The work makes it possible to tell the story of the fusion of genomes that gave rise to the world’s most consumed
The Power of Genomic Knowledge
“With the knowledge of the genome, it is possible to obtain information that allows us to go in two directions: the development of varieties by directing crossbreeding, in other words, as a reference to guide us in future crossbreeding that produces new varieties; and more direct interventions, such as modifying a gene specifically,” summarizes Douglas Domingues, currently a researcher at the Plant Genomics and Transcriptomics Group of the Luiz de Queiroz School of Agriculture at the University of São Paulo (ESALQ-USP), in Brazil, and one of the authors of the paper (developed when he was still working at the Rio Claro campus of the São Paulo State University).
According to him, there was a bit of a race to sequence the genome. “The price of sequencing has come down a lot, and coffee was one of the few commodities that hadn’t had its reference genome sequenced. There were other groups trying, and there was a paper published just before ours. But most of them used the standard strategy: choosing an interesting plant for cultivation and sequencing its genome,” he reports.
Unique Approach to Sequencing
The group to which Domingues belongs has sequenced a plant that is not interesting from an agronomic point of view but has a lot to offer from a genetic point of view. “The advantage of our reference genome is that it’s derived from a ’dihaploid’ individual. This results in a homogeneous reference genome that will be a superior standard for future research,” explains Patrick Descombes, coordinator of the work and senior expert in genomics at the Nestlé Institute of Food Safety & Analytical Sciences. He explains that Arabica coffee is a tetraploid: it has two genomes in one because it is the fusion of two other species.
By sequencing a dihaploid derived from Arabica coffee compared to a common tetraploid variety, scientists get a clearer and more simplified view of the genome. This makes it possible to identify variations between similar genes with greater precision, facilitating the use of molecular information for improvement studies.
Historical Insights Through DNA
In this study, the group was able to determine more precisely when this fusion took place: no more than 600,000 years ago, C. canephora and C. eugenioides fused to form this tetraploid hybrid, which continued its evolutionary path. “We came to this conclusion using
“We used the latest genomic technologies, i.e. long reads from the high-fidelity PacBio system [for gene sequencing] and proximity ligation with short reads from Illumina [an integrated system for analyzing genetic variation and biological function], to generate the chromosome assembly. This combination resulted in a chromosome-level assembly of the highest quality and integrity,” says Descombes.
The Quest for Disease Resistance
According to the ESALQ-USP professor, among the cultivated species, something very important for breeding was the introduction of genes for resistance to coffee leaf rust. “In the 1930s, Brazil played an important role in this regard. And the IAC [Agronomic Institute of Campinas, also in the state of São Paulo] is a pioneering center for studies and breeding. IAC researchers provided us with plants that predate the institution’s breeding program, which dates back to the 1930s. Disease-oriented breeding emerged between the 1960s and 1970s, and the main work was to cross a rust-resistant Arabica plant, the so-called Timor hybrid, with plants grown in various countries so that the new varieties would be resistant. But it wasn’t known which genes were responsible for the resistance.”
Discovered in the fields of Timor Island in the 1920s, the Timor hybrid is naturally resistant to rust and other diseases. “In addition to rust, coffee berry disease, coffee berry borer and coffee stem borer are three other major pests affecting production in many regions of the world. Climate change is also a key concern in the control of pests and diseases, as it allows them to spread to new regions. The trade of green coffee beans between different regions is another factor that can facilitate the spread of certain pests and diseases to new areas,” reveals Maud Lepelley, manager of the Plant Genetics and Chemistry group at the Nestlé Institute of Agricultural Sciences.
In the paper now published, the group has managed to find sets of genes already linked in the literature to disease resistance that are only present in post-improvement varieties. “Somehow the Timor hybrid managed to get these resistance genes, and now we know which ones. There are dozens of them, but we’ve narrowed the search. Arabica coffee has 69,000 genes; we’ve narrowed it down to just under 30 genes. Being able to identify these candidate resistance genes, which were previously unknown, is an unprecedented achievement in our research,” points out Domingues.
But the work is far from over, as these genes have yet to be tested. “More research will be needed to identify and create varieties that are resistant to these and other coffee pests and diseases,” says Lepelley.
Using molecular genetics, the consortium was also able to make a triple separation, showing that the genetic diversity of Ethiopia’s wild plants differs from that of the coffee grown today, probably due to a bottleneck effect and domestication, as few plants were selected for this process. “We’ve shown here that the genetic diversity was already very low among wild specimens due to multiple pre-domestication bottlenecks, and that the genotypes selected for cultivation by man, both the ancient local Ethiopian varieties and the more recent ones, were already somewhat mixed between divergent lineages,” the scientists state.
Gene Expression and Coffee Aroma
At the same time, Domingues’ group was able to observe some events related to the expression of genes linked to coffee quality, especially aroma. They studied the terpene synthase enzymes, which in plants are related to defense against insects, as well as a gene related to lipid compounds in coffee, which codes for fatty DOI: 10.1038/s41588-024-01695-w