Ancestry and morphoagronomical traits of cacao clones from the Cuban genebank reveal the diversity and potential for breeding of national genetic resources

Cacao breeding programs relying on a wide genetic base could contribute to increase the sustainability of cacao production. In Cuba, a short list of cacao clones was endorsed for breeding and farming practices; all of them were imported from other countries and show low genetic diversity. Cacao National Genebank (CNGB) conserves plants derived from breeding experiments and from in-farm prospections, which could be considered as national genetic resources (Cuban clones). The limited characterization of these resources has hampered their use for breeding purposes. This study aimed (1) to characterize the diversity of 89 clones from CNGB on the basis of both cacao ancestry and 22 morphoagronomical descriptors and (2) to identify national genetic resources with the highest potential for breeding considering their genetic and morphoagronomical traits. Cacao ancestry analysis using SNP markers, mainly identified seven lineages in the studied clones: Amelonado, Contamana, Criollo, Iquitos, Marañón, Nacional and Nanay. Most clones were hybrids of Amelonado with another ancestry. Cuban clones were more diverse in terms of cacao ancestry than clones currently used in breeding. A wide morphoagronomical variability was observed among the 89 clones and for most traits, Cuban clones were not significantly different from the imported ones. Clones with high values in agronomical-relevant traits (e.g. seed and fruit weight-related) tended to be hybrids (Q < 0.7), while low values of these descriptors were frequently observed in plants with high membership (Q > 0.7) to certain cacao ancestries. Seven Cuban clones showed values of seed weight-related traits similar to the clones currently exploited in breeding and farming practices, but they were more diverse considering their cacao ancestries. Six clones had light or pale colored cotyledons, which has been associated to a better sensorial quality of cocoa, and most of them showed high membership to Amelonado ancestry. Cuban genetic resources of Theobroma cacao L. from CNGB show a wide diversity which could contribute to broaden the genetic base of the breeding program. Several Cuban clones showed ancestry and seed-related traits that support their use to breed new cacao varieties to increase the sustainability of cacao production.