Study finds all Arabica coffee derives from a single ancestor

A new study published on 13 March used modern genetics tools to trace the history of the Coffea arabica species, the most common and economically important commercial coffee crop species worldwide.

Researchers confirmed the significant likelihood that C. arabica derived from a single speciation event.

This suggests a spontaneous coupling of two different species — Coffea canephora and Coffea eugenioids —brought together the two genomes to create a new species. All C. arabica grown around the world today therefore originated from a single plant an estimated 10,000 to 20,000 years ago.

“This means that a single plant, a super-individual, has given birth to the whole C. Arabica species and to the millions of trees that are cultivated today all over the world in the intertropical belt,” says co-author and coffee breeder Benoit Bertrand of the French Agricultural Research Centre for International Development (CIRAD).

The very recent birth of the C. arabica species and the extreme form of genetic bottleneck resulting from this singular speciation event supports the researchers’ other main finding that C. arabica has lower genetic diversity that any other major crop species in the world.

“Researchers have known for a long time that the genetic diversity of Arabica coffee is low,” says World Coffee Research (WCR) CEO Dr. Jennifer “Vern” Long.

“This paper provides clear, definitive evidence that the diversity is even lower than we thought. This is tremendously concerning for a crop as important as coffee. It reveals a profound vulnerability for any business that depends on coffee. At the same time, the paper points to key pathways for reducing that vulnerability through the breeding of F1 hybrid Arabica varieties that utilise Arabica’s existing but underexploited genetic diversity, as well as for breeding with other species in the coffee family. Both activities are urgent. The good news is that both are underway.”

The study was published in Nature Scientific Reports. The research was led by World Coffee Research, Istituto di Genomica Applicata (IGA) in Italy, and CIRAD, in collaboration with the Italian Universities of Trieste, Udine, Padova, and Verona, and with key contributions from Tropical Agricultural Research and Higher Education Center, the University of Sana’a in Yemen, Texas A&M University.

The paper’s first co-authors are IGA Technology Services Agrigenomics Lead Simone Scalabrin and WCR Molecular Breeder Lucile Toniutti. Italian coffee companies illycaffè and Lavazza funded the study for the purpose of enhancing scientific knowledge to ensure the future of coffee agriculture.

WCR says the results have important implications for the future of coffee breeding programs worldwide, which typically seek to exploit genetic diversity to help farmers meet challenges ranging from a changing climate to diseases and pests. Many of the approaches used by breeders in other crops will not work for Arabica, given its dramatically low diversity.

The findings suggest that long-term, breeders will need to look to related species in the Coffea family to find adequate genetic diversity to meet the challenges ahead — especially climate change — and to use modern breeding approaches to introduce novel diversity.

Despite this, the authors also suggest that there is untapped diversity for breeders to take advantage of “hybrid vigour” by crossing Arabicas from divergent genetic groups to create new F1 hybrid varieties.

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