Chromosome-level assembly reveals low genetic diversity of Arabica coffee | Top Vip News

Based on an assembly at the chromosome level, a study published in Nature Communications reveals the sources of genetic diversity in Arabica coffee; Genetic diversity may contribute to its unique flavor and resistance to pathogens. About 60% of the world’s coffee production comes 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 hybridization between the ancestors of today’s Robusta coffee and another closely related coffee species, Coffea eugeniodes. This hybridization resulted in the flavor of Arabica coffee and its large, complex genome, which poses challenges for genetic and breeding studies. Several partial genomic assemblies of Arabica coffee are currently available, but the mechanisms generating its genetic diversity are unclear.

Michele Morgante of the Istituto di Genomica Applicata, Udine, Italy, and others employed the latest sequencing technologies to generate a more complete genome assembly of Arabica coffee, allowing detailed analysis of the structure of its chromosomes. By analyzing the genome, including previously inaccessible regions, such as those surrounding the centromeres, they found differences in the structure, function and evolution of the genomes contributed by their two progenitor species, especially in the genes involved in caffeine biosynthesis. The authors also analyzed the genomes of 174 samples collected from different species within the genus Coffea and noted a very low level of genetic diversity within Arabica coffee.

“The very recent origin of C. arabica does not allow us to determine whether at least some of the non-shared insertions occurred after the allopolyplodization event and could contribute to permanent sequence variation in C. arabica,” they write.

Diversity was found to increase in some Arabica coffee cultivars in 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 flavor of Arabica coffee.

The authors suggest that the genetic diversity of Arabica coffee is essential to its commercial success, and the findings may help develop new coffee varieties with desirable traits, such as disease resistance or different flavor profiles.