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United States Department of Agriculture

Agricultural Research Service

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

Location: Sustainable Perennial Crops

Title: Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers

Authors
item Ji, Kun -
item Takrama, Jemmy -
item Meinhardt, Lyndel
item Mischke, Barbara
item Opoku, Stephen -
item Padi, Francis -
item Zhang, Dapeng

Submitted to: African Journal of Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 8, 2014
Publication Date: May 21, 2014
Citation: Ji, K., Takrama, J., Meinhardt, L.W., Mischke, B.S., Opoku, S., Padi, F., Zhang, D. 2014. Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers. African Journal of Biotechnology. 13(21):2127-2136.

Interpretive Summary: Ghana is the 2nd largest cocoa producing countries in the world with an annual production of 850,000 tons. Accurate identification of cacao varieties is an urgent need for Ghana’s cacao breeding program, germplasm collection, and seed gardens. Using a new generation of DNA fingerprinting technology, we evaluated a panel of molecular markers and applied this panel on 160 cacao trees in the Ghana cacao collection. Some of these accessions were introduced from the Americas in the 1940s. This new genotyping protocol unambiguously identified mislabeled trees and verified the recorded pedigree. Our study shows that this new DNA fingerprints can provide a robust and accurate result for cacao tree identification. This protocol can be applied for large-scale genotyping of cacao as well as for many other crops. This information will be used by plant breeders, scientists and extension people to improve cacao production around the world.

Technical Abstract: Accurate identification of individual genotypes is important for cacao (Theobroma cacao L.) breeding, germplasm conservation and seed propagation. The development of single nucleotide polymorphism (SNP) markers in cacao offers an effective way to use a high-throughput genotyping system for cacao genotype verification. In the present study, high-throughput genotyping with SNP markers was used to fingerprint 160 cacao trees in the CRIG germplasm collection. These accessions had been originally introduced from international germplasm collections in Trinidad and Costa Rica as long as 70 years ago. The multilocus SNP profiles, generated by the Sequenom Mass Spectrometry platform, were compared with the SNP profiles of reference trees maintained in the international cacao collections. The comparison unambiguously identified mislabeled trees. For materials introduced as hybrid seeds without an available reference genotype, parentage analysis and model-based assignment were applied to verify their recorded parentage and genetic background. 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.

Last Modified: 10/22/2014
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