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

item Boza, Edward
item Irish, Brian
item Meerow, Alan
item RODRIGUEZ, O - Dominican Institute For Agricultural And Forestry Research (IDIAF)
item VENTURA-LOPEZ, MARISOL - Dominican Institute For Agricultural And Forestry Research (IDIAF)
item GOMEZ, JAIME - Dominican Institute For Agricultural And Forestry Research
item Moore, John
item Zhang, Dapeng
item MOTAMAYOR, JUAN - M & M Mars Company - United States
item Schnell Ii, Raymond

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2012
Publication Date: 7/7/2012
Citation: Boza, E.J., Irish, B.M., Meerow, A.W., Rodriguez, O.A., Ventura-Lopez, M., Gomez, J.A., Moore, J.M., Zhang, D., Motamayor, J.C., Schnell Ii, R.J. 2012. Genetic diversity, population structure, conservation and utilization of Theobroma cacao L., genetic resources in the Dominican Republic. Tree Genetics and Genomes. Available:

Interpretive Summary: Cacao germplasm collections are known to have high levels of misidentified clones and this has lead to many problems when using germplasm accessions as parents in cacao breeding programs. In this study we used 14 microsatellite molecular markers to genetically fingerprint each of 803 trees in the germplasm collection maintained by the Instituto Dominicano de Investigaciones Agropecuarias y Forestales (IDIAF) at their research station in Mata Larga, Dominican Republic. We also genetically characterized 152 trees from Local Farmer Selections (LFS) developed by the Confederacion Nacional de Cacaocultuores Donimicanos, Inc. (CONACADO), Mata Larga Dominican Republic and by IDIAP. The 803 trees represent 59 genetic accessions that were reported to be in the collection. Using the 14 molecular markers 40.9% of the germplasm accessions were found to be incorrectly labeled and this percentage is consistent with other studies conducted to characterize clonal cacao germplasm collections. Among the 42 correctly identified accessions a population structure analysis using known genetic structure groups confirmed the correct identification. Among the LFS the 152 trees represent 110 selections which translates into a 17.4% error rate in their propagation. Comparing the 110 LFS to the known population structure groups identified most as having high levels of Amelonado, Criollo, Iquitos and Nacional lineages. The Dominican Republic cacao has a niche production for organic cacao and excellent flavor characteristics. These genetic backgrounds are often associated with excellent organoleptic qualities and fine floral aroma. This is the first study using molecular markers to characterize the Dominican Republic germplasm collections and LFS and the results are being applied in the current breeding program to select more productive cultivars for the Dominican Republic cacao industry.

Technical Abstract: Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic, which ranks 11th in the world and number one in organic cacao exports. In an effort to identify propagation mistakes, and estimate genetic diversity and population structure in cacao germplasm accessions and local farmer selections (LFS), 14 SSR markers were employed to fingerprint 955 trees (803 germplasm accessions and 152 LFS trees). Comparisons of repeat plants across plots revealed a significant misidentification rate estimated to be 40.9% for germplasm accessions and 17.4% for LFS. Fifteen synonymous groups (SYN GROUPs) were resolved in the germplasm collection and 13 SYN GROUPs within the 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 high levels of variation were detected among the LFS where a total of 113 alleles amplified with a mean of 8.07 alleles per locus and PIC of 0.57. The observed heterozygozity (Hobs) was 0.67 for the germplasm collection and 0.60 for LFS, representing a high allelic diversity in both these populations. SSR marker mTcCir37 was the most informative locus, amplifying 12 alleles in the germplasm accessions and 11 in the LFS, while mTcCir1was the least informative amplifying four and three alleles in the germplasm accessions and LFS, respectively. Based on population structure analysis and comparison to ten recently described cacao genetic groups, a majority (43.9% for germplasm accessions, 72.1% for LFS) showed a predominant Amelonado ancestry. Criollo ancestry was present in 7.6% and 9.5% for germplasm and LFS, respectively. Criollo is associated with the white or light purple seeded trait and organoleptic properties such as reduced bitterness, fine aroma and higher fat content. The Contamana, Nacional, and Iquitos backgrounds were also observed in both populations, but the Curaray background was only seen in the germplasm accessions. No Purús or Guiana ancestry was found in either of the populations. Many of the farmer selections had mixed genetic ancestry of hybrid nature i.e. Trinitarios. Overall, this research identified significant genetic diversity among the germplasm accessions, which could be exploited in the Dominican Republic breeding and selection programs.