Cacao Genome Sequence Released


CUGI partnered with Mars Incorporated and the United States Department of Agriculture to produce the whole genome sequence of Theobroma cacao. This plant produces cocoa beans, the key ingredient in chocolate. The ultimate goal is to improve current chocolate varieties to include a higher resistance to disease, more robust growth, and even better taste.

CUGI produced a comprehensive integrated genomic framework in support of the project. An anchored physical map with correlated genetic and sequence data can drastically improve the quality and coverage of a whole genome project. Three deep coverage, large-insert BAC libraries were constructed and subjected to high information content fingerprinting (HICF). A large number of the BACs were end sequenced by the high quality, longer read Sanger method. The small sequence contigs that often result from next generation sequencing techniques were positioned onto the physical map by comparison to BAC end sequence, electronic fingerprints and other lab-based methods. This physical map and its corresponding BAC-end sequences proved invaluable in assembling, scaffolding and orienting the next generation sequence data into a comprehensive whole genome.

The genetic markers from the genetic recombination map are being located on the physical map by overgo hybridization. This will allow mapping studies associating important traits in cacao to be immediately evaluated against the actual cacao genome sequence for candidate genes to target. The combination of genetic and genomic resources now available for the cacao plant will allow breeders to quickly and efficiently produce new varieties and fulfill the world's desire for sustainable, delicious chocolate.

CUGI Physical Mapping
Cacao Genome Database