BUFFALO — The key to growing coffee plants that can better resist climate change in the decades to come may lie in the ancient past.
Researchers co-led by the University at Buffalo 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, to be published today in Nature Genetics, suggest that Coffea arabica developed more than 600,000 years ago in the forests of Ethiopia via natural mating between two other coffee species. Arabica’s population waxed and waned throughout Earth’s heating and cooling periods over thousands of years, the study found, 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,” says the study’s co-corresponding author, Victor Albert, PhD, Empire Innovation Professor in the UB Department of Biological Sciences, within the College of Arts and Sciences.
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 only be cultivated 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 says.
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.
The reference genome is now available in a publicly available digital database.
“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.
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.
While breeders have tried replicating this crossbreeding to boost pathogen defense, the new Arabica reference genome allowed the present researchers to pinpoint a novel region harboring members of the RPP8 resistance gene family, as well as a general regulator of resistance genes, CPR1.
“These results suggest a novel target locus for potentially improving pathogen resistance in Arabica,” Salojärvi says.
The genome provided other new findings as well, like which wild varieties are closest to modern, cultivated Arabica coffee. They also found that the Typica variety, an early Dutch cultivar originating from either India or Sri Lanka, is likely the parent of the Bourbon variety, principally cultivated by the French.
“Our work has not been unlike reconstructing the family tree of a very important family,” Albert says.
Tom Dinki