Genetic diversity and population structure of anciently introduced Cuban cacao Theobroma cacao plants

Abstract

Cacao is widespread in eastern Cuba, but rarely grown in its central region. The origin, location and date of earliest introduction are under debate, with cacao hypothesized to have arrived in central Cuba from Central America in 1540 or in the eastern part of the island from Haiti between 1781 and 1803. Controlled introductions have taken place during recent decades, but the genetic diversity of earlier introductions has never been investigated. A representative sample of 537 Cuban cacao plants of ancient origin and 107 plants representing 10 genetic reference groups and Trinitario genotypes were fingerprinted using 15 international standard microsatellite markers. Overall, 139 alleles—9.267 alleles per locus on average—were amplified. Mean polymorphism information content, observed heterozygosity and expected heterozygosity were 0.379, 0.367 and 0.419, respectively. The Garza–Williamson index was 0.379, indicating a bottleneck in the history of Cuban cacao. Cuban plants exhibited low coefficients of membership in the 10 reference groups, with Amelonado (61.64 %) and Criollo (27.34 %) predominating, followed by Maran˜o´n (5.40 %), Iquitos (2.23 %), Contamana (1.49 %), Nanay (1.12 %) and Nacional (0.75 %). Additionally, 48.23 % of plants were an admixture of Amelonado and Criollo, i.e., of the Trinitario type. The Cuban plants were separated into two clusters, one comprising plants mainly from eastern Cuba from groups Criollo, Amelonado and Maran˜o´n, and the other mainly from central Cuba represented by plants from groups Criollo, Amelonado, Maran˜o´n, Iquitos, Contamana, Nanay and Nacional. These results should aid the design of rational conservation and utilization strategies for ancient Cuban cacao.