2007 Annual Report 1a.Objectives (from AD-416) This project will first address the critical need to correctly identify individual accessions in the ICG,T using DNA fingerprinting, and provide this information to international databases. Secondly, it will assess population structure and genetic variation in the collection using tools of population genetics and bioinformatics, with the intent to identify gaps for which new cocoa germplasm could be collected. Thirdly, this project will test the application of association genetics to link important agronomic traits to molecular diversity. Results of this project will contribute to more efficient organization and management of field genebanks and better use of cocoa germplasm for cocoa genetic improvement. 1b.Approach (from AD-416) This project will first complete the reference DNA profiles for the original cocoa trees in the Americas. Where it is possible, the authenticity of some genetic groups needs to be verified through the comparison with their original sources (i.e., the John Allen collection in Napo, Ecuador). Based on the reference DNA profiles, all the trees at the University Cocoa Research Station, Centeno, Trinidad (UCRS, which is the site of the ICG,T) will be checked to identify off-types. In total, 11,500 trees will be assessed. Initially fruit and flower morphology will be compared and, in cases of doubt, DNA fingerprints will be compared. After resolving any mislabeling within the collection, the genetic diversity in the ICG,T will be assessed. Allelic diversity in different populations and genetic groups will be quantified using the multi-locus SSR data. Where possible, population structure and genetic relatedness will be assessed, and pedigree relationship will be reconstructed using multi-locus SSR data. A set of 200-300 diverse cocoa accessions with multi-year agronomic and phenotypic data will be selected. Associations between important agronomic traits and SSR genotype then will be tested. The mapping result will be compared with those from classical mapping strategy using segregating populations. 3.Progress Report This report serves to document research conducted under a Specific Cooperative Agreement between ARS and the Cocoa Research Unit of the University of West Indies located at Augustine, Trinidad. Additional details of research can be found in the report for the parent project 1275-21000-177-00D, Molecular characterization and diversity assessment of cacao germplasm in the Americas. This specific cooperative agreement was set up to provide a mechanism to fund collaborative research on the DNA fingerprinting of cocoa germplasm in the International Cocoa Genebank, Trinidad. Since November 2005, a member of the research staff of CRU, has been hosted by SPCL, USDA-ARS/BARC for training in molecular marker technology. He has undertaken a project to fulfill the requirement for a Ph.D. from the University of West Indies, using DNA samples collected and extracted from UCRS in Trinidad. After the elimination of mislabeled accessions, association mapping has started to explore the genetic diversity of cocoa butterfat, cocoa powder, as well as other related economic traits within the accessions at ICG,T. A total of 326 accessions from the ICG,T were evaluated for bean number, bean size, bean mass, butterfat content and pod index. The results clarified the interrelationship among the traits associated with cocoa butterfat and cocoa powder yield. They suggest that simultaneous improvement of bean mass and size can be achieved. Several promising candidates for future germplasm enhancement were selected for each trait, and thirteen accessions combining low pod index, high butterfat content, high bean mass with high bean size were identified. This project was monitored via e-mail and phones calls.