World Coffee Research reveals its latest study on Arabica’s lack of diversity

With the 2008 rust outbreak in Central and South America now behind us, many in the coffee industry will be wishing for a period of calm predictability. However, according to a new study from World Coffee Research (WCR), the Arabica species of coffee on which the industry relies for its high-end product remains at risk. According to WCR’s latest research, the plant is spectacularly ill-equipped to overcome the increasing challenges being thrown at it by factors such as climate change due to its extremely limited genetic diversity. Tim Schilling is the Executive Director of WCR, which has just completed the largest ever study of the genetic diversity of Arabica through the process of genotype sequencing. It was carried out in partnership with genomic technology company Nature Source Genetics. What they found was a lack of genetic diversity in the Arabica species – a fact that leaves the plant  vulnerable to our changing environmental conditions. “The amount of genetic diversity of Arabica is not adequate to face up to the challenges that we’re looking at in this century,” Schilling tells GCR Magazine. “I’m specifically referring to direct effects of climate change and climate-change-induced diseases and insects.” Schilling’s team sequenced 260 billion basepairs of DNA out of 1000 lines of coffee, including 800 original Ethiopian lines collected back in the 1960s by the Food and Agricultural Organisation of the United Nations and French plant explorers. These samples came from a collection held at the Tropical Agricultural Research and Higher Education Centre (CATIE) in Costa Rica. This collection was part of the Arabica World Collection that was gathered together by researchers working in Ethiopia in the 1950s and 60s. Dr. Vincent Petiard of Nature Source Genetics says that, as well as mapping the genetic make-up of Arabica, he hoped the research would suggest a more efficient means of maintaining this collection that has to be kept alive because coffee seeds cannot maintain their germination capability for more than one year. “Why maintain thousands of plants in a field collection and spend so much money doing so if one could protect most of the diversity with only 50 or 100 plants selected for their richness in original genes?” Petiard says. “The money that would be saved would be better used for breeding.” The results of the study showed that, of the 800 original Arabica accessions analysed, the level of genetic diversity was worryingly low, with 98.8 per cent similarity among the samples. This compares remarkably unfavourably to other major crops such as rice, maize, and wheat, which display between 75 – 80 per cent similarity, and far different to vegetables such as tomatoes, where the cultivated varieties represent just 2 per cent of the full scale of the plant’s genetic diversity. While the results of the study are cause for concern for the industry, they were somewhat expected, says Petiard: “When considering the origin of Arabica [the addition of two individuals from two different species] we expected this result but maybe not as little diversity as that.” This is because Arabica itself is the result of a one-off genetic event that occurred in Ethiopia some 10,000 years ago. “The birth of Arabica coffee came from, let’s say, a one-night stand – a single genetic event in Ethiopia 10,000 years ago,” says WCR’s Schilling. “Suddenly some pollen from the Coffea eugenioides species got onto the canephora [Robusta] plant and, lo and behold, the baby that came from that turned out to be Arabica and it thrived.” With Arabica proving to be the most prized of the many different species of the coffee plant due to the quality of its fruit, it spread around the world. Since researchers assembled the Arabica World Collection more than 50 years ago, the Ethiopian government has become far more protective of its most valued export, limiting outside access to its coffee resources in a bid to protect what they see as their nation’s intellectual property. However, Petiard says that the results of this research indicate that this protectiveness could be misguided. “In my opinion it would be very interesting to run the same project on the Ethiopian collection  and evaluate just how much more diversity, if any, it could add to what we have observed in the CATIE collection that is originated from Ethiopia and Yemen,” he says. “It very well could be that the Ethiopian collections are also diversity-constrained and that there is no treasure of original diversity in the coffee birth land. In addition to telling them what is important to preserve, a clear answer to this question will allow the Ethiopian scientists and authorities to establish clear strategies and make I hope the above decisions about the maintenance and the use of their collections.” In addition to the Ethiopian samples found in the Arabica World Collection at CATIE, WCR and Nature Source Genetics were able to analyse a number of samples of Yemeni Arabica from the University of Agriculture in Sana’a. These samples did show some positive signs of diversity that could be used to help WCR devise some short-term fixes for the challenges Arabica faces, according to Schilling. “Over the 1500 years that the Ethiopian varieties migrated into Yemen, there was natural selection in Yemen that wasn’t going on in Ethiopia and, given the harsh conditions of Yemen, we suspect that this is good news for Arabica coffee dealing with climate change because we feel that there might be some kind of discovery there in terms of drought resistance,” Schilling says. “The short-term strategy is utilising the variability that is there – including the Yemeni variability – for the creation of rust-resistant hybrids with high quality traits. We can do that within five years now.” Longer term, WCR intends to focus on other strategies to meet this challenge. “There’s a couple of things that we can do genetically. One is to re-do what nature did 10,000 years ago, but do it better,” Schilling says. “We’re taking several of those eugenioides and canephora species and crossing them.” Petiard of Nature Source Genetics says that the resilience and diversity in the Robusta species is key to coffee’s future. “My gut feeling tells me that it would be easier to breed for a good quality Robusta than for a sustainable Arabica,” he says. “Some of the roasters have already understood that and are looking for good cup quality from Robustas that originate from certain countries and are also treated the same as Arabica after harvest.” Professor Juan Medrano of the University of California, Davis, has viewed the results of the study and is relatively optimistic about the prospects for breeding coffee in the future due to the sophisticated DNA technology available. “Phenotyping [measuring genetic traits] of the accessions is the key to the future, ” he says. “For example, the Geisha variety of coffee was found in La Esmeralda in Panama from an accession brought from the CATIE collection. Geisha is a unique example of natural variation of quality and flavour and there may be other accessions with unique traits in this collection.”
Schilling says that this challenge comes at a time when people are becoming more concerned than ever about coffee quality, driving the need for action even more.
“People are waking up to the intricacies of the quality that exists out there, but at the same time the potential of being hit by a major pandemic or other epidemics is just getting higher and higher and we just do not have the tools that you need genetically to deal with it,” he says. Luckily, he says today’s technology makes it possible to carry out the cross breeding selectively, picking out some of the traits in Robusta, such as resistance to rust and tolerance of drought, that make it a desirable species for breeding, while keeping the quality of Arabica. “The challenge here is to integrate the Robusta into Arabica, keeping all of the positive traits of each,” he says. Schilling says that the technology available makes it reactively easy to carry out this process efficiently: “We can mark all of the genes or sequences that we’re interested in and then we’re able to spot them easily in their progeny because we can read their DNA.” GCR WCR would like to acknowledge the work of the Borlaug Institute at Texas A&M University and Nature Source Genetics, the subcontractor who did the diversity analysis.