Unlocking the potential for cultivating coffee plants resilient to climate change in the forthcoming decades may trace its roots back to ancient times.
A collaborative effort spearheaded by the University at Buffalo has yielded what is proclaimed the most superior reference genome for Arabica, the world’s most favoured coffee species. This feat has unearthed a wealth of knowledge regarding its lineage, spanning millennia and continents, shedding light on its evolutionary journey. The findings, published in Nature Genetics, unveil that Coffea arabica emerged over 600,000 years ago in the Ethiopian forests through natural hybridisation between two other coffee species. The population of Arabica underwent fluctuations across Earth’s climatic oscillations over thousands of years before being cultivated in Ethiopia and Yemen and subsequently disseminated globally.
“We’ve utilised genomic data from contemporary plants to delve into the past and construct the most precise narrative possible of Arabica’s extensive history, while also elucidating the relationships among modern cultivated varieties,” remarks Victor Albert, PhD, co-corresponding author of the study and Empire Innovation Professor in the UB Department of Biological Sciences.
Major coffee corporations such as Starbucks and Tim Hortons rely exclusively on Arabica beans for their millions of daily servings. However, Arabica’s susceptibility to pests and diseases stems from its low genetic diversity due to a history of inbreeding and small population size, which limits its cultivation to regions with lower pathogen threats and favourable climatic conditions.
“An intricate understanding of the origins and breeding history of contemporary varieties is imperative for developing new Arabica cultivars better suited to withstand climate change,” adds Albert.
Employing cutting-edge DNA sequencing technology and advanced data science, the research team accomplished the sequencing of 39 Arabica varieties and even an 18th-century specimen used by Swedish naturalist Carl Linnaeus to classify the species. The reference genome is now accessible in a publicly available digital database.
“While other public references for Arabica coffee do exist, the quality of our team’s work is exceptionally high,” notes Patrick Descombes, senior expert in genomics at Nestlé Research and one of the study’s co-leaders.
Humanity’s adoration for coffee evolved without human intervention. Arabica originated as a natural hybridisation between Coffea canephora and Coffea eugenioides, receiving genetic contributions from both parents. This event’s precise timing and location have long been debated, with estimates ranging from 10,000 to 1 million years ago.
To pinpoint evidence of this pivotal event, UB researchers and collaborators employed computational modelling to scrutinise various Arabica genomes for signatures of its foundation. The models delineate three population bottlenecks in Arabica’s history, with the oldest occurring approximately 610,000 years ago, suggesting that Arabica formed sometime before that, potentially between 610,000 to 1 million years ago.
“In essence, the formation of Arabica was a natural occurrence predating modern humans and the domestication of coffee,” asserts Albert.
Coffee plants have traditionally been believed to have originated in Ethiopia. However, the study’s examination of wild varieties collected around the Great Rift Valley reveals a distinct geographical split: wild varieties originated from the western side. In contrast, cultivated varieties originated from the eastern side near the Bab al-Mandab strait separating Africa and Yemen. This aligns with evidence suggesting that coffee cultivation likely commenced primarily in Yemen around the 15th century.
“It appears that Yemeni coffee diversity may serve as the progenitor of all major current varieties,” observes Descombes.
The study juxtaposes climate events with fluctuations in wild and cultivated Arabica populations over time. Modelling indicates a prolonged period of low population size between 20,000 and 100,000 years ago, corresponding to an extended drought and cooler climate in the region. The population surged approximately 6,000 to 15,000 years ago during the African humid period, coinciding with more favourable growth conditions. Around 30,000 years ago, wild varieties and those destined for human cultivation diverged.
Cultivated Arabica faces a looming threat due to its low genetic diversity. It is estimated to have an adequate population size of only 10,000 to 50,000 individuals. This vulnerability leaves it susceptible to decimation by pathogens such as coffee leaf rust, which causes annual losses of $1-2 billion.
The reference genome unveils insights into how one line of Arabica varieties acquired robust resistance to disease. The Timor variety, originating in Southeast Asia as a spontaneous hybrid between Arabica and its parent, Coffea canephora, possesses more excellent disease resistance than Arabica.
“Consequently, when Robusta hybridised back into Arabica on Timor, it brought along some of its pathogen defence genes,” explains Albert.
While breeders have endeavoured to replicate this crossbreeding to enhance pathogen resistance, the new Arabica reference genome has enabled researchers to pinpoint a novel region housing members of the RPP8 resistance gene family and a general regulator of resistance genes, CPR1.
“These findings indicate a novel target locus for potentially enhancing pathogen resistance in Arabica,” remarks Jarkko Salojärvi, assistant professor at Nanyang Technological University and co-corresponding author of the study.
Furthermore, the genome reveals other novel discoveries, including the closest wild varieties to modern cultivated Arabica and the likely parentage of the Typica variety. This early Dutch cultivar is believed to be the progenitor of the Bourbon variety.
“Our endeavour has been akin to reconstructing the genealogical tree of a highly significant family,” concludes Albert.
More information: Jarkko Salojärvi et al, The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars, Nature Genetics. DOI: 10.1101/2023.09.06.556570
Journal information: Nature Genetics Provided by University at Buffalo
