After more than 10 years of teamwork planning and two years of mapping genes, two separate research groups have announced the complete sequencing of the genomes of two of the major cacao tree varieties.
Much of the world’s chocolate comes from cocoa beans harvested from the Theobroma cacao tree. The Forastero variety—used mainly in the bulk of the world’s chocolate production, and Criollo—used for its exceptionally fine taste.
Unfortunately, almost all cacao trees are highly susceptible to disease and cacao growers are constantly fighting plant plagues and the disruption of the sources of supply.
Brazil’s cacao crop, which once dominated the world market, was been decimated by a fungal blight known as witch’s broom. The fungus probably co-evolved with the cacao tree in Amazonia. Once the domesticated trees were cultivated in fields of genetically similar plants, the fungus had a field day and spread uncontrollably.
So far, witch’s broom and its equally destructive cousin, frosty pod, have not spread to cacao trees in Africa, where 70 percent of the world’s cacao is now grown. The old world cacao fields are not disease-free, however. Other fungi, such as black pod, as well as viruses and insect plagues have also affected cocoa bean crops in Africa and now in the newer plantations in Southeast Asia.
Cocoa bean shortages resulting from these plagues cost farmers an estimated $700 million in losses each year and are of particular to concern to larger candy companies which account for more than three-quarters of all the chocolate products sold in the United States each year.
To help ensure the health of cacao trees all over the world, two years ago Mars and Hershey announced separate plans to fund the sequencing of the cacao tree genome. The group that received funds from Mars and the U.S. Department of Agriculture went after the Forastero genome while Hershey partnered with Penn State University and CIRAD, a French agency based in Paris that studies agricultural issues in developing countries, to work on the Criollo genome.
The goal isn’t to produce genetically modified candy bars. Rather, by sequencing the cacao tree genome, geneticists are providing plant breeders all over the world with a powerful new tool known as marker-assisted selection (MAS) that can be used to accelerate the breeding process for disease resistance and other valuable traits like drought tolerance and even flavor and texture.
Having the cacao genome in hand could also provide a unique opportunity to study genetic interactions between pathogens and hosts. Since scientists already have the genomes of witches broom and frosty pod allowing them to find the genetic triggers underlying the infection, that could be a very useful weapon in fighting disease.
However, even with these advancements, there is much work that remains to be done. The next step, identifying molecular markers, is a complicated and painstaking process. Sequencing is the easy part. Assembling the genome and identifying the markers is really the art form. It’s kind of like assembling a 3-dimensional jigsaw puzzle—one for each of the 10 chromosomes in the cacao genome, each comprised of 40 million puzzle pieces.
In the end, a team of 60 scientists working at 20 different institutes in six different countries were able to assemble 76 percent of the Criollo genome and identify 96 percent of the genes. The Forastero genome project met with even greater success, with 92 percent of the genome assembled, including 35,000 genes.
While the two simultaneous projects might recall the infamous race between Celera Genomics and the publicly financed Human Genome Project to sequence the human genome, both cacao genome groups compliment each other for providing the opportunity to compare the two closely related Forastero and Criollo varieties.
The Forastero genome recently became available online and the Criollo sequence will be posted on the National Center for Biotechnology Information (NCBI) website, also home to the human genome.
Both groups intend to continue perfecting their respective sequences, while moving into the next stage of translating the roughly 420 million-unit DNA sequences into heartier cacao plants around the world.
It’s not only about helping chocolate manufacturers make better products; it should also help farmers create a more reliable crop that can be grown in an environmentally sustainable way.
That’s great news for 3.5 million substance farmers who depend on growing cacao for a living, and for chocolate-loving people who can look forward to enjoying great chocolate for years to come.