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Genetic diversity of naturalized cacao (Theobroma cacao L.) in Puerto Rico

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Abstract

Identification of genetically diverse cacao with disease resistance, high productivity, and desirable organoleptic traits is vitally important to the agricultural crop’s long-term sustainability. Environmental changes, pests, and diseases as well as nation’s sovereign property rights have led to a decrease in accessibility and exchange of germplasm of interest. Having been introduced during colonial times, naturalized cacao in Puerto Rico could serve as an unexplored source of genetic diversity in improvement programs. An island-wide survey was carried out to identify naturalized trees and to determine their genetic associations to reference cacao accessions. Samples were genotyped with Expressed Sequence Tag-derived single nucleotide polymorphism (SNP) markers. Principal coordinate, cluster, and population structure analysis using the genotype data for both local and reference samples assigned individuals into five distinct genetic backgrounds: Criollo, Trinitario, Amelonado, Upper Amazon Forastero (UAF), and Nacional. Puerto Rican cacao fit into four (Criollo, Trinitario, Amelonado and UAF) of the five genetic backgrounds, being mainly composed of individuals of Criollo ancestry. Based on historical evidence, cacao of Criollo background was probably brought to Puerto Rico from Venezuela and/or Central America during colonial times. Trinitario, Amelonado, and UAF genetic backgrounds are most likely products of more modern introductions. Genotyping cacao in Puerto Rico provides information on the history and possible origin of the naturalized trees on the island. In addition, the assessment has allowed the targeting of material for incorporation and long-term conservation filling gaps in the existing collection and providing new germplasm to be evaluated for agronomic performance.

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Notes

  1. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.

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Acknowledgments

The authors thank Chocolove Inc., a Boulder, Colorado-based Chocolate company, for providing funding to support research conducted and for continued efforts in cacao conservation and use. In addition, the authors thank Drs. David Kuhn, Timothy Porch, and Chris Richards for their editorial comments. Lastly, authors thank the general public and all of the farmers (especially Mr. Juan Echevarria) who were instrumental in identifying cacao trees thought out the island and helped secure leaf and pod samples.

Data archiving statement

Expressed sequence tags which were used for developing the SNP markers have previously been deposited by Argout et al. (2008, 2011) into the European Nucleotide Archive (ENA) database under accession numbers CU469588 to CU633156. The current research does not plan on submitting any de novo sequence information to be accessioned into publicly available databases. However, a full list of cacao tree accessions collected and incorporated into the USDA-ARS TARS germplasm collection will be accessioned and their associated information loaded into the Germplasm Resources Information Network (GRIN) Global database and the crop specific International Cacao Germplasm Database (ICGD) http://www.icgd.reading.ac.uk/. In addition, a full list of accession numbers for sampled cacao trees is included as supplemental material in this manuscript.

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Authors and Affiliations

  1. USDA-ARS Tropical Agriculture Research Station, 2200 Pedro Albizu Campos Ave., Mayaguez, Puerto Rico

    S . Cosme, H. E. Cuevas & B. M. Irish

  2. Department of Biology, University of Puerto Rico at Mayaguez, Carr. 108, Barrio Miradero Km 1.3, Mayaguez, Puerto Rico

    S . Cosme & T. K. Oleksyk

  3. USDA-ARS Sustainable Perennial Crops Laboratory, 1300 Baltimore Ave., Bldg. 001, Rm. 223, BARC-West, Beltsville, MD, USA

    D. Zhang

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  1. S . Cosme
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  2. H. E. Cuevas
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Correspondence to B. M. Irish.

Additional information

Communicated by D. Grattapaglia

Electronic supplementary material

Supplemental Fig. 1.

Detection of the optimal number of clusters (the most likely value of K) inferred by the STRUCTURE software and set ΔK = mean (|L″(K)|)/sd (L(K)) as a function of K. ΔK was generated by the STRUCTURE HARVESTER, and is based on the approach of (Evanno et al. 2005). (GIF 16 kb)

High-resolution image (TIFF 190 kb)

Supplemental Fig. 2.

Radial dendrogram depicting relationships among and between Puerto Rican (90) cacao (Theobroma cacao L.) samples and reference samples (100). The blue labels represent synonymous groups (SYN 1-11; Table 1) within Puerto Rican cacao samples. Red labels are possible errors in reference samples. (GIF 114 kb)

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Supplementary Table 1

(DOCX 69.2 kb)

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Cosme, S..., Cuevas, H.E., Zhang, D. et al. Genetic diversity of naturalized cacao (Theobroma cacao L.) in Puerto Rico. Tree Genetics & Genomes 12, 88 (2016). https://doi.org/10.1007/s11295-016-1045-4

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  • DOI: https://doi.org/10.1007/s11295-016-1045-4

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