Based on a chromosome-level assembly, a study published in Nature Communications reveals the sources of genetic diversity of Arabica coffee; the genetic diversity may contribute to its unique flavour and resistance to pathogens. About 60% of global coffee production is from the Arabica coffee species.
Commercial coffee is mainly produced from Coffea canephora and Coffea arabica, known as Robusta and Arabica coffee, respectively. Arabica coffee is derived from the hybridization between the ancestors of present-day Robusta coffee and another closely related coffee species, Coffea eugeniodes. This hybridization resulted in Arabica’s coffee flavour and its large and complex genome, which poses challenges for breeding and genetic studies. Several partial genome assemblies of Arabica coffee are currently available, but the mechanisms generating its genetic diversity are unclear.
Michele Morgante from the Istituto di Genomica Applicata, Udine, Italy, and others employed the latest sequencing technologies to generate a more complete genome assembly for Arabica coffee, allowing for a detailed analysis of the structure of its chromosomes. When analysing the genome, including previously inaccessible regions, such as those around centromeres, they found differences in the structure, function and evolution of the genomes contributed by its two progenitor species, especially for genes involved in caffeine biosynthesis. The authors also analysed the genomes of 174 samples collected from different species within the Coffea genus and noticed a very low level of genetic diversity within Arabica coffee.
“The very recent origin of C. arabica does not allow us to determine if at least some of the non-shared insertions occurred after the allopolyplodisation event and could contribute to the standing sequence variation in C. arabica,” they write.
Diversity was found to increase in some Arabica coffee cultivars at specific genomic regions, due to two different sources of variation: chromosomal abnormalities and genetic segments donated by a Robusta-Arabica hybrid, known as the Timor Hybrid. This hybrid has become the parental line of many modern cultivars that combine the disease resistance trait of Robusta coffee and the unique flavour of Arabica coffee.
The authors suggest that the genetic diversity of Arabica coffee is essential for its commercial success, and the findings may help develop new coffee varieties with desirable traits, such as disease resistance or different flavour profiles.
