Aromatic Arabica coffee accounts for around 60 percent of the coffee consumed worldwide. Researchers have now analyzed the genetic details of this type of coffee. Although Coffea arabica has very little genetic diversity, the analysis shows how diverse variations still arise. The results can also help develop new coffee varieties with desirable properties such as disease resistance or a specific flavor profile.
There are around 100 different types of coffee plants worldwide. However, two varieties dominate the world market: the mild, aromatic Arabica coffee (Coffea arabica) and the stronger Robusta coffee (Coffea canephora). Robusta coffee is less susceptible to disease and can be grown at lower altitudes and at higher temperatures than Arabica coffee. The more sensitive Arabica coffee is considered to be more aromatic and easier to digest. It was created from a cross between the ancestors of today’s Robusta coffee and another type of coffee, Coffea eugeniodes.
Study commissioned by Lavazza and Illycafè
Since Coffea arabica is a hybrid breed, its genome is particularly complex. The plant carries both sets of chromosomes from both parent species, so it has a total of four instead of two copies of each chromosome. This poses a challenge for genetic studies because it makes it difficult to assign the sequenced DNA sections. To date, several partial genomes of Arabica coffee have already been available. However, it was unclear how exactly these are connected and which sections are assigned to which chromosomes.
Using a modern sequencing method that makes it possible to record longer sections of the genome in one go, a team led by Simone Scalabrin from the Italian biotechnology company IGA Technology Services in Udine has now created a complete genome of Arabica coffee for the first time. The researchers also recorded previously inaccessible regions of the genetic material. The study was financed by, among others, the coffee companies Lavazza and Illycafè.
Low genetic diversity
Consistent with previous analyses, the researchers found that Coffea arabica has very low overall genetic diversity. At the same time, however, they found an explanation why Arabica coffee can still show large variations in properties and aromas: “In a limited number of genomic regions, the diversity in some cultivated genotypes increases to a level similar to that in one of the progenitor species, Coffea canephora.” , report Scalabrin and his colleagues. The various Arabica cultivars therefore differ significantly in these few gene regions, although their genome otherwise shows little diversity.
From the research team’s point of view, the reason for this is likely that over the course of the recent history of Arabica coffee, some genes from another hybrid variety found their way into the plant’s genome. This is the so-called Timor hybrid – a cross between Coffea arabica and Coffea canephora, which is resistant to several plant diseases. On the one hand, these genes represent a source of new genetic diversity for Arabica coffee. On the other hand, the team warns: “The changes discovered appear to be due to recent contamination events of the current seed pool. They could pose a threat to genetic purity if new Arabica plantations were established with sexually propagated material from these sources.”
Sources of variation
In addition, Scalabrin and his team explored the origins of popular varieties of Arabica coffee, including Bourbon and Geisha. How could these arise despite the low genetic diversity? The genome analyzes show that there was a genetic exchange between individual chromosomes of Coffea arabica, both shortly after the origin of the species and more recently. Other changes on individual chromosomes could also be detected, including deleted or duplicated sections. “These changes could represent a significant source of genetic variation in such a low-variability species,” the team writes.
According to the researchers, the results can help develop new coffee varieties that have desirable properties, including resistance to common diseases or a special flavor profile.
Source: Simone Scalabrin (IGA Technology Services, Udine, Italy) et al., Nature Communications, doi: 10.1038/s41467-023-44449-8