Cucurbita moschata (Duchesne ex Lam.) Duchesne ex Poir. is an important crop in tropical areas. In Spain, the cultivation of this species is mainly based on landraces maintained for centuries. The Center for Conservation and Breeding of Agricultural Diversity (COMAV) maintains a germplasm collection with about 250 C. moschata landraces, primarily from the Canary Islands and the Spanish peninsula, including some accessions from Central and South America. The morphological characterization of 47 accessions showed considerable variability, comparable to that found in different C. moschata centers of diversity. Molecular analysis using AFLP (amplified fragment length polymorphism) markers, which analyze neutral genetic diversity, and SRAP (sequence-related amplified polymorphism) markers, which preferentially amplify gene regions, showed a genetic diversity concordant with the morphological variability. With both markers, the accessions clustered according to geographical origin: Central America, South America, and Spain, suggesting the existence of two independent domestications in both American areas, and/or introgressions from related species. In the principal coordinate analysis (PCoA), the Central and South American accessions grouped together by AFLPs, separately from the Spanish ones, while with SRAP the South American accessions grouped separately from the other accessions. This could be due to the different information provided by each marker system. The SRAP results agree with the more primitive traits showed by the South American landraces. In addition, the accessions from the Canary Islands grouped separately from those from the Spanish peninsula. This divergence could be due to an earlier adaptation of C. moschata to the tropical climate of the islands, together with a differential germplasm introduction from America.
