Assistant Professor Jarkko Salojarvi from the NTU School of Biological Sciences (SBS), together with an international team of scientists, have assembled high-quality genomes of Coffea arabica, Arabica coffee, and its parental species Coffea canephora, Robusta coffee, and Coffea eugenioides. They further used the genome information to study the specific adaptations in Arabica that have resulted in high quality coffee, and to track the history of cultivated Arabica. Finally, they identified new genomic loci in C. arabica x C. canephora hybrids that could contribute to the disease resistance amongst coffee plants. Their work was published in the journal Nature Genetics in April 2024.
Assistant Professor Jarkko Salojarvi from the NTU School of Biological Sciences (SBS).
A short introduction to coffee
For many people, coffee is a much beloved drink that wakes them up in the morning and fuels their day. It is one of the world’s most traded commodities, closing in at more than 10 million metric tons per year, and an important cash crop to countries in Southeast Asia, South America, and Africa.
The most cultivated, and appreciated, coffee type is Arabica, which accounts for more than 60 percent of the world’s coffee production. It is known for its sweeter, smoother taste with a range of fruity, nutty undertones. The remaining variety of coffee is produced from C. canephora, also known as Robusta coffee, which is stronger and more bitter, with woody undertones.
C. arabica’s historical bottlenecks
C. arabica’s biological lineage stems from a natural hybridization event between Robusta coffee and C. eugenioides, an event that the team has estimated to have taken place between 350,000-610,000 years ago.
Most Arabica cultivars today descend from two groups of plants. One is the Typica group, whose lineage comes from plants obtained from either Sri Lanka or India, and which were subsequently grown in Southeast Asia. The other is the Bourbon group, which were grown in the 17th century on the island of Bourbon, now Réunion Island, in the Indian Ocean. The team used genome data to show that the origins of all these plants can be tracked down to 16th century Yemen, which at the time held the world monopoly on coffee production.
Both groups experienced single-plant cultivation bottlenecks; one plant from the Typica group was given to the royal court in France in 1714 and its seeds were used to establish Arabica cultivation in the Caribbean, whereas only one plant from the Bourbon group had survived by 1720. This is besides the fact that all C. arabica plants descended from that single plant ancestor more than 350,000 years ago.
These bottlenecks in its cultivation history have resulted in in C. arabica suffering from low genetic diversity, making it susceptible to plant pests and diseases. Mostly due to its high susceptibility to coffee leaf rust disease, it can only be cultivated successfully in a few regions around the world that have suitable climates and where these pathogens have not yet established themselves. All it takes is for one strong disease to destroy all known C. arabica plants and to affect the livelihoods of all those who depend on it.
Coffee defenders, assemble!
In order to prevent a potentially disastrous wipeout of Arabica plants worldwide, an international team of scientists came together to study the genomic origins and breeding history of the plant. Assistant Professor Jarkko from NTU SBS collaborated with many other researchers and coffee breeders from Australia, Belgium, Brazil, Canada, China, Colombia, Finland, France, Germany, Indonesia, Italy, South Africa, Spain, Switzerland, and Uganda.
With the use of genomic analysis technologies such as PacBio High-Fidelity (HiFi) sequencing, which provides accurate long reads of up to tens of thousands of DNA base pairs, and chromosome conformation capture (Hi-C), which allows researchers to put together full chromosomes of the species, the team was able to assemble highly detailed genomic assemblies of C. arabica and the modern representatives of its progenitors, C. canephora and C. eugenioides. The team also sequenced the most common coffee cultivars, representing ca. 95% of the world’s coffee production, and a C. arabica x C. canephora hybrid discovered on the island of Timor in 1927. This hybrid demonstrates a strong resistance to coffee leaf rust, or Hemileia vastatrix, a destructive fungal disease that can result in defoliation of a coffee plant, affecting the quality and quantity of the coffee berries. Unfortunately, this Timor hybrid produces a lower quality coffee, and therefore subsequent breeding efforts have been targeted towards improving the cup quality.
With the highly detailed genomic assemblies, it will be possible to better predict the future performance of a seedling based on its genetic markers rather than wait years for the plant to bear fruit. The team was also able to identify candidate genomic regions that contribute to disease resistance against coffee leaf rust. The next step for the team is to breed new coffee plants that bear this disease resistance trait, but which are still able to produce the delicious goodness of Arabica coffee.
Commercial Collaboration
Nestlé strongly supported this research by using high quality genomics approaches – including long and short reads high throughput sequencing – to create this arabica reference. Plant scientists from Nestlé’s Institute of Agricultural Sciences collaborated with genomics experts from Nestlé’s Institute of Food Safety and Analytics to decode the genetic blueprint of this coffee species and dive into the details of arabica’s genetic makeup. This work contributes to Nestlé’s commitment to achieve net zero emissions by 2050 by ensuring a sustainable future for coffee cultivation through the exploration of new, higher yielding arabica varieties with greater resistance to disease and drought. You can find out more at Nestlé’s Research & Development YouTube and LinkedIn.