The Genetic Identity of Theobroma cacao L. CCN-51

Cacao (Theobroma cacao L.) is an important cash crop in several growing regions of the world and particularly for small cacao farmers.  Cacao production in the Americas constitutes ~13.0% of global production.  Ecuador is among the higher producers in South America and its cacao beans are well known for fine flavors, aroma, and fat content.  CCN-51 is one of the most planted varieties in Ecuador; its pedigree is complex and sometimes mistaken for the Nacional type.  Seventy simple sequence repeat (SSR) loci were used to determine the genetic identity of CCN-51; in which 80% (56) were heterozygous and 20% (14) were homozygous.  This finding of high heterozygocity for CCN-51 is not consistent with that of a Nacional type clone.  No Nacional specific alleles were found.  Comparison of agronomic characteristics between CCN-51 and several Nacional clones indicated significant differences in cacao dry bean weight, yield potential, production efficiency, healthy pods, and witches' broom disease reaction.  Additionally, physical, chemical, and organoleptic characteristics suggest that CCN-51 is different from those of Nacional lineage.  Based on population structure analysis, the predominant ancestries for CCN-51 are Iquitos (45.4%), Criollo (22.2%), and Amelonado (21.5%).  Moreover, results of parentage and phylogenetic analyses using neighbor joining and unweighted pair group method with arithmetic mean (UPGMA) yielding high bootstrap values strongly support the relatedness of CCN-51 with Iquitos, Criollo and Amelonado.  CCN-51 constitutes a valuable genetic resource that is currently used not only in its country of origin, but also in many other national breeding and selection programs worldwide.