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United States Department of Agriculture

Agricultural Research Service

Research Project: SEQUENCING, ANNOTATION, AND DATABASE MANAGEMENT OF THE GENOME OF THEOBROMA CACAO

Location: Subtropical Horticulture Research

2011 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.

This is the fourth year of a five year commitment from Mars Inc. on this project.

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 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.


Last Modified: 12/20/2014
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