Editor’s Note: This article first appeared in Roast Magazine‘s July/August 2019 issue, and is reprinted here with permission. You can view the original piece in a free online preview here and download a pdf of the article, courtesy Roast Magazine.

Coffee Leaf Rust: Past, Present and Future in the Fight Against Fungus

Part II

By Chris Kornman


Recent research on Hemileia vastatrix, presented by Juan Carlos Herrera at the biannual ASIC (Association for Science and Information in Coffee) convention in October 2018, in Portland, Oregon, shed new light on the blight’s behaviors. Cenicafé, the science arm of the Federación Nacional de Cafeteros de Colombia (FNC, Colombian Coffee Federation), found that stressors—including too much sunlight and too little nitrogen in the soil—can increase coffee’s susceptibility to the rust fungus. It’s worth noting that non-hybrid arabica varieties like Bourbon and Caturra were especially prone to stress-related increases in infection. Planting different species of coffee in the field together, such as robusta and arabica, surprisingly increased rust’s potency.

Agronomists’ first response to rust, regardless of the species or its host, has overwhelmingly been to select and breed resistance. In 1911, one of coffee’s earliest known selections was made on Doddengooda Estate in Mysore, India, from a Typica tree that showed an uncanny ability to withstand the fungus. Named Kent—likely the surname of the man who discovered it—the cultivar became popular in India, Uganda, Tanzania and Kenya (all British colonies) in the 1920s and ’30s, and was an early ingredient in resistant hybrid “recipes,” most notably contributing its genes to Jember (S795), still planted widely in Indonesia. Kent is just part of Jember’s genetic base, however. The other half is a selection known stoically as S228, a wildly underwhelming name for an extraordinary spontaneous interspecific hybrid of West Africa’s native liberica species with Ethiopia’s indigenous arabica.

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One of the laboratories at Cenicafé. Photo courtesy of Chris Kornman

Breeding and selection take significant time, evidenced by Kent’s decade-plus lag between discovery and proliferation. Unsurprisingly, in areas affected by the 19th-century rust epidemic, the notion of waiting for the plodding science to answer a pressing economic concern was unpopular. Impatient and desperate, farmers turned to rust-resistant coffee species Coffea liberica, which had been only sparingly planted before rust. It was quickly distributed through Indonesia and the Philippines. In Indonesia, the Dutch also began experimenting with robusta.

Robusta (Coffea canephora), well known to indigenous groups near its genetic origins along the modern border of Tanzania, Uganda and the Democratic Republic of Congo, wasn’t added to botanical taxonomies until the end of the 19th century. Having now mapped both the arabica and robusta genome, scientists are confident that robusta is one of arabica’s genetic parents. The other is a commercially unviable species called eugenioides.

When robusta was introduced to Southeast Asia, it would make another important genetic contribution to arabica. The improbable occurred on the Pacific island called Timor, now split between Indonesian sovereignty and that of the independent nation of Timor-Leste. There, arabica spontaneously cross-bred with robusta, creating a new interspecific hybrid. This was a singular feat: Arabica is tetraploid; it has four sets of chromosomes. This makes it theoretically incompatible for natural breeding with its diploid (two sets) ancestor.

Regardless of plausibility, the Timor hybrid, often called “Tim Tim” locally, became a regional favorite shortly after it was first observed in the early 20th century. It now provides the baseline genetic source for nearly all disease-resistant arabica cultivars, the most common of which are collectively referred to as Catimors and Sarchimors. Despite their robusta heritage, these cultivar groups are classified genetically as arabica and are widely planted throughout the world.

Resistance, interlinked with genetic complexity and variation, continues as the foundation of farmer support research worldwide. Many specialty coffee professionals are familiar with World Coffee Research (WCR), whose genetic collection network includes seed and tree banks in Costa Rica (CATIE), Cote D’Ivoire (CNRA), Ethiopia (EBI) and Madagascar (FOFIFA), each of which has developed its own resistant hybrids and selections. Ethiopia’s Jimma Agricultural Research Center (JARC) is one of the world’s most important gene banks for coffee. There are numerous others. These few examples stand testament to the fact that nearly every coffee-producing country has at least one such organization.

A 6-cent-per-pound tax on exported coffees funds the FNC—one of the world’s largest and most high-profile coffee organizations. Laser-focused on improving volumes and prices countrywide, the FNC has been developing and releasing productive coffee cultivars for decades under its Cenicafé research division.

In Colombia’s central department of Caldas, just a few hours’ drive from Bogotá, a beautiful brick compound nestled into the green rolling hills of Chinchiná serves as Cenicafé’s flagship and neurocenter.

Along its balconies, visitors can stroll among rare coffee plants, potted and labeled, laden with ripening fruits that passersby might be tempted to pick. Within its halls, however, white lab coats are the norm, and a hushed, bent-back urgency muffles the echoes as specialists go about the serious business of coffee science.

