The USDA-SCRI CucCAP Projects: Building Genomic, Breeding and Disease Management Tools for Cucurbit Crops

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 US 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 National Institute of Food and Agriculture–Specialty Crop Research Initiative funded CucCAP (Cucurbit Coordinated Agricultural Project) 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 projects produced extensive genomic resources and bioinformatic tools including genome assemblies and pan-genomes for cucurbit species; genetically characterized the full US National Plant Germplasm System (NPGS) collections for watermelon, melon, cucumber, and squash; developed deeply resequenced core populations for these crops; identified single nucleotide polymorphism and structural variants; and developed the Cucurbit Genomics database (CuGenDB, http://cucurbitgenomics.org/v2/ ). New sources of resistance were identified for 17 cucurbit crop/disease combinations; quantitative trait loci were mapped and molecular markers developed for 24 combinations; and 15 breeding lines with resistances to various diseases were released. New detection methodology was developed for several pathogens; extensive disease monitoring and multilocation 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 coinvestigators 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 outputs, 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 postdoctoral researchers.