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Photo: Chocolate, which comes from cacao.
Agricultural Research Service scientists, in partnership with Mars Inc. are applying modern molecular genetic techniques to developing disease-resistant and productive cacao (Theobroma cacao) trees. Photo courtesy of Microsoft clipart.

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Sequencing the Cacao Genome to Safeguard Chocolate

By Alfredo Flores
June 26, 2008

During the past 15 years, the global cocoa industry has confronted a trio of devastating fungal diseases that cost growers an estimated $700 million in losses annually. Now scientists at the Agricultural Research Service (ARS) Subtropical Horticultural Research Station (SHRS) in Miami, Fla., are developing productive cacao (Theobroma cacao) trees resistant to these diseases: witches' broom, frosty pod and black pod.

The research has been based upon traditional varietal selection and breeding, enhanced by the use of molecular (DNA-derived) markers associated with disease resistance.

Field trials involving foreign cooperators are under way in South America, West Africa, Central America and Papua New Guinea to evaluate potential disease-resistant cocoa trees. Several of these tree selections were based upon disease-tolerance genes discovered in Miami.

Since 1999, ARS researchers at the SHRS, led by plant geneticist Ray Schnell, have worked in partnership with Mars Inc., the world’s largest manufacturer of chocolate-related products, to apply modern molecular genetic techniques to cocoa production.

This research, in collaboration with institutes in the Americas and Africa, has produced genetic linkage maps for cacao populations, segregating for resistance to the three fungal diseases. Today a new partnership was announced between ARS, Mars Inc., and IBM with the goal of sequencing the entire cacao genome. Once completed, the research results will be released into the public domain.

The partnership to sequence the cacao genome is financially backed and coordinated by Mars Inc. of McLean, Va. Scientific support is provided by SHRS in Miami, in collaboration with scientists at IBM’s Thomas J. Watson Research Center in Yorktown Heights, N.Y. The IBM team will use its Blue Gene supercomputer to analyze the cocoa genome. This is the first time that all three research groups are collaborating.

In addition to the three major partners, Washington State University will assist Schnell in developing detailed genetic maps and assembling the sequence fragments into the complete genome sequence.

ARS is a scientific research agency of the U.S. Department of Agriculture.