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Why the end of the world’s most popular coffee could be nigh

Without a fix, climate change and disease are poised to kill off the most prized variety

by Alex Scott
February 12, 2018 | A version of this story appeared in Volume 96, Issue 7

A greenhouse with coffee plants inside.
Credit: Coffee World Research
Conventional breeders and genetic engineers are both trying to make arabica coffee plants more robust.

Mark Dunhill, CEO of English coffee, tea, and cocoa retailer Whittard of Chelsea, is obsessed with sourcing the finest ingredients. His kitchen brims with parcels of dark chocolate and tea caddies full of exotic varieties.

But Dunhill’s even bigger obsession appears to be coffee. Every 10 days, a silver pouch packed with freshly grown and roasted coffee beans arrive from countries such as Guatemala, Tanzania and the Congo. He carefully weighs and grinds the beans before pouring them into an espresso machine that hisses as it delivers caffeine-powered perfection.

For Dunhill, as for most of the world’s billion or so coffee drinkers, coffee has to be made with beans from Coffea arabica—a shrub discovered hundreds of years ago in the southwestern highlands of Ethiopia—or not at all. To switch to the bitter beans of C. canephora, also known as robusta, would be anathema.

“Arabica beans provide a radically different and infinitely more pleasurable drinking experience,” Dunhill says. Robusta is typically relegated to instant coffee.

Unfortunately for the coffee world, arabica is also genetically predisposed for extinction. Cultivated arabica plants have a genetic diversity of just 1.2%, compared with more than 20% for crops such as rice and soy, making it less able to adapt to changing conditions. And it is a fragile, weakling of a variety that is susceptible to disease, including coffee leaf rust caused by the fungus Hemileia vastatrix, and pests such as the coffee borer beetle.

Compounding the problem, climate change in coffee-growing areas is forecast to increase stress on arabica, making it more vulnerable to pests and disease.

Stirred to action, coffee producers are working to protect arabica by crossbreeding it with more resilient Coffea varieties. But a debate on the rescue plan is heating up, with some scientists criticizing crossbreeding for being slow and inaccurate. They say genetic modification is the best way to ensure arabica does not go the way of the Gros Michel, a tasty species of banana wiped out by a fungus in the mid-20th century.

Coffee breeders reject this notion as well as any increased reliance on pesticides. They are counting on crossbreeding and better farming techniques to ensure arabica’s survival.

Time isn’t on arabica’s side. A leaf rust epidemic that began around 2008 wiped out large tracts of production across Central America. As long ago as 1890, rust killed off most of the arabica plants in Sri Lanka, until then a major coffee supplier to the U.K. It forced Sri Lankan growers to start growing tea, a move that is widely believed to have turned England into the nation of tea drinkers it is today.

According to research published by London’s Royal Botanic Gardens last year in the journal Nature Plants (2017, DOI: 10.1038/nplants.2017.81), climate change will make up to 60% of the growing land in Ethiopia—a major supplier—unsuitable for coffee cultivation by the end of the century.

Spilling the beans on Coffea arabica

5.8 million metric tons: Production in 2017
1.2%: Arabica’s genetic diversity
15%: Share of production lost to rust
10–14 days: Time it takes for rust to appear after first infection.
1990: Year coffee leaf rust became a global problem
40%: Share of Colombia’s coffee crop wiped out in 2008 by rust
3 billion: Number of trees Colombian growers have had to replant since 2008.

Sources: The American Phytopathological Society, International Coffee Organization, London’s Royal Botanic Gardens.

Across the world, arabica crops are already being “chased up the hillside” to cooler climes, says World Coffee Research, an organization set up in 2012 by coffee producers to protect and enhance supplies of quality coffee. WCR has since begun a program to breed a resilient variety of arabica. Coffee retailers such as Starbucks have also introduced programs to breed arabica with greater disease resistance.

WCR is working with experts around the world to identify wild arabica relatives in Ethiopia, or varieties maintained in agricultural institutes, that resist disease such as rust and crossbreed them with the weakling varieties we get our coffee beans from today.

The group has already created 46 arabica hybrids designed for enhanced resistance to fungal diseases and is now testing them in the field. It plans to introduce the best performers commercially in 2023.

WCR’s scientific director, Christophe Montagnon, acknowledges that the main focus is disease resistance and that heat tolerance won’t be bred into arabica soon.

“It is very unlikely that we find now the very plant that will be necessary in 2050. We are improving the coffee populations step-by-step,” Montagnon says.

But the crossbreeding advocated by Montagnon is not just slow but also somewhat clumsy, according to some scientists. “They are basically trying to breed a racehorse with a donkey. And it takes many, many years of backcrossing to get rid of the donkey,” says Brande Wulff, crop genetics project leader for the U.K.’s John Innes Centre, whose grandfather happened to be a tea grower in Sri Lanka.

