Brewing Up a Better Cup

Every day, millions of cups of coffee are served at corporate giants like Starbucks and Tim Hortons to help people power through their mornings. The beans used for this daily caffeine fix are almost exclusively from Coffea arabica, the most popular coffee species in the world.

But as the climate rapidly changes, Arabica is at risk.

To better understand its history and safeguard its survival, a study co-led by researchers at the University at Buffalo has created what they say is the highest-quality reference genome of Arabica.

It turns out the key to growing coffee plants that can better resist climate change may lie in their ancient past.

Coffea arabica developed more than 600,000 years ago in Ethiopia, the researchers’ findings suggest. Its population waxed and waned throughout Earth’s heating and cooling periods over thousands of years, before it was eventually cultivated in Ethiopia and Yemen and then spread across the globe.

“We’ve used genomic information in plants alive today to go back in time and paint the most accurate picture possible of Arabica’s long history, as well as determine how modern cultivated varieties are related to each other,” said Victor Albert, Empire Innovation Professor in UB’s Department of Biological Sciences and the study’s co-corresponding author.

What’s notable in the story of Arabica’s development is a history of inbreeding and small population size, resulting in a low genetic diversity that makes it susceptible to pests and diseases. That means it can be cultivated in only a few places in the world where pathogen threats are lower and climate conditions are more favorable.

Understanding this, said Albert, is critical to developing new varieties that are better adapted to climate change.

For their study, the research team used cutting-edge DNA sequencing technology and advanced data science to create their reference genome, which enabled them to sequence and carefully study 39 additional Arabica varieties.

These genomic data shed light on how one line of Arabica varieties obtained strong resistance to coffee leaf rust, a disease that causes $1 billion to $2 billion in losses annually.

This Timor variety formed in Southeast Asia as a hybrid between Arabica and one of its parents, Coffea canephora. Also known as Robusta and used primarily for instant coffee (although it is sometimes mixed in with Arabica), this species is more resistant to disease than Arabica.

“Thus, when Robusta hybridized itself back into Arabica on Timor,” explained Albert, “it brought some of its pathogen defense genes along with it.”

While breeders have tried replicating this crossbreeding to boost pathogen defense, the new Arabica reference genome allowed the present researchers to pinpoint a specific region harboring genes critical for disease resistance.

“Our work has not been unlike reconstructing the genealogical tree of a very important family of people,” Albert said.