Project Number: 1275-21000-264-01
Project Type: Specific Cooperative Agreement

Start Date: Jul 01, 2005
End Date: Jul 01, 2010

Objective:
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. An amendment to this agreement was implemented in 2008 to address the critical needs of our cooperator with regard to collecting specific agronomic data. A number of bean quality traits must be analyzed via HPLC. These compounds must be analyzed immediately after harvesting to guarantee accurate uniform measurements. The measurements are vital for bean quality traits and must be collected over multi-years to develop seed quality trait profiles. To address this need it is in the best interest of the agency to provide a HPLC to ICG,T. The HPLC, pumps, detector and accessories presently held in surplus with SPCL will be sent to the cooperator for the duration of the agreement and any subsequent agreements. Due to the age of the apparatus, which was purchased in the late 1980s, and the projected usage that it will receive during this agreement, we believe that it is in the best interest of the agency that the title will vest with the collaborator at the end of this agreement. SPCL will send ICG,T a HP integrator Model 3395 B, SN CN00008209 and accessories; a Waters 490E multichannel absorbance detector and a Spectral Physics 8800 ternary HPLC pump and accessories.

Approach:
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. This project was determined to be Exempt from NIH Guidelines on 8/5/02.