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Genetic diversity, conservation, and utilization of Theobroma cacao L.: genetic resources in the Dominican Republic

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Abstract

Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic, which ranks 11th in the world for cacao exports. To estimate genetic diversity, determine genetic identity, and identify any labeling errors, 14 SSR markers were employed to fingerprint 955 trees among cacao germplasm accessions and local farmer selections (LFS). Comparisons of homonymous plants across plots revealed a significant misidentification rate estimated to be 40.9 % for germplasm accessions and 17.4 % for LFS. The 14 SSRs amplified a total of 117 alleles with a mean allelic richness of 8.36 alleles per locus and average polymorphism information content (PIC) value of 0.67 for the germplasm collection. Similar levels of variation were detected among the LFS where a total of 113 alleles were amplified with a mean of 8.07 alleles per locus and PIC of 0.57. The observed heterozygosity (Hobs) was 0.67 for the germplasm collection and 0.60 for LFS. Based on population structure analysis 43.9 % of the germplasm accessions and 72.1 % of the LFS are predominantly of the Amelonado ancestry. Among these Amelonado, 51.7 % for the germplasm collection and 50.6 % for LFS corresponded to Trinitario hybrid lineage. Criollo ancestry was found in 7.6 and 9.5 % of the germplasm accessions and LFS, respectively. The Contamana, Nacional, and Iquitos backgrounds were also observed in both populations, but the Curaray background was only detected in the germplasm accessions. No Purús or Guiana ancestry was found in either of the populations. Overall, significant genetic diversity, which could be exploited in the Dominican Republic breeding and selection programs, was identified among the germplasm accessions and LFS.

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Acknowledgments

The authors would like to thank Land O’Lakes, Inc., International Development, for their collaborative efforts and partial financial support through the USAID-funded Cooperative Development Program (CDP). We also would like to thank MARS, Inc., for funding Trust Agreement #58-6631-6-123: Genetic Improvement of Theobroma cacao, and the USDA-ARS SHRS cacao program for their partial financial support. We would like to extend our appreciation to Drs. Belinda Martineau and Tomás Ayala-Silva for their constructive comments and suggestions to the manuscript.

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Authors and Affiliations

  1. C/O USDA-ARS Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL, 33158, USA

    Edward J. Boza, Alan W. Meerow, Cecile L. Tondo, J. Michael Moore, Juan Carlos Motamayor & Raymond J. Schnell

  2. USDA-ARS Tropical Agriculture Research Station, 2200 P. A. Campos Ave., Suite 201, Mayagüez, PR, 00680, USA

    Brian M. Irish

  3. Instituto Dominicano de Investigaciones Agropecuarias y Forestales (IDIAF), Mata Larga, San Francisco de Macorís, Dominican Republic

    Orlando A. Rodríguez & Marisol Ventura-López

  4. Confederación Nacional de Cacaocultores Dominicanos, Inc. (CONACADO), Calle Altagracia Saviñon No. 11, Los Prados, Santo Domingo, Dominican Republic

    Jaime A. Gómez

  5. USDA-ARS Sustainable Perennial Crops Laboratory, 10300 Baltimore Avenue, Bldg 001 BARC-West, Beltsville, MD, 20705, USA

    Dapeng Zhang

  6. MARS, Inc., Hackettstown, NJ, USA

    Juan Carlos Motamayor

  7. MARS, Inc., Elizabethtown, PA, USA

    Raymond J. Schnell

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  1. Edward J. Boza
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10722_2012_9860_MOESM2_ESM.tif

Population structure and nine ancestry groups within the cacao (Theobroma cacao L.) germplasm collection from IDIAF Mata Larga research station, Dominican Republic, produced using Structure v2.3.3. Each individual vertical line represents a genotype. Admixed individuals are denoted with multiple colors representing the ancestry groups (see color key). Note: Lowercase letters (a, b, c, or d) indicate an accession had more than one multi-locus genotype (MLG); §misidentified genotypes; §§accessions for which no reference genetic profiles were available; §§§SYN GROUPs including members without reference genotypes, true-to-type, or misidentified members; accession names with no symbol are true-to-type. (TIFF 105 kb)

10722_2012_9860_MOESM3_ESM.tif

Population structure and seven ancestry groups within the Dominican Republic cacao (Theobroma cacao L.) local farmer selections (LFS) produced using Structure v2.3.3. Each individual vertical line represents a genotype. Admixed individuals are denoted with multiple colors representing the ancestry groups (see color key). Note: Lowercase letters (a or b) means accession had more than one multi-locus genotype (MLG). (TIFF 96 kb)

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Boza, E.J., Irish, B.M., Meerow, A.W. et al. Genetic diversity, conservation, and utilization of Theobroma cacao L.: genetic resources in the Dominican Republic. Genet Resour Crop Evol 60, 605–619 (2013). https://doi.org/10.1007/s10722-012-9860-4

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