Scientists have sequenced the highest quality reference genome to date of the most popular coffee variety, Arabica, revealing secrets of its lineage, spanning millennia and continents.Arabica
Their findings, published in Nature Genetics, suggest that Coffea arabica developed over 600,000 years ago in the forests of Ethiopia through natural crossbreeding between two other coffee species. The study found that the Arabica population increased and decreased during Earth’s warming and cooling periods for thousands of years, before being cultivated in Ethiopia and Yemen, and then spread worldwide.
“We have used genomic information from living plants today to go back in time and paint the most accurate picture possible of Arabica’s long history, as well as to determine how modern cultivated varieties are related to each other,” says study co-author Victor Albert, a professor in the Department of Biological Sciences at the University of Buffalo, in a statement.
Coffee giants like Starbucks and Tim Hortons exclusively use Arabica plant beans to prepare the millions of cups of coffee they serve every day; however, partly due to low genetic diversity derived from a history of inbreeding and a small population size, Arabica is susceptible to many pests and diseases and can only be grown in a few places in the world where pathogen threats are lower and climatic conditions are more favorable.
“A detailed understanding of the origins and history of modern cultivated varieties is crucial for developing new Arabica cultivars better adapted to climate change,” says Albert in a statement.
From their new reference genome, achieved using cutting-edge DNA sequencing technology and advanced data science, the team was able to sequence 39 Arabica varieties and even a specimen from the 18th century used by the Swedish naturalist Carl Linnaeus to name the species.
The reference genome is now available in a publicly accessible digital database.
“Although there are other public references on Arabica coffee, the quality of our team’s work is extremely high,” says study co-director Patrick Descombes, a senior genomics expert at Nestlé Research. “We used state-of-the-art genomic approaches, including high-throughput long- and short-read DNA sequencing, to create the most advanced, complete, and continuous Arabica reference genome to date.”
Represents 60% of the world’s coffee
Arabica is the source of approximately 60% of the world’s total coffee products, and its seeds help millions of people start their day or stay awake late. However, the initial crossbreeding that created it occurred without any human intervention.
Arabica formed as a natural hybridization between Coffea canephora and Coffea eugenioides, where it received two sets of chromosomes from each parent. Scientists have struggled to determine exactly when and where this allopolyploidization event took place, with estimates ranging from 10,000 to 1 million years ago.
To find evidence of the original event, UB researchers and their partners ran their various Arabica genomes through a computational modeling program to search for species-specific signatures. The models show three demographic bottlenecks throughout Arabica’s history; the oldest occurred about 29,000 generations ago (or 610,000 years). This suggests that Arabica formed at some point earlier, between 610,000 and 1 million years ago, say the researchers.
“In other words, the crossbreeding that created Arabica was not something humans did,” says Albert. “It is quite clear that this polyploidy event predates modern humans and coffee cultivation.”
It was long thought that coffee plants developed in Ethiopia, but the varieties the team collected around the Great Rift Valley, which stretches from southeast Africa to Asia, showed a clear geographic division. All wild varieties studied originated on the western side, while all cultivated varieties originated on the eastern side, closer to the Bab al-Mandab Strait that separates Africa and Yemen.
This would coincide with evidence that coffee cultivation may have primarily begun in Yemen around the 15th century. It is believed that the Indian monk Baba Budan smuggled the legendary “seven seeds” from Yemen around 1600, establishing Indian Arabica crops and setting the stage for the global reach of coffee today.
“It seems that Yemeni coffee diversity may be the founder of all major current varieties,” says Descombes. “Coffee is not a crop that has been heavily crossed, like corn or wheat, to create new varieties. People mainly chose a variety they liked and then cultivated it. So the varieties we have today likely have existed for a long time.”
