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Title: Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by Single Nucleotide Polymorphism (SNP) markers

Author
item JI, KUN - Southwest University
item Zhang, Dapeng
item MOTILAL, LAMBERT - Cocoa Research Unit - Trinidad
item BOCCARA, MICHEL - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item LACHENAUD, PHILIPPE - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item Meinhardt, Lyndel

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2012
Publication Date: 6/6/2012
Citation: Ji, K., Zhang, D., Motilal, L., Boccara, M., Lachenaud, P., Meinhardt, L.W. 2012. Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by Single Nucleotide Polymorphism (SNP) markers. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-012-9847-1.

Interpretive Summary: Cacao beans from Theobroma cacao are the source of cocoa powder and cocoa butter, which are used in the multibillion dollar chocolate and confectionery industries. Cacao was domesticated in Mesoamerica as far back as 3000 yrs ago. Traditional varieties suitable for the production of fine flavor chocolate still exist in farmers’ fields in this region, but these varieties are thinly scattered among ordinary bulk varieties and are being rapidly replaced by exotic varieties. Accurate identification of these rare and valuable varieties is essential for sustainable production of fine flavored cacao beans and contributes to in situ/on-farm conservation of these premium cacao germplam. Using a new DNA fingerprinting method, we analyzed fine-flavored farmer varieties collected from traditional cacao farms in Honduras and Nicaragua. Our result revealed a high level of genetic diversity in these farmer varieties. A significant proportion of these varieties were confirmed as fine-flavored landraces. This information thus will be used by cacao farmers and breeders for conservation and utilization of cacao germplasm in Mesoamerica.

Technical Abstract: Cacao (Theobroma cacao L.) is the main source for chocolate with an annual production of four million tons worldwide. This Neotropical tree crop was domesticated in Mesoamerica as far back as 3,000 years ago. Knowledge of genetic diversity and population structure in farmer varieties of cacao in the center of domestication is essential for sustainable production of fine-flavored cacao beans and contributes to in situ/on-farm conservation of farmer varieties. Using 100 Single Nucleic Polymorphism (SNP) markers, we analyzed 84 fine-flavored farmer varieties collected from traditional cacao farms in Honduras and Nicaragua. The SNP based multilocus matching identified six synonymous groups, including 14 Criollo and two Amelonado varieties. A moderately high level of genetic diversity was observed in these farmer varieties, indicating the possibility to further explore intra-population variation and breed for fine-flavored cocoa. Multivariate analysis clarified the genetic identity of these varieties and the result largely supports farmer perceived classification, especially for ancient Criollo and Amelonado. Parentage analysis shows that Amelonado made most parentage contribution to the Trinitario type farmer varieties, whereas ancient Criollo had little influence on the Trinitario farmer varieties from Honduras and Nicaragua. The results demonstrate the efficacy of using a small set of SNP makers for cacao germplasm characterization, and further depict the diverse origins and parentage in farmer varieties from Mesoamerica. This information thus will be highly useful for conservation and utilization of cacao germplasm from this region.