Arabica Coffee Originated More Than 600,000 Years Ago in Ethiopia: Study https://www.sci.news/genetics/coffea-ar ... 12861.html
An international team of scientists has generated the highest quality reference genome to date of the world’s most popular coffee species, Arabica coffee (Coffea arabica). Their results suggest that this species developed more than 600,000 years ago in the forests of Ethiopia via natural mating between two other coffee species: Coffea eugenioides and Robusta coffee (Coffea canephora).
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. Arabica’s population 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, as well as determine how modern cultivated varieties are related to each other,” said University at Buffalo’s Professor Victor Albert. From their new reference genome, accomplished using cutting-edge DNA sequencing technology and advanced data science, Professor Albert and his colleagues were 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,” said Nestlé Research’s Dr. Patrick Descombes. “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.” Coffea arabica formed as a natural hybridization between Coffea canephora and Coffea eugenioides, whereupon it received two sets of chromosomes from each parent. Scientists have had a hard time pinpointing exactly when — and where — this allopolyploidization event took place, with estimates ranging everywhere from 10,000 to 1 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 Coffea arabica formed sometime before that, anywhere from 610,000 to 1 million years ago. “In other words, the crossbreeding that created Arabica wasn’t something that humans did. It’s pretty clear that this polyploidy event predated modern humans and the cultivation of coffee,” Professor Albert said.
Coffee plants have long been thought to have developed in Ethiopia, but varieties that the team collected around the Great Rift Valley, which 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 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 CE, 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,” Dr. Descombes said. “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.”
East Africa’s geoclimatic history is well documented due to research on human origins, so researchers could contrast climate events with how the wild and cultivated Arabica populations fluctuated over time. Modeling shows a long period of low population size between 20,000 and 100,000 years ago, which roughly coincides with an extended drought and cooler climate believed to have hit the region between 40,000-70,000 years ago. The population then increased during the African humid period, around 6,000-15,000 years ago, when growth conditions were likely more beneficial. During this same time, around 30,000 years ago, the wild varieties and the varieties that would eventually become cultivated by humans split from each other. “They still occasionally bred with each other, but likely stopped around the end of the African humid period and the widening of the strait due to rising sea levels around 8,000 to 9,000 years ago,” said Dr. Jarkko Salojärvi, a researcher at Nanyang Technological University.
The results appear online this week in the journal Nature Genetics. J. Salojärvi et al. 2024. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet 56, 721-731; doi: 10.1038/s41588-024-01695-w
Coffee Leaf Rust Battle on Kona
Suzanne Shriner picking coffee. Courtesy of Suzanne Shriner
Coffee leaf rust, or Hemileia vastatrix, was first identified in Sri Lanka in the 1860s and has impacted nearly every coffee-growing nation in the world since then. It's a fungus that debilitates and destroys coffee trees; it thrives in warm, wet conditions, and travels on the wind.
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