Cosme-Reyes, Stephanie M.

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    Genetic diversity assessment of naturalized cacao (Theobroma cacao L.) in Puerto Rico using single nucleotide polymorphisms
    (2014) Cosme-Reyes, Stephanie M.; Oleksyk, Taras K.; College of Arts and Sciences - Sciences; Siritunga, Dimuth; Martínez-Cruzado, Juan Carlos; Irish, Brian M.; Department of Biology; Wessel Beaver, Linda
    Cacao (Theobroma cacao L.) is an important tropical perennial crop on which the multimillion dollar chocolate industry is based. Identification of genetically diverse cacao with disease resistance, high productivity and desirable organoleptic traits is critically important for the sustainability of this crop. Environmental changes, pests and diseases as well as sovereign property rights have lead to a decrease in accessibility and exchange of germplasm of interest. Naturalized cacao in Puerto Rico could be a valuable, unexplored source of genetic diversity in crop selection and improvement programs. An island-wide survey was carried out to indentify naturalized cacao trees and collect leaf samples. Efforts allowed to survey 32 municipalities and collect a total of 180 samples. Single nucleotide polymorphism (SNP) genotyping was employed to assess local genetic diversity of naturalized T. cacao. Genetic profiles generated for the sampled cacao in Puerto Rico were compared to known reference accessions. A total of 87 EST- derived SNP markers were successfully amplified (≥90% allele calls) for 145 samples. When reference samples were included, genotype data analysis using Structure software assigned individuals into five distinct genetic backgrounds: Criollo, Trinitario, Amelonado, Upper Amazon Forastero (UAF) and Nacional. Distance based PCoA and cluster analysis results generally agreed with Structure findings, identifying the same five genetic backgrounds. Puerto Rican cacao samples fit into four of the five genetic backgrounds with no local samples belonging to the Nacional cluster. Naturalized Puerto Rican cacao was found to be mainly composed of Criollo ancestry individuals (71 out 180 total samples). Criollo background cacao was probably introduced from Venezuela and/or Central America during Spanish colonial times. Trinitario, Amelonado and UAF genetic backgrounds are most likely products of modern or more recent introductions. Fingerprinting of naturalized cacao in Puerto Rico has allowed targeting of material for germplasm incorporation and long term conservation as well as to fill gaps in existing germplasm collections. The assessment also provides knowledge on the available resources for the conservation and/or utilization of cacao germplasm in Puerto Rico.