The world loves chocolate, but thousands of years of selective breeding have drastically changed the genome of the trees from which chocolate is made. The plants now produce tastier chocolate, but they also make less due to harmful mutations.
The key ingredient in chocolate is cocoa powder. This is made from the seeds of the cocoa tree or cacao tree (), which is native to tropical forests in Central and South America.
Now a team led by , a geneticist at food giant Mars Incorporated, has sequenced 200 genomes of wild and domestic trees to explore their evolutionary history. It is the first study of cocoa trees on such a scale.
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A spokesperson for Mars explained that they fund Motomayor’s work to help protect their business. “There are extreme challenges to cocoa as a crop,” the spokesperson said. “Obviously, as a chocolate company… we want to protect cocoa.”
3600 years of cocoa
The researchers found deleterious mutations in many trees from different varieties, which affect the productivity of the crop. These mutations were particularly pronounced in a rare variety called Criollo, which has a nutty flavour and is used to make some of the world’s most expensive chocolate.
This could be a result of breeding efforts to produce cocoa that tastes less bitter, says Motomayor. “That created an accumulation of mutations that led to a loss of fitness, where these cocoa trees produce very little.”
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Most chocolate is made using other varieties, often dubbed “Forastero”. However, genetic material from Criollo is found in many of them. For example, one key cultivar used for breeding in Latin America, CCN-51, .
The researchers believe they can pinpoint the beginning of Criollo’s domestication to 3,600 years ago. In line with this, pottery from the Olmec city of San Lorenzo in what is now Mexico, dating to 1600-1800BC, – a chemical found in cocoa.
When the team compared genomes from today’s Criollo and other trees, they found that the domesticated Criollo had genes that are possibly associated with lower levels of chemicals called polyphenols. If so, that could account for its cocoa tasting less bitter than it once did.
Once the study is peer-reviewed, it will represent “a huge contribution to cacao genomics science”, says molecular biologist at Pennsylvania State University in Philadelphia. Understanding the cocoa tree’s genetic diversity will help breeders develop disease-resistant plants, he says.
Chocolate shortage
The global chocolate market is worth , according to research firm Markets and Markets, and .
However, the trees are notoriously tricky to grow. They are susceptible to many diseases and become less productive as they age. Currently there is a small global surplus of cocoa, but some fear as soon as 2020.
“We have an indication that the surplus is in decline because of increasing demand in emerging markets [such as China and India],” says at market research firm Euromonitor. If supply can’t meet demand, the price of chocolate would likely rise.
We need to breed robustness back into cocoa trees, says at the University of Florida in Gainesville. The 200 genomes will hopefully allow advantageous traits in wild trees to be brought to domesticated populations, he says.
“It’s probably an emergency because the tree takes so long to grow,” says Folta.
This is especially important in west Africa, which produces around two-thirds of the global cocoa supply. Cocoa trees are not native to this region, so the represents yet another genetic bottleneck – and is experiencing reduced disease resistance and lower crop yields.
“Right now, we’re fitting one variety to God knows how many landscapes, soils, water and climate regimes,” says , an agriculture advisor at Concern Worldwide in London, UK. “It would be nice if farmers and the agriculture industries in these countries had a few different things to work with when they’re plant breeding.”
bioRxiv