Cenicafé’s early rust-resistant cultivars—Tabi and Colombia, essentially backcrossed Catimors—were longstanding and somewhat popular alternatives to the country’s aging stock of Typica and Caturra. However, Colombia captured the world’s attention in 2005 with the release of Castillo. That cultivar is now the most commonly grown plant in the country, thanks in part to heavy marketing, national taste competition victories, and subsidized seed pricing.

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Castillo is bred for resistance to coffee leaf rust. Photo courtesy of Chris Kornman

Castillo’s benefits include high yields and disease resistance, but it is its multi-line composite of fifth-generation (F5) breeding that allows for genetic diversity sufficient to resist rust and other diseases holistically within a single field of trees. On a monoculture Caturra farm, in the increasingly likely event of a “super-roya” epidemic, the entire field would succumb to such a monstrous predator.

However, only part of the Castillo grove would be susceptible because—despite being 100 percent Castillo—there are multiple variations, each made up of thoroughly unique genetic compositions, in each bag of seeds. Additionally, Castillo has been divided into 16 “regional” quality variations in addition to a “general” profile. Genetic variation was injected into the very fabric of Castillo’s rust resistance.


Shortly after Castillo arrived in Colombia, so did rust. Beginning in 2008 in Colombia, and sweeping across Central America by 2012, an especially virulent strain of CLR caught international attention. Guatemala, Costa Rica and Honduras declared states of phytosanitary emergency. The losses in coffee harvest from Central America in the 2012–2013 season were estimated to be close to 2.7 million bags, around $500 million in unrealized revenue. Colombia’s harvest was down 31 percent from 2008 to 2011, Central America’s production was reduced by 16 percent in 2013, and another 10 percent the following season. Compound this with lost labor opportunities on the farms, harvest failures in following years (Promecafe estimated El Salvador’s harvest decreased by 54 percent in 2013–14, primarily due to rust), and the Mesoamerican coffee-growing world was in the midst of a substantial crisis.

Concurrent with CLR’s re-emergence in Colombia in 2008, the global economy took a long walk off a short pier, plunging into a worldwide recession. To add financial insult to rust’s injury, coffee farmers were hit with price increases for fertilizers. And Mother Nature did not cooperate—tropical anomalies contributed to problematic rainfall and temperature conditions, and strong winds spread the rust spores mercilessly (Avelino, J., Cristancho, M., Georgiou, S. et al. Food Sec. (2015) 7: 303. doi.org/10.1007/s12571-015-0446-9). As if this weren’t enough, scientists across the world reported the evolution of more virulent strains of many species of rust fungi as we sprinted through the early decades of the 21st century.

The epidemic of 2008–2013 was devastating. Even worse, its potential to resurface is not simply a probability, but an assured reality.

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Coffee leaf rust in Guatemala. Photo by Lily Kubota


If the fight against rust starts with resistant cultivars, then it is hamstrung by specialty coffee cuppers’ tendency to regard those same cultivars as qualitatively inferior.

Castillo’s introduction in Colombia catalyzed a wave of reaction in the roasting sector, as terrified cuppers speculated that traditional varieties would go extinct in the shadow of the FNC’s drive for hardy plants. Castillo became a flashpoint that encapsulates the clash between genetic research and the specialty coffee roaster.

Setting out to test the presuppositions of willing participants, in 2014 Michael Sheridan (now Intelligentsia Coffee’s director of sourcing and sustainability, then affiliated with Catholic Relief Services as the director of the Borderlands Coffee Project), set up a series of blind trials in partnership with the Center for Tropical Agriculture (CIAT) in Colombia, WCR and the Sensory Analysis Center at Kansas State University (KSU). Twenty-five smallholder farmers in Nariño separated their Castillo and Caturra harvests, and these coffees were sent to trial by taster.

Hosted at Intelligentsia’s Chicago Roasting Works, with tasting structure designed by veteran Cup of Excellence head judge Paul Songer, the panel included a strong showing of respected quality specialists: Roman Bondarenko (Keurig), Aleco Chigounis (Red Fox), Timothy Hill (Counter Culture), Jennifer Howell (George Howell), Doug Langworthy (Starbucks), Adam McClellan (Stumptown), Néstor Perilla (FNC) and Geoff Watts (Intelligentsia). I was there, too, as Intelli’s national quality control manager (and like many above, my employment is now elsewhere). QC lab specialist at the time, Amanda Seaver—who roasted every coffee twice—and I, with a great deal of help from Watts’s wife Vivi, dropped everything for a week in November, set all the tables, cupped every coffee, joined the discussion, and cleaned every cup.

Theories floated lazily around the cupping room like coffee grounds in the cooling glassware: Castillo might taste better with riper cherries and longer fermentation times, and probably had a lower quality ceiling. George Howell’s phrase “tail of the devil”—which he famously used to describe Castillo’s fabled harsh, astringent, or mouth-drying finish—was repeated with frequency. But at the end of a double-blind session, after cupping each set twice, the cultivars were in a virtual dead heat.
Cuppers were startled. The results seemed implausible. The panel agreed to reconvene and taste the same coffees, the same way, in January 2015. Perhaps Castillo would lose its edge after a few months of aging.

