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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: Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authenticity and traceability

Authors
item Fang, Wanping -
item MEINHARDT, LYNDEL
item MISCHKE, BARBARA
item Bellato, Claudia -
item Motilal, Lambert -
item ZHANG, DAPENG

Submitted to: Journal of Agricultural and Food Chemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 19, 2013
Publication Date: December 19, 2013
Citation: Fang, W., Meinhardt, L.W., Mischke, B.S., Bellato, C., Motilal, L., Zhang, D. 2013. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authenticity and traceability. Journal of Agricultural and Food Chemistry. 62:481-487.

Interpretive Summary: Cacao is an important tropical crop since it is the source of cocoa butter and powder for the confectionery industry. Production and marketing of differentiated high-value cocoa provide social-economical opportunities for cacao growers, the chocolate industry and consumers. From the conservation perspective, the higher farm-gate revenues from premium markets can provide economic incentives for demand-driven in situ/on-farm conservation of cacao genetic diversity. However, among premium cacao varieties, adulteration is common and happened at different steps of the cocoa chain. Using a a nanofluidic DNA genotyping system, we developed a protocol for cocoa traceability based on a small quantity of DNA extracted from the seed coat of single cacao beans.This approach is accurate and robust for authenticity verification of gourmet cacao varieties. This information will be used by researchers, cocoa producers and chocolate industry to accurately determine cocoa traceability and authenticity.

Technical Abstract: Cacao (Theobroma cacao L.) is an important tropical crop since it is the source of cocoa butter and powder for the confectionery industry. Production and marketing of premium high-value fine flavored cacao provide opportunities for cacao growers, the chocolate industry and consumers. The higher farm-gate revenues from premium market can also provide economic incentives for demand-driven in situ/on-farm conservation of cacao genetic diversity. One problem with the premium cacao market is the mixing of off-types that adulterate the raw material. Accurate determination of genetic identity of a single cacao bean using molecular markers is essential for ensuring cocoa traceability and authenticity. Using a panel of 48 SNP markers and a nanofluidic SNP genotyping system, we generated SNP fingerprints for a small quantity of DNA extracted from the seed coat of single cacao beans. Based on the SNP profiles, an assumed adulterate variety was unambiguously identified from the authentic beans by multi-locus matching. Assignment test based on both Bayesian clustering analysis and allele frequency classified all 30 authentic samples into one homogenous cluster, which separated them from the non-authentic samples. The result was further supported by distance-based principle coordinate analysis. The nanofluidic array of SNP protocol based on single beans, together with forensic statistical tools, are robust enough to establish the authenticity and verification of gourmet cacao varieties and therefore, it shows significant potential for practical application.

Last Modified: 9/10/2014
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