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United States Department of Agriculture

Agricultural Research Service


Location: Subtropical Horticulture Research

2009 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 objective of the in-house project: 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 is the first year of a five year commitment from Mars Inc. on this project. Several 454 runs have been made on the accession Matina 1-6 and the sequences have been annotated. The Physical Map has been completed including placing over 200 microsatellite and candidate gene markers from the linkage map onto the physical map. BAC end sequences for the minimum tiling path are being sequenced and will aid in genome assembly. A new website funded by Specific Cooperative Agreement (SCA) 58-6631-9-200 ( has been designed and all the sequence information for the cacao genome sequencing project is currently available to project members. A single nucleotide polymorphism (SNP) discovery project funded by SCA 58-6631-9-203 is close to completion with RNA isolated at SHRS from leaves of genetically diverse accessions of cacao being sequenced at NCGR. Access to the SNP data is available through the cacaogenomedb website. Project was monitored through a monthly conference call and two meetings per year. A postdoctoral fellow has been hired to coordinate the conversion of the SNP data into a SNP assay tool.

4. Accomplishments

Last Modified: 10/16/2017
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