The USDA-SCRI CucCAP projects - Building genomic, breeding and disease management tools for cucurbit crops

Authors: GRUMET, REBECCA - Michigan State University; FEI, ZHANGJUN - Cornell University; Levi, Amnon; MAZOUREK, MICHAEL - Cornell University; McCreight, James; QUESADA-OCAMPO, LINA - North Carolina State University; Weng, Yiqun; BRANHAM, SANDRA - Clemson University; HAUSBECK, MARY - Michigan State University; KEINATH, ANTHONY - Clemson University; Wintermantel, William; Kousik, Chandrasekar; Ling, Kai Shu; KNUTH, MELINDA - North Carolina State University; RAMIREZ, ANGELA - University Of Puerto Rico; MCGREGOR, CECILIA - University Of Georgia; MERU, GEOFFREY - University Of Florida; PALMA, MARCO - Texas A&M University; REDDY, UMESH - West Virginia State University; RIBERA, LOUIS - Texas A&M University; SCHULTHEIS, JONATHAN - North Carolina State University; SMART, CHRISTINE - Cornell University; TREGEAGLE, DANIE - North Carolina State University; WECHTER, WILLIAM - Clemson University; WEHNER, TOOD - North Carolina State University; WESSEL-BEAVER, LINDA - University Of Puerto Rico; WU, SHAN - Cornell University

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/21/2026
Publication Date: 2/18/2026
Citation: Grumet, R., Fei, Z., Levi, A., Mazourek, M., Mccreight, J.D., Quesada-Ocampo, L., Weng, Y., Branham, S., Hausbeck, M., Keinath, A., Wintermantel, W.M., Kousik, C.S., Ling, K., Knuth, M., Ramirez, A.L., Mcgregor, C., Meru, G., Palma, M., Reddy, U., Ribera, L., Schultheis, J., Smart, C., Tregeagle, D., Wechter, W., Wehner, T., Wessel-Beaver, L., Wu, S. 2026. The USDA-SCRI CucCAP projects - Building genomic, breeding and disease management tools for cucurbit crops. Journal of the American Society for Horticultural Science. https://doi.org/10.21273/JASHS05562-25.
DOI: https://doi.org/10.21273/JASHS05562-25

Interpretive Summary: Cucurbit crops, including watermelon, melon, cucumber, squash, and pumpkin are of high nutritional value and widely cultivated across the United States. National production totals 109 million metric tons on 229,000 hectares, with a farm gate value of $1.43 billion. However, diseases caused by fungal, bacterial, and viral pathogens remain the primary challenge to U.S. cucurbit production, reducing both yield and quality. To address these challenges, USDA-ARS and university scientists launched two USDA-NIFA-SCRI funded projects: CucCAP1 (2015–2020): Leveraging applied genomics to improve disease resistance in cucurbit crops; CucCAP2 (2020–2025): Harnessing genomic resources for disease resistance and management in cucurbit crops – bringing the tools to the field. Over ten years, these coordinated projects brought together ARS and University scientists, experts in genomics, genetics, breeding, plant pathology, integrated disease management, and economics. Together, they achieved significant outcomes, including 1) development of extensive genomic resources, including cucurbit pan-genomes, 2) genetic characterization of U.S. National Plant Germplasm System (NPGS) cucurbit collections, 3) Identification of novel disease resistance sources and resistance gene loci, 4) development of molecular markers for resistance gene loci and release of 20+ breeding lines with disease resistance, 5) development of detection methodologies and large-scale disease monitoring, 6) establishment of the CucCAP web portal (cuccap.org) and broad extension and outreach. Together, CucCAP1 and CucCAP2 advanced cucurbit disease resistance research and delivered practical tools to breeders, pathologists, and growers, strengthening the resilience and sustainability of cucurbit production in the U.S.

Technical Abstract: Cucurbit crops including watermelon (Citrullus lanatus), melon (Cucumis melo), cucumber (Cucumis sativus), squash and pumpkin (Cucurbita spp.) make important nutritional and flavorful contributions to the human diet. The primary challenge for U.S. cucurbit production is disease caused by numerous fungal, oomycete, bacterial and viral pathogens that reduce crop yield and quality and engender costly control measures. The USDA-NIFA-SCRI funded CucCAP projects, “CucCAP: Leveraging applied genomics to improve disease resistance in cucurbit crops” and “CucCAP2: Harnessing genomic resources for disease resistance and management in cucurbit crops – bringing the tools to the field”, brought together members of the cucurbit community across the country with expertise in genomics, bioinformatics, breeding, genetics, plant pathology, integrated disease management, and economics to address these disease challenges. Collectively, the project produced extensive genomic resources and bioinformatic tools including genome assemblies and pan-genomes for cucurbit species; genetically characterized the U.S. National Plant Germplasm System (NPGS) collections for watermelon, melon, cucumber and squash; developed deeply re-sequenced core populations for these crops; identified single nucleotide (SNP) and structural variants; and developed the Cucurbit Genomics database (CuGenDB, http://cucurbitgenomics.org/v2/). New sources of resistance were identified for sixteen cucurbit crop/disease combinations; QTLs were mapped and molecular markers developed for 24 combinations; and more than 20 breeding lines with resistances to various diseases were released. New detection methodology was developed for several pathogens; extensive disease monitoring and multi-location disease management trials and resistance tests were performed; a centralized web portal (https://cuccap.org) was developed to provide cucurbit disease information in English and Spanish; and disease management information was shared with growers, commodity groups and industry organizations through publications and presentations at conferences, field days, and extension schools delivered at more than 100 venues in 24 states. The CucCAP projects were carried out through joint efforts among 26 university and USDA co-investigators and their research groups along with valued input and assistance from NPGS cucurbit crop curators, seed industry collaborators, cucurbit growers, external evaluators, and international collaborators. In addition to the specific genomic, breeding, and disease management goals, the CucCAP projects have had broader impacts including use of the new genomic tools to provide insights into cucurbit biology, synergistic effects resulting from a more cohesive cucurbit community, and scientific training of a cadre of students and post-doctoral researchers.