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Arabica Coffee: scientists obtain the highest quality reference genome of the most popular coffee in the world

A team of scientists has obtained the reference genome – and of highest quality to date, they say – of the coffee most popular in the world, Arabica, and to achieve this they have studied the evolution of this species for millennia and on several continents.

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The authors of the study, whose details were published this Monday in the journal Nature Genetics, argue that the work will help cultivate coffee plants capable of resisting climate change in the future.

The study, co-led by the University at Buffalo (UB), suggests that Coffea arabica emerged more than 600,000 years ago in the forests of Ethiopia from the natural hybridization of two other coffee species.

Then, for thousands of years, the Arabica population rose and fell depending on the Earth’s climatic events, until it ended up being cultivated in Ethiopia and Yemen, later expanding to the rest of the planet.

“We have used genomic information from living plants to go back in time and draw as precise a picture as possible of the long history of Arabica, as well as to determine the relationship between the varieties cultivated today,” explains the co-author of the study and professor from the Faculty of Letters and Sciences of the University of Buffalo, Víctor Albert.

Using their new reference genome, obtained through 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 to the species.

The reference genome is now available in a publicly accessible digital database.

A natural origin

Arabica emerged from a natural hybridization between Coffea canephora and Coffea eugenioides but scientists did not know when – and where – it happened.

To find out, the team subjected several Arabica genomes to a computational modeling program and determined that this variety was formed at some earlier time, between 610,000 and a million years ago, and that it was a natural interbreeding, prior to modern humans.

The study also showed a clear geographical division in the varieties collected around the Great Rift Valley, which runs from southeast Africa to Asia: All the wild varieties were on the western side and the cultivated ones were on the eastern side, closer to the Strait of Bab al-Mandab, which separates Africa from Yemen.

This agrees with previous evidence that coffee cultivation may have begun mainly in Yemen, around the 15th century. (It is believed that the Indian monk Baba Budan smuggled some seeds from Yemen around the year 1600, which began the globalization of this plant.)

“It seems that the diversity of Yemeni coffee may be the founder of all the main current varieties,” says Patrick Descombes, a genomics expert at Nestlé and co-author of the study.

“Coffee is not a crop that has been crossed much, like corn or wheat, to create new varieties. People chose a variety they liked and grew it. So the varieties we have today have probably existed for a long time,” says the researcher.

Genetic diversity and resistance

The reference genome also helped discover how a line of Arabica varieties gained strong resistance to the disease.

The Timor variety was formed in Southeast Asia as a spontaneous hybrid between Arabica and one of its parents, Coffea canephora. Also known as Robusta and used primarily for instant coffee, this species is more resistant to disease than Arabica.

“So, when Robusta hybridized again with Arabica in Timor, it brought with it some of its defense genes against pathogens,” explains Albert, who also co-led the sequencing of the Robusta genome in 2014.

The new Arabica reference genome allowed the team to locate a new region that harbors members of the RPP8 resistance gene family, as well as a general regulator of resistance genes, CPR1.

“These results suggest a new target locus to potentially improve pathogen resistance in Arabica,” says Salojärvi.

The genome also provided other new data, such as which wild varieties are most similar to currently cultivated Arabica coffee. They also discovered that the Typica variety, an old Dutch cultivar originating in India or Sri Lanka, is probably the mother of the Bourbon variety, cultivated primarily by the French.

“Our work has been no different from reconstructing the family tree of a very important family,” says Albert.

Source: Elcomercio

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