From an afternoon candy bar to a delicious helping of ice cream, chocolate has undoubtedly become one of humankind’s favorite indulgences. But the seductive sweet’s journey begins long before it reaches your taste buds. It starts with a single fragile cocoa bean—the key ingredient in chocolate—that takes nearly five years to mature into a fruit-producing cocoa tree. During these years, the world’s 6.5 million cocoa farmers lose roughly one-third of their crop to drought, disease and pests.
An unfortunate fact of life? Science says not so fast. In 2008, IBM teamed up with the United States Department of Agriculture’s Agricultural Research Service (USDA-ARS) and the world’s largest producer of chocolate products, Mars, Incorporated, to sequence the cocoa genome in an effort to help the cocoa farmer grow heartier, more disease-resistant and more productive cocoa trees.
The Mayans first domesticated cocoa nearly 3000 years ago in Central America, but roughly 70 percent of today’s global cocoa production is produced in equatorial Africa. There are more than 2,000,000 small-scale farms in West Africa alone. The majority of these farms are family-owned plots with fewer than five acres of land. Suppliers in the trade typically come from a long line of farmers with intimate knowledge of the land. But modest plot sizes leave farmers and their families susceptible to the environmental challenges that can dramatically affect farmers’ cocoa crops—and thus their livelihood.
As it stands today, roughly one-third of all cocoa produced in Africa is lost to drought, pests and fungal disease. This adds up to an estimated annual loss of US$700,000,000 to US$800,000,000. Faced with such devastation, farmers must work harder and devote more of their limited arable land to cocoa in order to stay profitable.
Quickly, the core of the problem became apparent. Mars researchers needed to explore the genetics of the cocoa plant. If they could take the best of the different varieties of cocoa trees and combine them into more resilient and productive cultivars, that could help improve the crops. They had to sequence the cocoa genome. This process would require a deep understanding of genetic processes, as well as an enormous amount of computing power. While Mars certainly had a deep understanding of cocoa and chocolate, and the USDA had extensive experience in breeding crops, the group needed a highly specialized technology expertise for this undertaking. They found it in IBM’s Computational Biology Laboratory, which had the computing power and analytics expertise to tackle the problem.
“In late 2007, it became very apparent to me that we would not have a continuous supply of cocoa going into the future if we did not intervene on a massive scale to secure our supply chain.”
“Cocoa Genome ‘Will Save Chocolate Industry’,” BBC NewsNovember, 14, 2010
“This effort, which will allow fast and accurate traditional breeding, is about applying the best of what science has to offer in taking an under-served crop and under-served population and giving them both the chance to flourish.”
“Mars Inc, IBM and USDA map genome for cocoa plant,” ReutersSeptember 15, 2010
“By assembling the sequence fragments into the complete genome sequence and developing a detailed genetic map, we can help maximize the potential yield and income for cocoa farmers and catalyze future research and endeavors involving the cacao tree.”
“Mars Inc, IBM, USDA map genome for cocoa plant,” ReutersSeptember 15, 2010
“Sequencing the genomes of agriculture crops is a critical step if we want to better understand and improve a crop.”
“USDA-ARS, Mars and IBM Intend to Sequence and Study the Cocoa Genome,” IBM Press ReleaseJune 26, 2008
“You still need the basic biology and work in the greenhouse, but we can help plant experts zoom in. At the end of the day, the desirable traits being sought in cocoa are all genetic sequences.”
“A Genetic Quest for Better Chocolate,” New York TimesJune 25, 2008
“The knowledge of the genome will not only change the future of its cultivation, but stands to throw light on its past: a genetic rationale for when it was domesticated; its then and now close relatives in the Amazonian family and many more such intriguing questions.”
Launched in 2008, the collaboration among Mars, the USDA and IBM set off to sequence the cocoa genome in order to identify and isolate specific gene variations that correlate to desirable hereditary traits. One gene sequence might give a tree its ability to tolerate drought, while another variant helps tolerate pests. One might give the cocoa its rich taste, while yet another translates into higher yield.
Thus, completing the cocoa genome sequencing would help give Mars scientists the tools they need to eliminate the trial-and-error of traditional hybridization, enabling them to breed improved crops faster. “You don’t have to wait an entire crop cycle to find out if you selected the right plant or not,” said Ajay Royyuru, head of IBM’s Computational Biology Center. Howard-Yana Shapiro, global head of plant science and research at Mars, estimates the new genome information will cut breeding times from five to seven years down to 18 months.
The accelerated breeding time is not simply a luxury for botanists or a cost-savings for chocolate makers. The development of a stronger, more productive cocoa strain is first and foremost critical to the livelihoods of the millions of farmers who supply the world market with good, quality cocoa. But the team is also on a strict timeline to keep up with global demand for chocolate. As Shapiro notes, “Cote d’Ivoire is the largest producer of cocoa in the world. Mars has bought cocoa from there for sixty years. ... In 10 years, under a 2% increase in consumption we will need (an area corresponding to) another Cote d’Ivoire.” In short, there are no more places to grow cocoa; there is no more arable land with the right mix of soil and weather conditions for cocoa to thrive. The chocolate industry has to do more with less land. Reducing the one-third of crop production currently lost to drought and disease will go a long way to help.
What was originally billed as a five-year engagement was completed three years ahead of schedule—due in no small part to the smart analytics developed at IBM. On September 15, 2010, Mars released preliminary findings into the public domain through the Public Intellectual Property Resource for Agriculture, which supports agricultural innovation for both humanitarian and small-scale commercial purposes. The initial release accounted for 92 percent of the cocoa genome and approximately 35,000 genes, which can now be used by any other researcher, agronomist, government agency or company seeking to improve the cocoa crop.
The work is far from over. The foundation of understanding the cocoa tree has been laid with the unraveling of its genome. Bioinformaticians and computational biologists are now wading through the next level of data (RNA), while biologists and botanists are getting their hands dirty in the greenhouse, creating, testing and improving genetic variations through breeding. They are growing hybrid plants, and hybrids of hybrids, to select the right variants that will stand up to the rigors of the world outside the greenhouse.
With the help of IBM, the sequencing of the cocoa genome will change the future of its cultivation—so the storied taste of chocolate can become a more sustainable product for the world to enjoy for generations to come.
Selected team members who contributed to this Icon of Progress:
IBM Computational Biology Laboratory
- Ajay Royyuru Senior Manager, IBM Computational Biology Center
- Niina Haiminen Research Scientist, Computational Biology
- Laxmi Parida Manager, Computational Genomics
- Isidore Rigoutsos Professor, Jefferson Medical College
- Howard-Yana Shapiro Global Head of Plant Science and Research, Mars, Incorporated
United States Department of Agriculture-Agricultural Research Service
- Judy St. John USDA-ARS Deputy Administrator for Crop Production and Protection