Population Structure and Genetic Diversity of the Trinitario Cacao ( Theobroma cacao L.) from Trinidad and Tobago

Population structure of the old Trinitario cacao (Theobroma cacao L.) in Trinidad was evaluated from the 35-microsatellite multilocus profi le of 32 relict clones from abandoned cocoa estates in Trinidad (TRD) and 88 Imperial College selections (ICS) clones conserved in the International Cocoa Genebank, Trinidad. Ancestry was derived by comparison to 34 representative genotypes of Criollo, Central American, and Lower and Upper Amazon origin. The 154 individuals separated into four populations in this study, labeled Population 1—Upper Amazon; Population 2—Ecuadorian; Population 3—Lower Amazon; and Population 4—Trinitario. Over 90% of the individuals demonstrated 70 to 99% membership to their respective populations. The ICS and TRD clones formed a genetically homogenous group, 84% of which clustered in Population 4 with clones of pure Criollo descent. Another 10% clustered in Population 1 containing clones of Upper Amazon descent. The cacao population of Trinidad is genetically different from clones of Ecuadorian and Lower Amazon descent, Populations 2 and 3, respectively. The 10 most discriminating loci for each population were different as shown by polymorphism information content values for each of the 35 microsatellite loci. This is the fi rst report to provide a strong genetic basis for the industry fl avor distinction of Trinitario and Ecuadorian cacaos. These fi ndings signifi cantly impact germplasm fi ngerprinting and curatorship and maintenance of industry fl avor classes while breeding for disease resistance in cacao.