Microsatellite Fingerprinting of the USDA-ARS Tropical Agriculture Research Station Cacao (Theobroma cacao L.) Germplasm Collection

Cacao (Theobroma cacao L.) is an important cash crop in many tropical countries. Cacao accessions must be propagated vegetatively to conserve genetic integrity due to its allogamous nature and its seed recalcitrance (lack of dormancy). Therefore, cacao germplasm is usually maintained as living trees in field collections and has resulted in varying rates of misidentification and duplication. Using a high throughput genotyping system with 15 microsatellite loci, all 924 trees in the USDA-ARS Mayaguez cacao collection were fingerprinted. Nineteen accessions (12.3%) were found to have intraplant errors while 14 (9.1%) synonymous sets were identified that included replicates of 49 accessions. The average number of alleles (8.8; SE = 0.56) and gene diversity (HObs = 0.65; SE = 0.026) indicate a high allelic diversity in this collection. A distance-based cluster analysis and a Bayesian assignment test showed that the cacao accessions can be classified into four distinct clusters, with their geographical origins covering most of the cacao growing regions in the Americas. Assessment of the representative diversity of the collection led to the identification of several genetic gaps, including underrepresented genetic populations and particular traits of economic and agronomic value. The improved understanding of identities and structure in the USDA-ARS cacao collection will contribute to more efficient use of cacao in conservation and breeding.