Tinkering with cocoa genes won't change the flavor of chocolate, but it could lead to stronger trees.
The genetic secrets of the cacao tree are expected to lead to healthier trees and more healthful chocolate.
Another benefit of the genetic work could be better livelihoods for millions of cocoa farmers.
But chocolate lovers needn't fear: tinkering with the flavor of chocolate is not the aim of the research.
"In my opinion chocolate tastes pretty good right now," said molecular biologist Mark Guiltinan of Pennsylvania State University. "We don't want to mess it up." Guiltinan is one of the many coauthors of a paper reporting the work in the latest issue of the journal Nature Genetics.
Scientific tweaking of favorite food plants has resulted in some historical failures that serve as cautionary tales to Guiltinan and his colleagues: such as tomatoes that look great, last long in stores, but are flavorless; and "improved" strawberries that fared no better.
"We don't want to do that to chocolate," Guiltinan told Discovery News. On the other hand, knowing what genes to breed for will likely lead to more healthy chocolate plants.
Right now the Criollo variety of Theobroma cacao accounts for only about five percent of the world's cacao production. Thirty to 40 percent of that cacao crop is lost every year to fungal infections, Guiltinan said.
"The variety that was sequenced is known for its very high quality flavor," said Siela Maximova, another coauthor and also a researcher at Penn State. "Unfortunately that variety is very susceptible to disease."
For that reason the Criollo is commonly been crossed with the lesser prized, but more disease-resistant Forastero variety.
The new genetic analysis of Criollo has already uncovered hundreds of genes involved in resisting pathogens, said Maximova. The work has also shed light on the genetic basis of the synthesis of oil, flavonoids, antioxidants, hormones, pigments and aromas.
Their discoveries could lead to cocoa beans that yield more butter and even more healthful antioxidants and flavonoids.
But that does not mean Dove bars will be made from GM cocoa beans, said Guiltinan.
"I'm not concerned that this work could be utilized for such research," said Lyndel W. Meinhardt, research leader of the U.S. Department of Agriculture's Sustainable Perennial Crops Lab. "Overall, the cocoa industry and cocoa growers are not supportive of cultivating genetically-engineered cacao. I'm more excited about the potential that this work brings to improve cacao."
Most the cacao grown around the world has a very limited genetic background and so this work will help set the stage to make significant genetic improvements, Meinhardt told Discovery News.
"Mainly we're talking about classical breeding," said Guiltinan, clarifying that direct genetic improvement can be done the old-fashioned way, but sped up with the help of molecular research that allows young plants to be analyzed for traits instead of waiting for them to mature.
Ultimately, then, the biggest winners from this research should be cocoa farmers and cocoa companies.
"The cocoa genome project...is an important tool which will help researchers to identify and breed cocoa trees which are more disease and pest tolerant," said Bill Guyton of the World Cocoa Foundation, which promotes sustainable cocoa economy. "Improved productivity will ultimately result in better incomes for the millions of the small-scale farmers who grow the crop."