Arabica is a hybrid of Coffea eugenioides and Robusta (Coffea canephora). While C. eugenioides and Robusta are normal diploid species, Arabica is an allotetraploid, meaning that it has two chromosome sets derived from the diploid parental species. Polyploid genomes are difficult to assemble, which is why Arabica was one of the last major crop species without a genome assembly.
Approximately 60 per cent of the world’s coffee products are from Coffea arabica. From an evolutionary perspective, its two parental species diverged relatively recently, only approximately 4.5 to 7 million years ago, meaning that they can still form viable hybrids such as Arabica. The Arabica speciation was a single spontaneous event that happened between 20,000 and 1 million years ago, according to previous estimates.
”At the beginning of our work, the Arabica genome had not yet been properly assembled, and the existing genome of Robusta was also far from complete,” Jarkko Salojärvi from the University of Helsinki comments. Jarkko was the principal investigator of the project. The research consortium assembled the genomes of Arabica and its two parental species and used these resources to study the evolutionary history of Arabica. Specifically, what happened to the newly established allopolyploid and what was the population history underlying the cultivated coffee species.
The consortium refined the origins of Arabica to around 350,000–610,000 years ago. They discovered that the hybridization that founded Arabica did not cause a genomic shock, an incompatibility due to a conflict between genomes from two different species, but instead evolution has proceeded at the same pace as in its diploid parental species.
The research found that Arabica has undergone several population bottlenecks – periods of low genetic variation – during its history over the recent hundreds of thousands of years. ”With the means of genomics we also tracked the history of cultivated coffee, and found out that the most famous Arabica lineages, Bourbon and Typica, are closely related. They also share history with Indian coffee variants. This finding supports the historical tale of an Indian monk Baba Budan who smuggled the so-called seven seeds from Yemen in his beard, breaking the world-wide coffee monopoly that Yemen held at the time,” Salojärvi describes.
Better taste and resistance to coffee leaf rust
Because the cultivated coffee species are all closely related, their genomes are very similar. This is why they are very prone for different kinds of pathogens. The most severe one is coffee leaf rust (Hemileia vastatrix) which obliterated the coffee empire of Ceylon (presently Sri Lanka) in less than a decade in the 1870s.
Fortunately for all the coffee drinkers, in 1927 a spontaneously formed Coffea canephora x Coffea arabica hybrid was found in Timor, Southeast Asia. Most of the current leaf rust-resistant coffee varieties are descendants of this plant.
“Unfortunately, the quality of coffee from the Timor hybrid is lower than from the classic Arabica variants. Our genome assembly will be useful in coffee breeding, as it will be faster to develop a variety that is both resistant to leaf rust and also produces high quality coffee,” Salojärvi tells.
The researchers identified a shared genomic region in the Timor hybrid-based cultivars that may convey resistance to coffee leaf rust. The region originates from Robusta (Coffea canephora) and it contains resistance genes that are expressed in leaf rust resistant varieties but not in susceptible cultivars. The genomic region is being further studied for rust resistance. The researchers also identified possible causes for the decreased taste from gene families that affect the quality and palatability of coffee.
“Brazilian coffee breeders, who were also co-authors in this publication, are already using the coffee genome in their daily work,” Salojärvi adds.
Original article