An international team of scientists has generated the highest quality reference genome to date for coffee arabica, the world's most popular coffee species (arabica coffee tree). Their results suggest that this species developed through natural hybridization between two other coffee species in the forests of Ethiopia more than 600,000 years ago. coffee tree and robusta coffee (Coffea genus).
Arabica is the source of approximately 60% of all coffee products in the world, and its seeds help millions of people start their day and stay up late.
Arabica populations waxed and waned throughout millennia of Earth's heating and cooling periods, eventually being cultivated in Ethiopia and Yemen and then spreading around the world.
Professor Victor Albert of the University at Buffalo said: “We are using genomic information from living plants to go back in time and map the long history of Arabica as accurately as possible, and to understand how modern cultivars have evolved. “We have clarified whether the two are interrelated.'' .
From a new reference genome created using state-of-the-art DNA sequencing technology and advanced data science, Professor Albert and his colleagues identified 39 Arabica species and the 18 that Swedish naturalist Carl Linnaeus used to name the species. Even century specimens could be sequenced.
“Although other public references exist on Arabica coffee, the quality of our team's research is very high,” said Dr. Patrick Descombe from Nestlé Research.
“We used state-of-the-art genomics approaches, including long-read and short-read high-throughput DNA sequencing, to create the most advanced, complete and continuous Arabica reference genome to date.”
arabica coffee tree It is formed as a natural hybrid between Coffea genus and coffee treethen received two sets of chromosomes from each parent.
Scientists have struggled to pinpoint exactly when and where this allopolyploidization phenomenon occurred, with estimates ranging from 10,000 years ago to 1 million years ago.
To find evidence of the original event, the researchers ran the genomes of various Arabica species through a computational modeling program, looking for traces of the species' foundation.
The model shows three population bottlenecks in the history of Arabica, the oldest of which occurred about 29,000 generations, or 610,000 years ago.
this suggests arabica coffee tree It was formed shortly before that, between 610,000 and 1 million years ago.
“So the hybridization that produced Arabica was not human-made. It is clear that this polyploidy phenomenon predates modern humans and coffee cultivation,” Professor Albert said.
Coffee trees were long thought to have developed in Ethiopia, but the varieties the researchers collected around the Great Rift Valley, which stretches from southeastern Africa to Asia, showed a clear geographic divide.
The wild species studied all originate from the western side, whereas all cultivated varieties originate from the eastern side, closest to the Bab al-Mandab strait that separates Africa and Yemen.
This is consistent with evidence that coffee cultivation may have originated primarily in Yemen around the 15th century.
Indian monk Baba Budhan believed it Around 1600 AD, the legendary “seven seeds” were smuggled out of Yemen, establishing the Indian Arabica variety and setting the stage for today's global spread of coffee.
“It appears that Yemen's coffee diversity may be the originator of all of today's major varieties,” Dr. Descombe said.
“Coffee is not a crop that has been highly hybridized to create new varieties, like corn or wheat.”
“People mainly chose their favorite varieties and grew them. So the varieties we have today have probably been around for a long time.”
East Africa's geo-climatic history is well documented through research on human origins, allowing researchers to understand how climate change and wild and cultivated Arabica populations have fluctuated over time. can be compared.
Modeling shows a long period of low population size between 20,000 and 100,000 years ago, combined with a prolonged drought that is thought to have hit the region between 40,000 and 70,000 years ago. This almost corresponds to a cold climate.
The population then increased during the Wet Period in Africa, about 6,000 to 15,000 years ago, and growing conditions are thought to have become more favorable.
Around the same time, about 30,000 years ago, wild species diverged from the varieties that would eventually become domesticated by humans.
“They still occasionally breed with each other, but this probably stopped around 8,000 to 9,000 years ago, around the end of the African Humid Period and the widening of the straits due to rising sea levels,” said Yarko, a researcher at the Southern Ocean Institute of Technology. Dr. Sarojärvi said. University.
of result Published in an online journal this week natural genetics.
_____
J. Sarojärvi other. 2024. Allopolyploid genomes and population genomics arabica coffee tree Uncovering the history of modern coffee variety diversification. Nat Genet 56, 721-731; doi: 10.1038/s41588-024-01695-w
Source: www.sci.news
