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A taste of the chocolate genome

Competing teams announce impending completion of cacao DNA sequence

5:31pm, September 15, 2010
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The genetic blueprint of the chocolate tree is at hand, but not quite in mouth.

Two independent teams have completed drafts of the DNA sequence of the cacao tree, the source of chocolate, scientists announced September 15. Both efforts will eventually help breed plants that resist disease yet still bear superior beans, the researchers claim.

Neither group has published results in a scientific journal, so it’s difficult to discern what’s been discovered. Both teams assert that their data are as rich as a slab of Belgium’s finest dark. But what’s been released publicly may be more like a watery cup of hot cocoa.

A team led by candy maker Mars, Inc., the U.S. Department of Agriculture and IBM announced the unveiling of a preliminary genome of the cacao tree, Theobroma cacao, that’s available to the research community at www.cacaogenomedb.org. The other genome draft, completed by an international consortium of 20 different institutions in six countries, is currently under review in a scientific journal and will soon be published.

Chocolate is more than a pleasant afterthought to cacao farmers, who must contend with pathogens that cause frosty pod and black pod, diseases that can wipe out 80 percent of a crop. The hope is the new sequence data will help link resistance to these blights to actual genes, allowing farmers to breed stout plants that still bear beans rich in cocoa butter, the ingredient that gives chocolate its creamy melt-in-your-mouthiness.

The draft genome made available by the Mars team is a rough physical map of the cacao tree’s 10 chromosomes. Roughly 400 million “letters” of code have been arranged into chunks of about 150,000 letters each. This rough map will allow scientists to search for genes associated with particular traits, says Juan Carlos Motamayor, chief cacao scientist for Mars. The researchers have already figured out where some genes of interest reside, but they aren’t making that information available yet, he says.

The second team has a very detailed draft, says plant molecular biologist Mark Guiltinan of Pennsylvania State University in University Park. He and his collaborators have discovered hundreds of genes associated with disease resistance and with high-quality pods. If the available Mars genome is like a barely completed building with wired rooms and drywall, the International Cocoa Genome Sequencing Consortium’s draft is furniture-ready. All it needs is to pass that scientific version of the building inspection known as peer review.


Cacao genome unwrapped: International consortium of plant scientists sequence the cocoa genome. Press release, Sept. 15, 2010. International Cocoa Genome Sequencing Consortium.
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MARS, USDA-ARS and IBM publicly release preliminary cacao genome sequence three years ahead of schedule. Press release, Sept. 15, 2010.
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Further Reading

The International Cocoa Genome Sequencing Consortium website:
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The Cacao Genome Database website:
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R. Ehrenberg. Chocolate may have arrived early to U.S. Southwest. Science News. Vol. 175, Feb. 28, 2009, p. 14. Available online:
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J. Raloff. Medicinal chocolate…Part 1. Science News Online, Feb. 27, 2008.
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J. Raloff. Medicinal chocolate…Part 2. Science News Online, Feb 28, 2008.
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