Coffee plants are very sensitive to their environment, which is why they are not grown everywhere. With climate change, will farmers who grow the precious beans always be able to do so?
Researchers from the University at Buffalo declared that the key to growing coffee plants that can better resist climate change in the decades to come may lie in the ancient past. They have created what they say is the highest quality reference genome to date of the world’s most popular coffee species, Arabica, unearthing secrets about its lineage that span millennia and continents.
Their findings, just published in the prestigious journal Nature Genetics under the title “The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars,” suggest that this species developed more than 600,000 years ago in the forests of Ethiopia through natural mating between two other coffee species. The study found that the number of this plant waxed and waned throughout Earth’s heating and cooling periods over thousands of years before eventually being cultivated in Ethiopia and Yemen and then spread over 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 and determine how modern cultivated varieties are related to each other,” said the study’s co-corresponding author, biology Prof. Victor Albert.
Coffee giants like Starbucks and Tim Hortons exclusively use beans from Arabica plants to brew the millions of cups of coffee they serve everyday, yet, in part due to a low genetic diversity stemming from a history of inbreeding and small population size, Arabica is susceptible to many pests and diseases and can be cultivated only in a few places in the world where pathogen threats are lower and climate conditions are more favorable.
“A detailed understanding of the origins and breeding history of contemporary varieties are crucial to developing new Arabica cultivars better adapted to climate change,” Albert noted.
Arabica genome breakthrough
From their new reference genome, accomplished using cutting-edge DNA sequencing technology and advanced data science, the team was able to sequence 39 Arabica varieties and even an 18th century specimen used by Swedish naturalist Carl Linnaeus to name the species.
“While other public references for Arabica coffee do exist, the quality of our team’s work is extremely high,” says one of the study’s co-leaders, Patrick Descombes, senior expert in genomics at Nestlé Research. “We used state-of-the-art genomics approaches - including long- and short-read high throughput DNA sequencing - to create the most advanced, complete and continuous Arabica reference genome to date.”
Arabica is the source of approximately 60% of the world’s total coffee products, with its seeds helping millions start their day or stay up late. However, the initial crossbreeding that created it was done without any intervention from humans, the researchers wrote.
Arabica formed as a natural hybridization between Coffea canephora and Coffea eugenioides, when it received two sets of chromosomes from each parent. Scientists have had a hard time pinpointing exactly when and where this event took place, with estimates ranging everywhere from 10,000 to one million years ago.
To find evidence for the original event, the researchers ran their various Arabica genomes through a computational modeling program to look for signatures of the species’ foundation. The models show three population bottlenecks during Arabica’s history, with the oldest happening some 29,000 generations -or 610,000 years - ago. This suggests Arabica formed sometime before that, anywhere from 610,000 to a million years ago. “In other words, the crossbreeding that created Arabica wasn’t something that humans did,” said Albert. “It’s quite clear that this event predated modern humans and the cultivation of coffee.”
Coffee plants have long been thought to have developed in Ethiopia, but varieties that the team collected around the Great Rift Valley that stretches from Southeast Africa to Asia, displayed a clear geographic split. The wild varieties studied all originated from the western side, while the cultivated varieties all originated from the eastern side closest to the Bab al-Mandab (“Gait of Tears”) strait that separates Africa and Yemen.
That would align with evidence that coffee cultivation may have started principally in Yemen, around the 15th century. Indian monk Baba Budan is believed to have smuggled the fabled “seven seeds” out of Yemen around 1600, establishing Indian Arabica cultivars and setting the stage for coffee’s global reach today.
“It looks like Yemeni coffee diversity may be the founder of all of the current major varieties,” Descombes suggested. “Coffee is not a crop that has been heavily crossbred, such as maize or wheat, to create new varieties. People mainly chose a variety they liked and then grew it - so the varieties we have today have probably been around for a long time.”
“Our work has not been unlike reconstructing the family tree of a very important family,” Albert concluded.