Coffee’s Prehistoric Origins Revealed Through Genome Sequencing

April 18, 2024

A report has highlighted the ancient origins of Coffea arabica, the world’s most popular coffee species, through genome sequencing. The findings suggest that Arabica coffee developed over 600,000 years ago in the forests of Ethiopia via natural hybridization between two other coffee species, Coffea canephora and Coffea eugenioides. This makes Arabica coffee significantly older than modern humans.

What is genome sequencing?

Genome sequencing is the process of determining the complete DNA sequence of an organism’s genome. In the context of coffee’s prehistoric origins, researchers used genome sequencing to analyze the DNA of various coffee species, including Coffea arabica. By comparing the genetic information, they discovered that Arabica coffee originated from a natural hybridization between two other coffee species around 600,000 years ago in the forests of Ethiopia, providing insight into its evolutionary history.

Tracing Arabica’s Lineage and Population History

By sequencing the genomes of 39 Arabica varieties, including an 18th century specimen used by Carl Linnaeus to name the species, researchers were able to create the highest quality Arabica reference genome to date. Analysis revealed that Arabica’s population fluctuated in response to Earth’s climatic changes over millennia. The population declined during an extended drought 40,000-70,000 years ago before increasing again during the African Humid Period 6,000-15,000 years ago when growing conditions improved.

Cultivation and Spread of Arabica Coffee

While Arabica coffee evolved naturally, it was later cultivated by humans, likely starting in Ethiopia and Yemen around the 15th century. According to legend, Indian monk Baba Budan smuggled seven coffee seeds out of Yemen around 1600, establishing Indian Arabica cultivars. This paved the way for coffee’s global spread. Today, coffee giants like Starbucks and Tim Hortons exclusively use Arabica beans.

Threats to Arabica Coffee Due to Low Genetic Diversity

Cultivated Arabica has a low genetic diversity stemming from its history of inbreeding and small population size. This makes it vulnerable to decimation by pests and diseases like coffee leaf rust which causes $1-2 billion in annual losses. The Arabica reference genome identified a region containing pathogen defense genes obtained when a disease-resistant Robusta variety hybridized with Arabica in Timor. This could provide a target for improving Arabica’s pathogen resistance.

Additional Facts of Arabica Coffee

Over 2.25 billion cups of coffee are consumed worldwide every day
Brazil is the world’s largest coffee producer, accounting for one-third of global production
In India, coffee is traditionally grown in the Western Ghats in the south, with the states of Karnataka, Kerala and Tamil Nadu being major producers
Two main varieties are cultivated in India 1) Arabica and 2)Robusta. Arabica is grown at higher elevations while Robusta is grown in warmer climates closer to sea level
Indian filter coffee, made by mixing frothed and boiled milk with the infusion obtained by percolation brewing of finely ground coffee powder, is a popular beverage

The new genomic insights into Arabica coffee’s prehistoric origins and population history provide a foundation for developing varieties that can withstand the impacts of climate change and ensure the beloved beverage’s future.

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