International Business Machines Corp. is working with candy maker Mars Inc. and the American government to study the genetic code of cocoa trees to safeguard the world’s chocolate supply.

Closely held Mars, the maker of M&M candies and Snickers bars, and the U.S. Agriculture Department will sequence the entire cocoa genome, deciphering the plant’s biological map. IBM will analyze the results using Blue Gene, the world’s second-fastest supercomputer, the company said yesterday in a statement.

Political unrest and plant diseases in Africa, home to two-thirds of cocoa production, have driven up prices more than 50% in the past year. Cocoa trees in Africa and Asia have become increasingly stunted from fungus, insects, and drought, triggering supply shortfalls.

“Mars is trying to improve the reliability of the cocoa supply and IBM is looking for new ways to market its Blue Gene supercomputer power,” an analyst for AMR Research in Boston, Lora Cecere, said. IBM can apply the same tools to other food staples falling short of demand, such as corn, she said.

Sequencing the genome will let scientists isolate hardier plant types that can withstand fungal strains, boring insects, and the drier environments created by drought and global warming, a senior computational manager at IBM, the world’s biggest computer-services company, Ajay Royyuru, said.

The five-year project will help the more than 6.5 million family farmers — most of them in Africa, South America, and Asia — who depend on cocoa, according to Armonk, N.Y.-based IBM. A spokeswoman from IBM, Jenny Hunter, declined to reveal the value of the company’s contract with Mars.

“This is not just science for the sake of science,” Mr. Royyuru said. “This is IBM making an impact in markets way beyond what we would traditionally look at.”

Cocoa demand will outpace supply by 29,000 tons this season, Fortis Bank said June 6, up from a prior forecast of 6,000 tons. The bank expects a 21,000-ton shortfall for the 2008-09 season, a third straight annual deficit.