Cacao genome workshop makes debut at genetics conference, Chocolate is world's sixth largest crop and a fragile one

The annual International Conference on the Status of Plant and Animal Genome Research, which this year was held January 10-14 in San Diego, initiated a Cacao Genome Sequencing Workshop session which took place January 11.

The conference was organized by David Kuhn of the US Department of Agriculture’s Agricultural Research Service (USDA-ARS).

Presenters included Dr. Howard Shapiro, the global director of plant science and external research for Mars, Inc., whose talk was titled “The Role of Public-Private Collaboration in Sequencing the Cacao Genome,” and Dr. Raymond Schnell of the USDA-ARS Subtropical Horticultural Research Station in Miami, who addressed the topic “The Cacao International Breeding Program and the Need for Cacao Genome Sequence.”

Shapiro referenced, both orally and on a slide presentation, a document from 1631 which mentioned threats to the cacao crop.

“They recognized in 1631 that this is a particularly fragile crop,” he said. “Even in 1631 they were having trouble with this crop.”

Cacao, whose primary product is chocolate, is the world’s sixth-largest crop. The cacao tree can be cultivated in a sustainable agro-forestry system.

Four main genetic groups of cacao are traditionally classified as Criollo, Trinitario, Lower Amazon Forastero, and Upper Amazon Forastero.

“Cacao’s considered food of the gods, but it doesn’t come from another planet,” Schnell said. “It’s produced on small farms.”

Production of cacao in tropical America has been severely affected by two fungal pathogens: witches’ broom and frosty pod. Both pathogens destroy the bean.

Those two diseases, along with the fungal disease black pod, were responsible for losses exceeding $700 million (in US dollar equivalent) in 2001.

Witches’ broom wasn’t found in Brazil until about 1987. Before the infestation, Brazil was the second-largest producer of cacao beans in the world and the third-largest exporter.

“It helped develop a flavor which you see in the M&Ms,” Shapiro said.

Within 10 years Brazil was a net importer of cacao. Witches’ broom reduced Brazil’s cacao production by between 400,000 and 800,000 tons.

“It was a shock to us,” Shapiro said. “It was a huge source for us.”

Witches’ broom and frosty pod are currently confined to tropical America, but commercial populations in West Africa and South Asia are highly susceptible to both diseases.

The cocoa pod borer is currently confined to Indonesia.

West Africa currently produces approximately 70 percent of the world’s cacao. “If any of the diseases go here the game’s over,” Shapiro said.

Shapiro noted that potential threats to the world’s chocolate supply include not only a bird’s wing but also the possibility of bioterrorism which would intentionally seek to destroy cacao production.

“This got us really concerned,” he said. “Chocolate is the heart and soul of Mars, Incorporated.”

Mars, Inc. was founded in 1911 and originally produced handmade chocolate. Its first product, Milky Way, was first sold in 1923. The company also produces M&Ms, Snickers, Three Musketeers, Twix, and Dove Chocolate.

A separate food division produces the Uncle Ben’s rice brand, and the corporation’s pet food division sells Whiskas, Pedigree, and Sheba.

In 1999, the USDA-ARS, in collaboration with Mars, Inc., initiated a project to apply modern molecular genetic techniques to cacao breeding.

The objective was to develop an international marker assisted selection breeding program focusing on disease resistance.

The project began with a five-year cooperative research and development agreement (CRADA) and was renewed by a second five-year agreement. A third agreement is expected shortly.

“We wanted to accelerate breeding and not just through disease resistance,” Shapiro said. “We wanted to deal with yield, quality of flavor, water and nutrient use efficiency, tree architecture, and drought tolerance.”

Traditional cacao breeding programs have been marginally successful in producing resistant material with suitable commercial characteristics.

While some small cross-breeding improvements to crop yield have been made by the French and Dutch, the progress doesn’t compare to that of corn, citrus, or almond yield.

“The quality and flavor’s been falling off,” said Shapiro, who noted that many chocolate companies now blend to retain flavor.

Although the CRADA work is not proprietary, Mars, Inc. is a privately held corporation and does not face demands for dividends.

“They understand the public domain,” Shapiro said. “The more that gets out there, the more useful it is.”

That additional information could bring additional benefits to the chocolate industry in the long run.

“We also wanted to attract a new generation of cocoa geneticists,” Shapiro said.

Approximately 98 percent of the world’s chocolate production is within 18 degrees latitude of the Equator.

In the United States cacao is grown only in Hawaii, Puerto Rico, and the USDA-ARS laboratory in Miami.

The United States agricultural interests in chocolate, however, include the production of milk and peanuts.

“You add it all together and there was a huge danger,” Shapiro said.

The CRADA specifies working with regional partners in Africa, Asia, Central America, and South America to understand regional needs.

In West Africa, 20 percent of the trees produce 80 percent of the yield.

While Asia has seen a gradual increase in yield over the past 30 years, no such increase in yield has taken place in Africa.

“Economic development, economic diversity will really take us a long way,” Shapiro said. “For six and a half million people it’s a critical path, and we all understand the urgency.”

Large evaluation trials are taking place in Costa Rica, Ecuador, Brazil, and Papua New Guinea with additional studies in Ghana, Nigeria, Costa Rica, and Ecuador.

The projects are all in collaboration with national agricultural institutes in the respective countries, and the international project has a goal of producing new disease-resistant cultivars by 2012.

Ten different cacao structure groups have been identified. “As part of the project we will sequence these as well,” Shapiro said.

“The genome is fairly small, so we thought this should be a doable proposal,” Schnell said.

The genetic work will also account for any temperature change. Between 1964 and 2002 the average temperature in the Ivory Coast rose from 79 degrees Fahrenheit to 80.5 degrees Fahrenheit.

“Without the genome you’re not going to be able to make the breakthrough to have a plant that grows well in these conditions,” Shapiro said.

The CRADA program also considers agro-forestry, agro-ecology, and agro-economics. “We also help protect the fragile environment where it’s grown,” Shapiro said.

On June 26, 2008, USDA-ARS, Mars, Inc., and IBM announced that they were combining their scientific resources to sequence and analyze the entire cacao tree.

“The whole goal, then, is to provide better cacao quicker,” Schnell said.

“We can’t wait 30 years to get to these goals,” Schnell said. “We need to develop these markers quickly.”

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