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United States Department of Agriculture

Agricultural Research Service


Location: Sustainable Perennial Crops

2013 Annual Report

1a.Objectives (from AD-416):
The goal of this project is to develop and implement scientific approaches for managing and facilitating the use of cacao germplasm. Over the next 5 years we will focus on the following objectives:

Objective 1: Rationalize ex situ cacao collections in international and non-U.S. national genebanks.

Sub-objective 1.A. Maximize diversity coverage and reduce mislabeling and redundancy in international and non-U.S. national collections. Sub-objective 1.B. Improve the integration and expand the scope of phenotype, pedigree, and molecular data in International Cacao Databases. This objective will assure that germplasm collections are representative of the diversity available and that breeders are using correctly labeled and described breeding parents.

Objective 2: Develop complementary conservation methods, including in situ and on-farm conservation methods that can improve cacao productivity while maintaining or enhancing genetic diversity. This will be carried out with partners in developing country centers of diversity.

Objective 3: Characterize and evaluate targeted economic/agronomic traits of cacao and identify likely sources of new genes for breeders. This will serve as a guide to breeders as to what germplasm may contain the traits in which they are interested.

1b.Approach (from AD-416):
The project will continue to genotype cacao samples from ex situ collections from various cocoa producing countries in Latin America. These genotypes developed with a standard set of 15 SSR markers will continue to be used to fingerprint the cacao collections from Ecuador, Colombia, Bolivia, and several small collections in Central America and the Caribbean, following our established protocol of DNA extraction, SSR analysis and allele sizing. The generated multi-locus SSR data, together with those previously obtained from the two International genebanks and other non-U.S. national collections will be compiled and used for the identification of duplicates within and among collections. After the elimination of mislabeled and duplicate accessions, summary statistics for measuring genetic diversity will be conducted to analyze the geographical distribution of cacao germplasm and identify “hotspots” and geographical areas that have complementary levels of diversity. A minimum of two gap-collecting expeditions will be carried out in areas lacking representation in the ex situ collections. The information on genetic identities obtained in Sub-objective 1.A will serve as the foundation for correcting the existing nomenclatures in the two international databases, as well as the International Cocoa Quarantine Centre, Reading (ICQC, R), which serves as the source for the dissemination of disease-free (post-quarantine) accessions for the global cacao community. Comparison of on-farm diversity with the natural populations in the Peruvian Amazon will be implemented using the populations previous collected from Ucayali, Huallaga, and Mararon River valleys to develop complementary conservation methods, including on-farm conservation methods. Finally phenotypic and genetic analyses will be conducted to characterize and evaluate targeted economic/agronomic traits of cacao and identify likely sources of new genes for breeders.

3.Progress Report:
In FY 2013, progress was made in molecular characterization of a large Ecuadorian cacao collection, the John Allen Collection, maintained in the National Agricultural Research Institute of Ecuador. The John Allen Collection holds wild cacao germplasm covering most of the Ecuadorian Amazon. Accessions were verified and spatial pattern of diversity distribution was analyzed based on SNP fingerprinting data and geographic coordinates. The resultant information significantly improves our understanding about the spatial distribution of cacao genetic diversity in the Amazon. Progress was also made in identification of traditional varieties and assessment of on-farm diversity in Peru. ‘Piura Porcelana’ is a traditional cacao variety from Peru that is cultivated for the gourmet chocolate market. However, the genetic identity of this traditional variety was unknown. Single Nucleic Polymorphism (SNP) analysis confirmed that ‘Piura Porcelana’ has a distinctive genetic profile and that it originated from the Andes foothills in northern Peru. This result provides new evidence of direct adoption of wild cacao germplasm in South America. The information is useful for in situ conservation and sustainable use of traditional cacao varieties in the Peruvian Amazon. Assessment of on-farm diversity also continued in Mesoamerica. SNP analysis was carried out for farmer selections from traditional farms in Izalco, Sonsonate and San Miguel regions in El Salvador. Landraces and traditional varieties, including ancient Criollo, Amelonado and Trinitario were identified using SNP analysis. The identification of local farmer selections provides needed information for conservation and sustainable use of the local landraces for the production of fine flavor cocoa beans. Genetic identity and parentage were tested for farmer selections from Sulawesi, Indonesia. Results of SNP analysis showed that only a small number of germplasm groups contributed to these farmer selections. New sources of resistance harbored in other germplasm groups need to be incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. Molecular characterization of international clones in the Ghana cacao germplasm collection was carried out in FY 2013. These international clones were introduced from Trinidad in 1940s and they have served as main parental clones in all the African cacao breeding programs. Mislabeled cacao trees in this collection were identified using SNP fingerprinting technology. The results provide basic information for improving the efficiency of the Ghanaian breeding programs and quality of seeds multiplication in Ghana. This project ended in March, 2013. The new project “Genetic Diversity Assessment of Cacao and Other Tropical Tree Crop Genetic Resources” (Project 1245-21000-267-00D) started in March 2013.

1. Identification of a traditional cacao variety in Peru. Traditional cacao varieties often have special quality and have good potential for external gourmet markets. However, there is a general trend that these varieties are being replaced by introduced bulk varieties in farmers’ fields. “Piura Porcelana” is a perceived traditional variety in northern Peru. In FY 2013, a survey was conducted in Piura, Peru and samples were taken from traditional farms and analyzed using Single Nucleic Polymorphism (SNP) markers. The results confirm that the ‘Piura Porcelana’ cacao type has a distinctive genetic profile and is closely associated with the native wild population in the Andean foothills. This variety shares a common origin with the “Nacional” cacao in Ecuador. This study is particularly valuable in providing needed information required for making decisions on in-situ conservation of cacao germplasm in the center of origin of this crop. This information will also be highly useful to the U.S. chocolate industry for the production of fine flavor chocolates.

Review Publications
Yang, J., Scascitelli, M., Motilal, L., Sveinsson, S., Engels, J., Kane, N., Dempewolf, H., Zhang, D., Maharaj, K., Cronk, Q. 2013. Complex origin of Trinitario-type Theobroma cacao (Malvaceae) revealed using plastid genomics. Tree Genetics and Genomes. 9(3):829-840.

Last Modified: 7/30/2014
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