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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Publications at this Location » Publication #426507
Research Project: Genotypic Characterization of Genetic Resources for Cacao, Coffee, and Other Tropical Perennial Crops Economically Important to the United States

Location: Sustainable Perennial Crops Laboratory

Title: Assessing genetic redundancy and diversity in Colombian cacao germplasm collections using SNP fingerprinting

Author
item OSORIO-GUARIN, JIME - Colombian Corporation Of Agriculture And Livestock- Agrosavia
item BERDUGO-CELY, JHON - Colombian Corporation Of Agriculture And Livestock- Agrosavia
item GARZON-MARTINEZ, GINA - Colombian Corporation Of Agriculture And Livestock- Agrosavia
item BAEZ-DAZA, ELIANA - Colombian Corporation Of Agriculture And Livestock- Agrosavia
item Park, Sunchung
item Meinhardt, Lyndel
item Zhang, Dapeng
item YOCKTENG, ROXANA - Colombian Corporation Of Agriculture And Livestock- Agrosavia

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2025
Publication Date: 7/4/2025
Citation: Osorio-Guarin, J.A., Berdugo-Cely, J.A., Garzon-Martinez, G.A., Baez-Daza, E.Y., Park, S., Meinhardt, L.W., Zhang, D., Yockteng, R. 2025. Assessing genetic redundancy and diversity in Colombian cacao germplasm collections using SNP fingerprinting. Frontiers in Plant Science. https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2025.1632888/full.
DOI: https://doi.org/10.3389/fpls.2025.1632888

Interpretive Summary: Cacao genetic resources are the foundation of sustainable chocolate production. Cacao researchers depend on these genetic resources to develop new varieties that produce more beans, have great flavor, and can survive tough environmental conditions. In this study, a team of Colombian and USDA-ARS researchers investigated the level of genetic redundancy or duplication (plants with the same pedigree) in two living cacao collections maintained at Palmira and La Suiza, Colombia. The research team analyzed the DNA fingerprints of 5,182 cacao trees and detected a significant number of mislabeled plants (12.4%) and a high level of genetic redundancy (53.1%). This research highlights the importance of keeping cacao collections well-organized and accurately labeled, with the assistance of DNA fingerprinting technology. The resulting information will be used by cacao researchers to improve the efficiency in management of cacao collections and develop new varieties that produce high-yields and desirable quality attributes.

Technical Abstract: Cacao germplasm is the cornerstone of sustainable cacao production, underpinning efforts to develop high-yielding, quality-rich, and climate-resilient varieties. This study aimed to evaluate the genetic redundancy and diversity of cacao germplasm banks maintained under field conditions at the Palmira and La Suiza research centers of the Colombian Corporation for Agricultural Research (AGROSAVIA). We genotyped 5,182 cacao trees from these two collections using single nucleotide polymorphism (SNP) markers. After removing missing data, 4,653 trees remained and were used for the analysis. Our analyses revealed that both collections exhibit similar genetic diversity patterns, allowing the Palmira collection to serve as a backup for the La Suiza collection. However, a substantial rate of intra-plot mislabeling (12.4%) and high genetic redundancy (53.1%) was detected, likely due to errors in collection, introduction, pre-planting labeling, and the use of rootstocks. The study demonstrates that it is crucial to generate accurate scientific information to maintain well-classified cacao collections with minimal genetic redundancy, thereby improving efficiency of cacao germplasm conservation. The improved accuracy and efficiency will also enhance the use of these germplasm to develop new cacao varieties with desirable agronomic traits and quality attributes.