HudsonAlpha Scientists Help Secure the Future of Chocolate with Improved Cacao Reference Genome

People around the world consumed nearly 7.7 million tons of chocolate in the last year, but the cacao crop that supports the production of these sweets is under significant environmental threat.

Millions of cacao farmers in West Africa, Southeast Asia and Latin America feel the pressures of ever-increasing consumption, a changing climate and devastating fungal infections. In 2017, The New York Times said there is “a battle to save the world’s favorite treat.”

Scientists at the HudsonAlpha Institute for Biotechnology with funding from Mars Wrigley Confectionery have created the newest weapon in that battle — an improved reference genome to help researchers and farmers develop healthier, more productive cacao crops.

Sweets Under Siege

The production of one of the world’s favorite delicacies relies on a particularly delicate plant. Cacao can only be grown within 20 degrees of the equator, and global studies suggest that the effects of climate change will shrink the farmland currently suitable for production even further. Increasing temperature and decreasing humidity in the areas that currently produce cacao will mean the crop must be grown at higher elevations.

Cacao also proves particularly vulnerable to fungi and diseases. It suffers from a number of menacingly named blights, including frosty pod rot, witches’ broom, black pod and cacao swollen-shoot virus. One fear is that if any of these blights spread from its native region, it could sweep through global crops, devastating worldwide production.

The Newest Weapon in the War to Save Cacao

HudsonAlpha scientists have completed and released an updated reference genome for the tree that produces cacao beans. Researchers generated this resource using advanced long-read sequencers to produce an updated reference genome than the first version, which was completed in 2010. 

A reference genome identifies parts of the genome to be carried through to the next generation of plants, such as genes that promote drought tolerance, increase yield or improve disease resistance. Then, researchers can sequence each generation of selectively bred plants to quickly find which ones carry the desirable traits.

This most recent effort was was led by HudsonAlpha faculty investigators Dr. Jane Grimwood and Jeremy Schmutz.

“As our technology improves, we’re able to produce more detailed, versatile reference genomes, which are critical for the kind of rapid crop improvement you want to see with cacao,” Schmutz said.

Farmers have used selective breeding to improve crops for centuries. The process works by crossbreeding two plants, hoping to combine desirable traits and make hardier plants. Then, the offspring with those traits are bred again. This selective breeding process takes time though, because each crop must mature. A cacao tree, for example, takes about five years to start generating fruit.

A Better “Chocolate Tree”

Cacao trees, like many modern crops, do not show much genetic diversity. Most of the cacao trees worldwide come from a handful of clones selected in the 1940s. Because the trees are so closely related, they have similar genetic weaknesses. If a disease reaches a group of cacao trees that doesn’t carry any genetic resistance to that disease, it can destroy the entire crop. 

“Having so little genetic diversity leaves the cacao tree vulnerable,” said Grimwood. “However, it also means that genes can be exchanged between trees, which gives researchers and farmers an opportunity.”

Using this new reference genome, researchers will be able to guide crossbreeding and hybridization efforts more quickly. That means traits such as drought tolerance can be bred into a population faster and disease resistances can be introduced more efficiently.

The “chocolate tree” remains under threat, but now scientists and farmers alike have a more complete tool kit to produce more robust cacao crops.