Forget curing cancer, solving global warming, or unraveling the origin of the universe. They’ve finally found the real killer app for supercomputing: advancing chocolate science. The United States Department of Agriculture, Mars Inc., and IBM have gotten together to sequence the genome of the cacao plant (Theobroma cacao) — the origin of cocoa and chocolate.

The IBM team at the T.J. Watson Research Center in Yorktown Heights will use a Blue Gene supercomputer and its expertise in computational biology to map and analyze the cocoa genome. The whole project is expected to take approximately five years, at which point plant breeders should have a much better understanding of what makes the cacao trees tick.

Apparently the plants are subject to a variety of diseases, pests, and environmental hardships in their tropical homeland, so if breeders had access to the decoded cacao genome they could manipulate the plant’s genetic traits to increase production. Global supplies of cocoa have been shrinking lately due to drought and disease outbreaks. At the same time, demand is increasing due to all the positive press about the health benefits of chocolate.

With the exception of a small amount of cacao grown in Hawaii, North America is not in the chocolate growing business. But other U.S. agricultural interests — almonds, raisins, peanuts, and so on — are partially dependent on chocolate confections. Mars, of course, has a huge interest in ensuring future cacao supplies. It’s annual revenue in 2007 was $25 billion, and is said to be investing $10 million in the genome project. For its part, Mars intends to make the research results freely available through the Public Intellectual Property Resource for Agriculture, a group that supports agricultural innovation for humanitarian and small-scale commercial purposes.

Although Mars and the USDA didn’t mention it, a possible hidden agenda in mapping the cacao genome is its application in genetic engineering. While the general public is currently suspicious of GMOs (genetically modified organisms), the potential value of transferring chocolate-making genes into temperate climate crops could be huge. Even with modern agricultural techniques and advanced breeding, tropical agriculture tends to be difficult to sustain for a variety of reasions. Being able to expand chocolate production into temperate agricultural regions would create a whole new business model for companies like Mars. And while plans for chocolate soybeans are probably not yet on the drawing board, that might be just the kind of GMO that the public could sink their teeth into.