The CucCAP project: leveraging applied genomics to improve disease resistance in cucurbit crops

R. Grumet, Z. Fei, A. Levi, M. Mazourek, J.D. McCreight, J. Schultheis, Y. Weng, M. Hausbeck, S. Kousik, K.S. Ling, A. Linares-Ramirez, C. McGregor, L. Quesada-Ocampo, U. Reddy, C. Smart, P. Wechter, T. Wehner, L. Wessel-Beaver, W.M. Wintermantel
The USDA-SCRI 'CucCAP' project is a collaborative effort by the US cucurbit community to develop genomic tools for the Cucurbitaceae family to facilitate introgression and pyramiding of disease resistance loci. Resource development includes genetic characterization of the National Plant Germplasm System (NPGS) plant introduction (PI) collections of watermelon (Citrullus spp.), melon (Cucumis melo), cucumber (Cucumis sativus), and squash (Cucurbita spp.). Genotyping-by-sequencing (GBS) of the collections (1000-2000 accessions/crop) provided 20,000-30,000 single nucleotide polymorphisms (SNPs) per species that are well distributed across the genomes. The SNPs were used to characterize genetic diversity, population structure, phylogenetic relationships, linkage disequilibrium, and population differentiation of the collections and perform genome wide association studies (GWAS) of horticulturally important traits. This information is currently being used to establish publicly available, re-sequenced functional panels of 300-400 accessions per crop representing >95% of the diversity present in the collections, along with key disease resistance, fruit quality, horticultural and agronomic traits. The CucCAP disease priorities for each crop were identified by the cucurbit industries and vary among crops. The participating research groups are characterizing resistances, identifying QTL, developing markers, and introgressing resistances for the different crop-disease combinations. Markers have been developed for resistances to angular leaf spot, anthracnose, downy mildew and powdery mildew in cucumber, Fusarium race 1 and 2 in watermelon, Fusarium race 1 in melon, and powdery mildew in squash. QTL identification and marker development is underway for multiple additional diseases and crops.
Grumet, R., Fei, Z., Levi, A., Mazourek, M., McCreight, J.D., Schultheis, J., Weng, Y., Hausbeck, M., Kousik, S., Ling, K.S., Linares-Ramirez, A., McGregor, C., Quesada-Ocampo, L., Reddy, U., Smart, C., Wechter, P., Wehner, T., Wessel-Beaver, L. and Wintermantel, W.M. (2020). The CucCAP project: leveraging applied genomics to improve disease resistance in cucurbit crops. Acta Hortic. 1294, 91-104
DOI: 10.17660/ActaHortic.2020.1294.12
cucumber, Citrullus, Cucumis, Cucurbita, melon, squash, pumpkin, watermelon, core collections

Acta Horticulturae