IU researchers improve cacao tree genome

Research performed by a non-departmental organization at IU could help sustain the world supply of chocolate — and the livelihoods of millions of farmers in West Africa and other regions.

The IU Center for Genomics and Bioinformatics aided in the completion of the first mapping of the cacao tree genome, which produces the beans used to make cocoa powder.

The map was released to the public Sept. 15 and allows producers to pinpoint beneficial crop traits and improve tree breeding.

“Putting a tree in the ground for your livelihood is a pretty big investment because it will take a while for you to benefit from that,” said Keithanne Mockaitis, leader of IU’s branch of the project. “With much better detail on the genome, breeders will be able to help farmers decide what to plant in their region that will be more likely to resist disease.”

Mars Inc., the U.S. Department of Agriculture, the CGB and several other organizations partnered for the project. The goal of the research is to aid in the breeding of disease-resistant cacao plants.

“You can’t really do that without a reference,” Mockaitis said. “We just built what is necessary to do all of these really informative experiments.”

Disease causes an estimated $700 million in dead-loss for cacao farmers each year, according to the USDA. In regions such as West Africa, which produces 70 percent of the world’s cocoa, such losses can cripple economic growth.

In 1989, Brazil provided a sobering example of what disease-related crop destruction can do to a nation’s economy. The country lost more than three-fourths of its cacao population to a tree-killing fungal disease known as witches’ broom.

“Brazil was the fourth-largest exporter of cocoa,” said David Kuhn, a molecular biologist with the USDA. “It became a net importer for its own domestic industry after witches’ broom swept through the cocoa-breeding region.”

Breeding based on genetic mapping, known as marker-assisted selection, helps growers improve their crop. As of now, Mockaitis said, this research is the best defense against fallout like that seen in Brazil.

“That wasn’t that long ago,” she said of Brazil’s outbreak. “It’s not like all of a sudden we have all of these agricultural technologies outside of the plant that are so effective against this stuff. We don’t. And that’s why the genetics is so important.”

The CGB began its work with the project in early 2009 and has provided several technological assets. The equipment available to the CGB is cutting-edge, Research Associate Zach Smith said. The three pieces of mapping equipment alone are worth more than $1 million, and several components are unavailable elsewhere.

These resources brought the CGB an extended grant from Mars Inc. that will last a full year.

The University also sees several benefits from the CGB’s work. Researchers who go to Mockaitis with genome sequencing projects don’t have to pay as much for the center’s time, and while the group is partially funded by IU, it supports itself for the most part.

Mockaitis said the current grant from Mars Inc. supplements the salaries of at least five people.

“Grants like this have a very positive effect on research here,” she said. “We’re able to provide the newest thing at a reasonable cost to researchers here. Some centers have to do the old thing that’s just written in the book because they can’t afford to
experiment.”

The success of the cacao project has also given national attention to the work of Mockaitis and her staff.

“A demonstrated ability to use the technologies has given us a higher profile for competing for funding for other types of projects,” Mockaitis said.

Kuhn credited the CGB researchers as essential contributors to mapping the genome and discovering the functions of genes.

“We would not have been able to assemble the genome without those two contributions,” he said. “That’s absolute fact.”