2012 Annual Report 1a.Objectives (from AD-416): The primary goal of this project is to use the most advanced techniques available to sequence, assemble, annotate, and curate the cacao genome. 1b.Approach (from AD-416): The cacao sequencing project will be organized and coordinated from the Miami lab using various vendors and collaborating partners. The project has two sub-objectives that will be accomplished over the next five years. First, the entire genome sequence of Matina 1-6 will be generated using a combination of various sequencing strategies. The annotated genome sequence will be deposited in a publicly available database. Second, an integrated web-based relational database will be developed, and curated. 3.Progress Report: This project is related to the inhouse objective: The development and implementation of an international marker assisted selection (MAS) program for cacao is the major objective of this project. This objective involves a combination of hypothesis-driven and non-hyothesis driven research and includes the training of scientists from cacao producing countries in plant breeding, genetics, and the use of molecular markers in a (MAS) program. Major sequencing of the cacao genome is complete and posted on the website (http://www.cacaogenomedb.org/). Re-sequencing has begun on a number of important cultivars that contain unique traits important in breeding, such as disease resistance. The genome sequence of these cultivars is being compared to the reference sequence of 'Matina 1-6' to determine differences that control these important traits. The genome sequence has been used to identify candidate genes for pod color. Fluorescent in situ hybridization has been used to identify each cacao chromosome. The project is managed by ARS scientists in Miami and coordinated through a monthly conference call and two meetings per year. A postdoctoral fellow has been hired to coordinate the conversion of the Single Nucleotide Polymorphism (SNP) data into a SNP assay tool.