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United States Department of Agriculture

Agricultural Research Service


Location: Subtropical Horticulture Research

2010 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 research relates to 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 is the third year of a five year commitment from Mars Inc. on this project. Major sequencing of the cacao genome is complete. Over 12x coverage using 454 and 50x coverage using Illumina technologies has been accomplished. Paired end libraries have been made and the ends sequenced to aid in the assembly (3 kb, 8 kb, and a fosmid library). A 3Mb 454 and Sanger sequencing pilot project was completed on linkage group 5. This area was assembled and genes involved with BP resistance and four horticultural traits are being annotated and identified. A new website funded by 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 SNP discovery project funded by SCA 58-6631-9-203 is close to completion with over 300K SNP discovered. Access to the SNP data is available through the cacaogenomedb website. A new 6,000 SNP chip, optimized for our mapping populations, has been produced and is being validated. Results from genotyping of 1100 individuals in the mapping populations should increase the resolution of the genetic recombination map by at least ten-fold. A postdoctoral fellow has been hired to coordinate the coversion of the SNP data into a SNP assay tool. Monitoring activities: The project is managed by ARS scientists in Miami and coordinated through a monthly conference call and two meetings per year.

4. Accomplishments

Last Modified: 10/17/2017
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