1.What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? What does it matter?
This project continued its focus on the accurate and consistent identification of the germplasm accessions of Theobroma cacao in the international and national genebanks and the assessment of genetic diversity in the Latin America gene pool.

Cacao germplasm, and its efficient use, is of major importance to the U.S. chocolate industry as well as developing countries. Cacao germplasm must be maintained as collections of live trees in the field, because storage of the recalcitrant seeds is impossible. Incorrect labeling of accessions has been a problem in national or international collections around the world. Many cacao accessions (perhaps as high as 40%) held in these collections are known to be mislabeled, duplicated, or have no assignment of identity at all. The level and structure of the genetic diversity in these collections, as well as in the overall Latin America genepool, are poorly understood. These constraints limit the ability of both U.S. and collaborating foreign scientists to acquire and exchange cacao germplasm, reduce efficiency in using cacao germplasm for breeding, and hinder the development of a rational strategy for the conservation of cacao genetic diversity in the Americas. This project will first address the critical need to correctly identify individual accessions in and across these collections for utilization in breeding programs and provide this information to international databases. Results will contribute to more efficient organization and management of field genebanks and better use of scarce resources for genebank maintenance. We will assess genetic variation in the cacao collections and in the Latin America genepool using DNA markers, with the intent to identify gaps for which new cacao germplasm could be collected.

Theobroma cacao doesn't grow in the continental US but, together with major quantities of milk, sugar, almonds and peanuts produced by U.S. farms, represents an 8.6 billion dollar chocolate industry. The confectionary industry in the U.S. would be severely affected by a shortage of cacao supply. Thus, the information gained during this project directly aids substantial U.S. agriculture.

The research to be undertaken falls under National Program 301- Plant Microbial and Insect Genetic Research, Genomics and Genetics and address goal 2.1 described in the National Program Action Plan. Specifically these are: 2.1.2.1 Plant Molecular and Cellular Genetics- Acquire knowledge concerning wide crosses, tissue culture, identification, location, and means to manipulate and transfer genes that regulate and control traits of economic importance in plant production/product quality to enhance modification of plant germplasm and achieve genetic progress and, 2.1.2.3 Plant Genome Mapping - Develop gene maps, gene markers, and cytogenetic knowledge of economically important plant species to enhance breeding programs.

2.List the milestones (indicators of progress) from your Project Plan.
Year 1 (2004) The extent of mislabeling in the CATIE collection and the original reference population in the Trinidad collection estimated. The effectiveness and accuracy of the 15 SSR loci for individual identification evaluated.

Year 2 (2005) Original reference trees in Trinidad and CATIE collections fingerprinted and mislabeling in the reference trees identified and corrected. Mislabeling in the USDA collection at Mayaguez, Puerto Rico identified and correct name re-assigned. On-farm diversity in Huallaga and Ucayali area of Peru assessed.

Year 3 (2006) Mislabeling and off-types within each clone identified in CATIE and Trinidad International collections. Intra- and inter- population variation in the wild populations from the Camopi and Tanpok basins of French Guiyana analyzed. A survey of on farm diversity in the Yungas, Bolivia started.

Year 4 (2007) The INIAP collection in Ecuador genotyped. Genetic background of the Ecuadorian population "National" clarified. On-farm diversity in Ecuador assessed. Linkage disequilibrium estimated in different cocoa populations and association mapping tested in cocoa.

Year 5 (2008) Taxonomic relationship among the Theobroma taxa clarified and gene flow between cultivated cocoa and the wild compartment analyzed. Phylogeography of cocoa in the Upper Amazon region analyzed. Existing gaps in national and international collections identified. Recommendation for on farm conservation of cocoa genetic resources proposed.

4a.What was the single most significant accomplishment this past year?
Genetic Identity International Cocoa Genebanks. Genetic identity of 2100 cocoa Genetic Identity International Cocoa Genebanks. Genetic identity of 2100 cocoa accessions from two international cocoa genebanks, the cocoa germplasm collection in Costa Rica and the collection in Trinidad, were verified using microsatellite DNA markers. The multi-locus fingerprints unambiguously identified 348 duplicates and 79 homonymous mislabeling from the two gene banks. Population admixture was detected in the Upper Amazonian and Trinitario genetic groups via assignment tests. Pedigree relationships were reconstructed for the wild cocoa populations collected from the Peruvian Amazon forest in the 1930's. This data will be used by breeders and cocoa researchers to identify and develop promising new material for release to farmers.

4b.List other significant accomplishments, if any.
On-farm diversity in Peru. A survey of on-farm variety and gene diversity were carried out in Huallaga valley, Peru, in collaboration with ICT - a local non-government organization. A high level of on-farm diversity was observed in this region. This high level on-farm diversity was due to the introduction of hybrids families derived from various indigenous and international clones. This finding demonstrates that the large number of farmer's selections in this region offers a good opportunity for rapid dissemination of promising clones in northeastern Peru. It also suggests that identification of productive trees through farmer participatory selection is a cost-effective approach for cocoa improvement.

5.Describe the major accomplishments over the life of the project, including their predicted or actual impact.
To date, this project has generated DNA profiles for approximately 2600 "reference trees" cocoa accessions maintained in the international cocoa collections. These reference profiles are essential for accurate identification of cocoa germplasm around the world. Based on the DNA profiles, we have also analyzed the population structure and reconstructed the pedigree relationship for several widely distributed cocoa populations. Incorrect labeling of accessions and lack of understanding on population structure have been major problems impedes the efficient management of cocoa germplasm. The identification of individual accessions and populations will significantly improve the accuracy and efficiency in cocoa germplasm conservation and utilization in breeding new varieties.

6.What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end-user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products?
The fingerprints data of about 2600 cacao accessions from various international and national cocoa germplasm collections, as well as the identified mislabeling, have been transferred to our collaborators. This information is being used by our collaborating institutions for the correction of the off-types.

7.List your most important publications in the popular press and presentations to organizations and articles written about your work. (NOTE: List your peer reviewed publications below).
There is no non-peer reviewed publication printed in the current reporting period.