Genetic heritage of Arabica coffee discovered

The key to growing coffee plants that will be more resilient to climate change in the coming decades may lie in our archaic past.

Scientists co-led by the University at Buffalo have created what they say is the highest-quality reference genome of the world’s most popular coffee variety, Arabica, revealing secrets about its lineage that spans millennia and continents.

Their findings, published today in Genetics of naturesuggest that Arabic coffee It evolved more than 600,000 years ago in the forests of Ethiopia through a natural cross between two other coffee species. Arabica’s population waxed and waned with the Earth’s warming and cooling for thousands of years, studies have shown, before eventually being cultivated in Ethiopia and Yemen and then spreading around the globe.

We used genomic information from plants living today to go back in time and build the most exact picture possible of Arabica’s long history, as well as to determine how current cultivars are related to each other.”

Victor Albert, Ph.D., corresponding author of the study, Empire Innovation Professor in the Department of Biological Sciences, College of Arts and Sciences at the University of Buffalo

Coffee giants like Starbucks and Tim Hortons employ only Arabica beans to brew the millions of cups of coffee they serve every day. However, due in part to low genetic diversity resulting from a history of inbreeding and compact population sizes, Arabica is susceptible to a range of pests and diseases and can only be grown in a few places in the world where pathogen threats are lower and climates are more favorable.

“A detailed understanding of the origins and breeding history of current varieties is crucial to developing recent Arabica varieties that are better adapted to climate change,” says Albert.

Using a recent reference genome, obtained using cutting-edge DNA sequencing technology and advanced data science, the team managed to sequence 39 Arabica varieties and even the 18th-century specimen that Swedish naturalist Carl Linnaeus based his name on.

The reference genome is now available in a publicly available digital database.

“While there are other public references for Arabica coffee, the quality of our team’s work is extremely high,” says co-leader Patrick Descombes, senior genomics expert at Nestlé Research. “We used state-of-the-art genomic approaches—including high-throughput, long-read DNA sequencing—to create the most advanced, complete, and continuous Arabica reference genome to date.”

Humanity’s Favorite Coffee Was Created Without Human Aid

Arabica is the source of about 60% of the world’s coffee, and its seeds facilitate millions of people start their day or stay up delayed. But the initial crossbreeding that created it happened without any human intervention.

To find evidence of the original event, UB scientists and their partners ran the genomes of different Arabica species through a computer modeling program to look for traces of a species substrate.

“In other words, the crossbreeding that created Arabica was not something humans did,” Albert says. “It’s pretty clear that this polyploid event preceded current humans and coffee cultivation.”

Coffee plants were long thought to have developed in Ethiopia, but the varieties the team collected from around the Great Rift Valley, which stretches from southeastern Africa to Asia, showed a distinct geographic divide. All the wild varieties studied came from the western side, while all the cultivated varieties came from the eastern side, closest to the Bab el-Mandab Strait, which separates Africa from Yemen.

This would be consistent with evidence that coffee cultivation may have begun primarily in Yemen, around the 15th century. It is believed that the Indian monk Baba Budan smuggled the legendary “seven seeds” out of Yemen around 1600, establishing the Indian Arabica varieties and setting the stage for coffee’s global reach today.

“It looks like the Yemeni coffee variety may have been the founder of all the major varieties we have today,” Descombes says. “Coffee is not a plant that has been heavily cross-bred, like corn or wheat, to create recent varieties. People basically chose the variety they liked and then grew it. So the varieties we have today probably have been around for a long time.”

How Climate Has Affected the Arabica Population

East Africa’s geoclimatic history is well documented through research into human origins, which has allowed scientists to compare climatic changes with population changes in wild and cultivated Arabica over time.

Modelling shows a long period of low population between 20,000 and 100,000 years ago, roughly coinciding with a prolonged drought and cooler climate that probably hit the region between 40,000 and 70,000 years ago. Then, populations increased during the Saturated Africa period, around 6,000–15,000 years ago, when growing conditions were probably more favourable.

At the same time, about 30,000 years ago, wild varieties diverged from the varieties that would eventually be cultivated by humans.

“They continued to breed occasionally, but they probably stopped breeding at the end of the African muggy period and with the widening of the strait due to sea level rise, around 8,000–9,000 years ago,” says Jarkko Salojärvi, an assistant professor at Nanyang Technological University in Singapore and a co-author of the paper.

Low genetic diversity threatens Arabica

The cultivated Arabica population is estimated to have an effective size of only 10,000 to 50,000 individuals. Its low genetic diversity means that it could be completely decimated, like a monoculture of Cavendish bananas, by pathogens such as coffee leaf rust, which causes losses of $1-2 billion per year.

The reference genome allowed for a more detailed explanation of how one line of Arabica varieties acquired robust resistance to the disease.

The Timor variety originated in Southeast Asia as a natural hybrid between an Arabica variety and one of its parent varieties, Canephora coffee. Also known as Robusta and used primarily for instant coffee, this variety is more disease resistant than Arabica.

“In this way, when Robusta recrossed with Arabica in Timor, it brought with it some of its pathogen defense genes,” says Albert, who co-led the 2014 sequencing of the Robusta genome. The current work by Albert and colleagues also presents a much improved version of the Robusta genome, as well as recent sequences from other Arabica progenitor species, Eugenia coffee.

While breeders tried to repeat this cross to enhance their defenses against pathogens, the recent Arabica reference genome allowed current scientists to pinpoint a recent region where members of the RPP8 resistance gene family and general resistance gene regulator, CPR1.

“These results indicate a recent target locus that has the potential to improve pathogen resistance in Arabica,” says Salojärvi.

The genome also yielded other recent findings, such as which wild varieties are closest to current, cultivated Arabica coffee. They also found that Typica, an early Dutch variety that originated in India or Sri Lanka, is likely the ancestor of Bourbon, a variety cultivated primarily by the French.

“Our work was like reconstructing the family tree of a very crucial family,” Albert says.