Genetic engineering is a quicker and more effective alternative to crossbreeding for heat tolerance and disease resistance, Wulff argues. “With genetic modification, you can go to the wild relatives, identify resistance genes that matter, take them out with molecular tweezers, and stick them straight into your elite material to clinically combine the best of both worlds,” he says.

Lessons already learned from applying genetic engineering to other plant species should be transferable to arabica, Wulff suggests. “Resistance genes are like eyes that see the presence of the pathogen, and when they detect a pathogen, they can turn on defense mechanisms,” he says.

A green coffee leaf infected with a fungus has orange, crusty patches.
Credit: Coffee Buyers Club
Arabica plants struggle against fungus, as seen here, and against rising temperatures.

Techniques such as CRISPR can be used to change a single or a few base pairs of DNA, but Wulff says traditional genetic engineering approaches are required to incorporate a full resistance gene, which is typically 30–100 DNA base pairs long.

A fungus might generate millions of spores, of which just one has a mutation that enables it to overcome a plant’s resistance. Two resistance genes would reduce the probability of the pathogen’s success to one in 1 trillion. Each new resistance gene can increase the odds against the pathogen’s success 1 million times. “If you introduce a stack of five genes, it should be durable for 100 years,” Wulff says.

The cost of cloning disease-resistance genes has tumbled in recent years and now stands at roughly $70,000 per gene. And the work could be done in a few months. “So it is becoming much more affordable to clone these agronomically important genes,” Wulff says.

University of California, Davis, researchers brought genetically modifying arabica coffee a step closer to reality in early 2017 when they released the genome sequence for the plant. “This new genome sequence for C. arabica contains information crucial for developing high-quality, disease-resistant coffee varieties that can adapt to the climate changes,” said UC Davis geneticist Juan Medrano, researcher on the sequencing effort, at the time of the publication.

But WCR, which has the backing of more than 30 coffee-producing organizations, maintains that genetic modification is not an option. “The coffee world and story is not yet compatible with genetic modification,” Montagnon says diplomatically. Indeed, at this time there is no genetically modified coffee on sale anywhere in the world and no major plan under way to introduce it.

Wulff admits that genetically modified coffee would face social and regulatory challenges. The big agricultural companies are the only ones that can afford the multi-million-dollar regulatory costs required to bring such a product to market, he says.

In the absence of genetic modification, three of the world’s biggest agrochemical firms—BASF, Bayer, and Syngenta—say they have pesticides and other technologies that will protect arabica.

Syngenta has introduced NuCoffee, a package of services that support best practices in coffee cultivation, including pesticide-use protocols. The approach is leading to significantly higher yields for coffee crops, says Daniel Bachner, a senior crop protection executive at Syngenta in Brazil.

Meanwhile, BASF says it has begun offering coffee producers a variety of the mineral kaolin, which forms a dusty coating that puts off pests while also protecting against sunburn and keeping plant canopies cooler. Named Surround, the material doubles bean yields in coffee bushes, according to Peter Barrows, international business director for BASF subsidiary TKI.

BASF is also targeting leaf rust with an array of pesticides. “We are planning to launch a host of new products across all indications by the end of the decade,” BASF says. One example is Revysol, a triazole-based antifungal that the firm hopes will be its next blockbuster fungicide.

WCR isn’t fond of these approaches either. “I don’t believe the solution is in pesticides,” Montagnon says. “I believe—and other scientists do—that we should be looking more at plant health.” Good use of fertilizer and farming practices such as promoting shade can be more efficient than the use of pesticides to protect rust-susceptible coffee plants, he argues.

Montagnon points to studies, including one being undertaken by Jacques Avelino, a plant pathologist at the French agricultural research institute CIRAD. According to Avelino, who has been studying coffee cultivation for 30 years and is an adviser to WCR, farming practices that promote shading of arabica bushes can be highly effective at reducing rust and other diseases.

Scientists like Wulff warn that farming improvements and crossbreeding, however well meaning, could fail to fight off climate change, pests, and disease. Consumers will then be forced to make a choice: Either switch to bitter robusta or wake up and smell the genetically modified coffee.

But Montagnon, who himself has 28 years of experience in breeding coffee plants and has published more than 100 articles on the subject, is confident that a combination of crossbreeding and better farming practices is the best way of ensuring arabica’s survival.

He’s also confident this approach will produce the exquisite-tasting coffee that consumers demand. Whittard’s Dunhill, among others, will be hoping that Montagnon is right and that shiny pouches of freshly roasted arabica beans will drop onto his doormat for years to come.


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