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United States Department of Agriculture

Agricultural Research Service


Location: Subtropical Horticulture Research

2013 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-hypothesis 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. This project has come to the end of the five year period and this will be the final progress report. Major sequencing of the cacao genome was completed and posted on the website ( September 15, 2010. 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. These findings have been reported in a recent publication The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color Genome Biology 2013, 14:R53 doi:10.1186/gb-2013-14-6-r53. The database associated with the cacao genome sequencing project has been migrated to a USDA server at Iowa State, but can still be found at "". Recently, two scientists were trained at the Generic Model Organism Database (GMOD) workshop to be better able to curate and manage the database. The Matina 1-6 genome sequence that was the product of this project has been chosen to represent Theobroma cacao in, the JGI compendium of plant genome sequences.

4. Accomplishments

Last Modified: 06/25/2017
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