Cracking the code: exploring the mysteries of flavor variation in genetically similar arabica coffee beans

In the realm of coffee, the unique nuances of a single-origin Colombian bean, when roasted and ground alongside its Ethiopian counterpart, evoke distinct flavors discernible to the astute coffee aficionado. Yet, a recent study has unveiled that these flavor disparities and other defining characteristics among coffee varieties worldwide do not solely stem from individual genetic variations, but rather, from extensive chromosomal reorganization encompassing swaps, deletions, and rearrangements.

Genetic Insights and Chromosomal Reorganization

The most exhaustive genome sequencing endeavor of Coffea arabica to date has unveiled minimal divergence in the 'letters' of DNA strands between different varieties. Michele Morgante, a plant geneticist from the University of Udine, Italy, and a key contributor to the study, remarks, "If you look at single nucleotide variations, the levels are anywhere from 10 to 100 times lower than any other species."

Employing cutting-edge next-generation sequencing technology capable of uninterrupted reading of DNA strands up to hundreds of thousands of base pairs in length, Morgante and his team have propelled significant advancements in coffee genetics. Their findings, published in Nature Communications, represent a paradigm shift in the understanding of coffee genetics.

“With those type of technologies, it becomes much easier to assemble the genome and you can also assemble regions that were previously inaccessible,” says Morgante.

The genetic makeup of coffee holds profound significance, as evidenced by the cultivation and sale of 10 million tonnes of the crop in the 2022–23 period. Coffee, deriving from two principal species—Coffea canephora, colloquially known as robusta, and Coffea arabica, recognized as arabica—often blends beans from both species. However, single-species beans are also prevalent, with arabica beans accounting for approximately 56% of total coffee sales.

Impact of Polyploidy on Arabica Coffee Diversity

Unlike most organisms where genetic variation primarily arises from hybridization with other species, C. arabica, characterized by polyploidy with multiple copies of each chromosome, experiences infrequent interbreeding. This contrasts with C. canephora, which possesses two copies of each chromosome, posing challenges for arabica's interbreeding.

Consequently, C. arabica's primary source of single nucleotide variation is mutation, occurring steadily over time. Despite its relative youth, emerging as a hybrid of robusta and Coffea eugenioides—a lesser-cultivated coffee species—within the past 50,000 years, C. arabica exhibits notable physical variation, including diverse flavor profiles and disease resistance.

“From that single plant, which has basically no variation, you create the whole species, and then the variation that you have is only the novel mutations that have occurred since that event,” Morgante says.

Juan Medrano, emeritus geneticist at the UC Davis Coffee Center, underscores the structural and chromosomal variability within C. arabica, noting, "We're always talking about low variability at the DNA level, but there is variability at the structural level, at the chromosomal level, at the level of deletions … and insertions."

The study unveils significant chromosomal rearrangements, particularly in the Bourbon varietal of C. arabica, showcasing deletions and even complete chromosome absences. Michele Morgante highlights instances where certain varieties exhibited only three chromosome copies, such as two canephora and one eugenioides, contrasting with others featuring five copies, including two eugenioides and three canephora.

Practical Implications for Coffee Breeders

Beyond elucidating C. arabica's phenotypic diversity, the sequenced genome holds immense value for coffee breeders amidst challenges posed by diseases and climate change. Kassahun Tesfaye, a plant geneticist at the Institute of Biotechnology at Addis Ababa University, emphasizes the genome's role in comprehending coffee's evolution and guiding breeding programs to select for desirable traits like disease resistance and low caffeine levels.

“Getting a proper in-depth understanding of the genome would basically help us to understand how the crop evolved and also understand the genomes of coffee in line with its parents,” remarks Tesfaye. This comprehensive understanding of the coffee genome serves as a compass guiding coffee breeding programs towards selecting traits like resistance to the notorious coffee rust fungus or the cultivation of beans with low caffeine levels, as highlighted by Tesfaye. However, the real challenge lies in translating this wealth of genomic knowledge into tangible outcomes for coffee breeders. “We need to equip breeders, mostly in the developing countries, with the toolkits to breed for low caffeine, to breed for specific disease [resistance], to breed for high productivity,” emphasizes Tesfaye.