape of gummy stem blight resistance in watermelon through QTL-Seq. Plant Biology. 24:1129. https://doi.org/10.1186/s12870-024-05839-2.
Kumar, R., Chanda, B., Mandal, M., Ikerd, J.L., Branham, S., Wechter, W., Wadl, P.A., Levi, A., Shaik, A., Reddy, U., Karthikeyan, R., Kousik, C.S. 2025. QTL mapping and KASP Marker Development for Powdery Mildew Resistance in Watermelon. Plant Disease. https://doi.org/10.1094/PDIS-04-25-0737-RE.
Ganaparthi, E., Wechter, W., Katawczik, M.L., Levi, A., Branham, S. 2025. Genome-wide association mapping and genomic predictions for bacterial fruit blotch resistance in the USDA Citrullus amarus collection. Plant Disease. https://doi.org/10.1094/PDIS-12-24-2665-RE.
Chattha, M.S., Ward, B.K., Kousik, C.S., Levi, A., Farmaha, B.S., Marshall, M.S., Bridges, W.C., Cutulle, M.A. 2025. Watermelon genotypes and weed response to chicken manure and molasses-induced anaerobic soil dis-infestation in high tunnels. Agronomy. https://doi.org/10.3390/agronomy15030705.
Branham, S., Ganaparthi, V., Wechter, W., Park, Y., Wehner, T., Davis, A., Tetteh, A.Y., Massey, L.M., Hammar, S., Grumet, R., Kousik, C.S., Levi, A. 2025. Extreme-Phenotype Genome-Wide Association Study (XP-GWAS) and Marker Development for Powdery Mildew Race 2W Tolerance in the USDA Citrullus Germplasm Collection. Scientific Reports. 15, Article number: 4781 (2025). https://doi.org/10.1038/s41598-025-89445-8.
Biswas, A., Wechter, W., Ganaparthi, V., Jarquin, D., Kousik, C.S., Branham, S., Levi, A. 2025. Comparative genomic prediction of resistance to fusarium wilt (Fusarium oxysporum f. sp. niveum race 2) in watermelon: insights from parametric and machine learning approaches. Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-024-04813-8.
Natarajan, P., Rathnagiri, A., Rivera-Burgos, L., Lopez-Ortiz, C., Nimmakayala, P., Sari, N., Wehner, T.C., Levi, A., Reddy, U. 2024. Elucidating the Genetic Architecture of Gummy Stem Blight Resistance in Watermelon via QTL-Seq and Bulked Segregant Analysis. BMC Plant Biology. 24:1129 (2024). https://doi.org/10.1186/s12870-024-05839-2.