A Sweet Sequence: The Cocoa Genome

By Amy Cowen on September 21, 2010 4:00 PM

Cocoa beans in a cocoa pod. Source: U.S. Department of Agriculture - Agricultural Research Service.

Cocoa is the key ingredient in chocolate, and while it may seem like the candy display at your local store is never at risk of running on empty, the U. S. Department of Agriculture-Agricultural Research Service (USDA-ARS) reports that "worldwide demand for cacao now exceeds production." Adding to the problem is the fact that cocoa farmers face a large number of environmental risks each year. Fungal diseases and pests that target cacao trees can cause widespread damage, destroying seed-bearing pods and contributing to hundreds of millions of dollars of lost sales each year. Drought, too, is responsible for the loss of cocoa crops each year.

Working Together

In 2008, the USDA-ARS, the Mars food company, and IBM announced collaborative plans to work on sequencing the cocoa genome, a project predicted to help more than 6.5 million farmers worldwide&emdash;and help pave the way for a more sustainable cocoa industry.

While the US chocolate industry weighs in at a hefty $17.3 billion a year, the economic reach of chocolate is worldwide. Labeled one of the top ten global agriculture commodities, 70% of the world's cocoa is farmed in Africa, where the cocoa industry is an important economic industry.

The hope is that sequencing the cocoa genome will allow targeted breeding of cocoa plants, enabling cocoa farmers to raise healthier crops with higher yields. This kind of breeding may also enable the development of crops that are more resistant to environmental changes and more pest and disease resistant.

Ahead of Schedule

The preliminary release of the cocoa genome sequence was announced last week, three years ahead of expectations. The sequence is called the Theobroma cacao Matina 1-6 genome sequence (referred to as Matina 1-6) and contains 1782 "supercontigs," the first ten of which account for approximately 92% of the genome. Work continues to sequence the complete genome, but the preliminary release involves 35,000 genes.

In addition to USDA-ARS, Mars, and IBM, National Center for Genome Resources (NCGR), Clemson University, HudsonAlpha Institute for Biotechnology, Indiana University, and Washington State University were involved in the researching and sequencing of Matina 1-6.

The gene sequence is freely available to the public at: http://www.cacaogenomedb.org/

Genomics at Work

With the public availability of Matina1-6, chocolate-loving students with an interest in genomics can join the investigation and build a science project around the search for specific types of resistance in genes. For example, students could predict which cacao pathogens the Matina 1-6 cacao plant is resistant to based on the genome sequence. One place to start might be to do background research on common threats to the cacao plant—fungi and other pathogens that commonly attack cacao. Then search for genes in other plants that are known to convey resistance to those pathogens. Examining Matinal 1-6 for similar genes would allow students to make predictions about resistance.

Those looking for an introduction to genomics will find science project ideas in the Science Buddies genetics & genomics section.

And, for those who like their chocolate unsequenced: