Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Publications at this Location » Publication #334234

Research Project: Genetic Diversity Assessment of Cacao and Other Tropical Tree Crop Genetic Resources

Location: Sustainable Perennial Crops Laboratory

Title: Assessing hidden parentage and genetic integrity of the “United Fruit Clones” of cacao (Theobroma cacao) from Costa Rica using SNP markers

Author
item MATA, ALLLAN - Catie Tropical Agricultural Research
item ARCINIEGAS, ADRIANA - Catie Tropical Agricultural Research
item PHILLIPS, WILBERTH - Catie Tropical Agricultural Research
item Meinhardt, Lyndel
item Mischke, Barbara
item Zhang, Dapeng

Submitted to: Breeding Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/14/2018
Publication Date: 12/1/2018
Citation: Mata, A., Arciniegas, A.L., Phillips, W.M., Meinhardt, L.W., Mischke, B.S., Zhang, D. 2018. Assessing hidden parentage and genetic integrity of the “United Fruit Clones” of cacao (Theobroma cacao) from Costa Rica using SNP markers. Breeding Science. 68:545-553.

Interpretive Summary: Cacao (Theobroma cacao L.) is a tropical rainforest tree that is the source of cocoa powder and butter used in the confectionary industry. The International cacao germplasm collection in CATIE contains nearly 1,200 accessions of cacao, mainly from the center of genetic diversity of this species. Among these accessions, the ‘United Fruit’ (UF) clones were developed by the United Fruit Company in Costa Rica, and they represent one of the earliest groups of improved cacao germplasm in the world. Some of these UF clones have been used as key progenitors for breeding resistance/tolerance to Frosty Pod and Black Pod diseases in the Americas. Accurate information on the identity and background of these clones is important for their effective use in breeding. We analyzed their DNA fingerprints based on SNPs and verified their integrity. Our results showed that approximately one third of the UF clones are duplicates and thus can be eliminated. Our study shows that a small set of polymorphic SNP markers can provide a robust and accurate result for cacao genotype identification. This protocol can be applied for large-scale genotyping of cacao as well as for many other crops. The UF clones are composed of Trinitario, ancient Nacional and hybrids between ancient Nacional and Amelonado. This result filled the information gap about the UF clones thus will be use by scientists and extension specialists to improve the management of cacao genetic resources.

Technical Abstract: Cacao (Theobroma cacao L.), the source of cocoa powder and cocoa butter used for chocolate, originated in the rainforests of South America. The International cacao germplasm collection in CATIE contains nearly 1,200 accessions of cacao, mainly from the center of genetic diversity of this species. Among these accessions, there are several groups of unique breeding lines which are important for supporting cacao breeding worldwide. The ‘United Fruit’ clones were developed by the United Fruit Company in Costa Rica, representing one of the earliest groups of improved cacao germplasm in the world. Some of these UF clones have been used as key progenitors for breeding resistance/tolerance to Frosty Pod and Black Pod diseases in the Americas. However their utilization in Asia and Africa has been minimal, partially due to the lack of information about their genetic background. The objective of this program is to assess the genetic integrity and clarify genetic background of this group of germplasm. Using Single Nucleotide Polymorphism (SNP) markers, we verified the true-to-type identity of UF clones in the CATIE cacao collection and analyzed their population memberships using maximum-likelihood-based approaches. Three duplicate groups, representing approximately 30% of the UF clones, were identified. Both distance and model-based clustering methods showed that the UF clones were mainly composed of Trinitario, ancient Nacional and hybrids between ancient Nacional and Amelonado. This result filled the information gap about the UF clones thus will improve their utilization for cacao breeding.