It didn’t. Overall, Castillo took three of the top five spots, with point scores brushing up against 90. However, Sheridan is quick to caution against moving to unjustified conclusions, as this single trial was by no means comprehensive. In his 2015 article for the Specialty Coffee Chronicle, he’s careful to mention that sampling from just 25 farms in a single Colombian department over the course of one harvest cycle is not statistically significant. “They represent a single sensory snapshot taken with a narrow-angle lens,” he states (scanews.coffee/2015/08/04/castillo-or-caturra-a-simple-question).

Yet, proof exists that resistant varieties don’t have to taste terrible. And so, it seems, the specialty coffee industry is at a crossroads. Science, slow as it may be, has forged a path toward resistant cultivars for farmers. Roasters, however, covet the romance and tradition of varieties like Caturra, Bourbon and Typica.

Between the rocky reality of leaf rust and the hard place of a roaster’s scorn, how can a farmer choose?
The economics are surprisingly straightforward: Even if planting Castillo means a loss of the price premium associated with traditional varieties, the hybrid’s higher average yield and resistance to rust practically guarantee a consistent annual income close to break-even. It’s too attractive to resist.

For an established farmer with the ability to specialize in differentiated quality, Castillo acts as a safety net for lean years. But for a subsistence Colombian farmer, planting Castillo may well make the difference between destitution and keeping food on the table and kids in school. The same is true with hybrid plantings across the Americas; for the vast majority of farmers, the choice of cultivar may be a foregone conclusion. Bourbons and Caturras are dinosaurs, too slow to adapt to rapidly changing climates and diseases.

Will specialty roasters embrace the resistance? Cup of Excellence (COE) Executive Director Darrin Daniel was especially proud of the 2017 results from Nicaragua, in which the second-place COE finalist used a fungus-resistant F1 hybrid called Centroamericano (a Sarchimor crossed with Sudan Rume), and “skeptical farmers were converted based on the competition results.” Maybe the tide is turning.

Roasters in the future may not have much of a choice, however, as resistant hybrids sweep the coffee landscape. In recent years, I’ve had a number of conversations on a wide range of topics with Alfred Klein, who runs the quality-focused Finca San Carlos in Chiapas, Mexico. His Jade Centennial micro-lot is outstanding, persistently sweet with a sparkling orange acidity and notes of pear and plum. He explained recently that “the incidence of roya has diminished … due to the fact that very susceptible varieties have died out, [and] many plantations have been renovated in the last years with resistant strains.”
Yet even in fields of resistant varieties, preventive maintenance remains an imperative. “It is impossible to foresee weather and rain patterns nowadays in order to take action against the disease once the infection has started,” Klein says. “Waiting until you see the symptoms means it’s already too late.”

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Alfred Klein, director of the quality-focused Finca San Carlos in Chiapas, Mexico. Photo courtesy of Royal Coffee

Resisting rust and maintaining an organic certification? Almost impossible. Finca San Carlos nearly decertified in 2017 in favor of rust prevention. Chemical solutions, too, have constraints. Klein laments that “different products the market offers are still controlling the disease, but the efficiency is not the same. All products basically come from a very small group of related chemical molecules, and sooner or later these molecules won’t work anymore. This has happened with almost all agrochemicals; it’s just a matter of time and spore mutation.

“The other side of the equation,” he continues, “is the cost of the product and its application. With the current coffee prices, not many growers can afford preventative control, and the issue of resistant varieties is also only a matter of time. Costa Rica 95, one of the more planted resistant varieties, has lost its resistance already in some places like Honduras.”

The 2008–2013 rust outbreak began in the midst of a global financial crisis. New York “C” futures prices, as of press time, are still unsustainably low—having spent most of 2019 under $1 per pound. The current coffee price crisis may well spark another rust outbreak; the numbers simply don’t add up for farmers to practice good prevention techniques if they can’t even meet the basic costs of production.

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Coffee leaf rust damage from 2012–2013, according to the International Coffee Organization. Image courtesy of Chris Kornman

Even with unlimited resources, the sad reality of resistance is that it is temporary. A survey of WCR’s variety catalog is riddled with cultivars, once fighters, that have since retired. Kent, Lempira, H3, K7, and even Gesha were once sought for their rust tolerance, a quality lost as climates have shifted and the fungus has evolved. Castillo, and every cultivar developed after it, will eventually be assimilated into the susceptible masses of relatively meager genetic diversity outside of Ethiopia’s naturally heterogeneous stock. Greg Meenahan, WCR’s partnership director, recently confirmed that the organization is removing the “resistant” language from all of its current variety catalog, as varieties once thought to be practically immune have proven susceptible to newly evolving strains of rust fungi.

Ultimately, if we can’t fix systems that stoke the flames of a fungal epidemic, resistance might be futile. So much stands blocking the gate beyond changing climate conditions and evolving fungi. Outdated colonial norms like monoculture plantations (like Sri Lanka in the 1800s) persist, as do supply chains that distance farmers from their consumer market and a general lack of infrastructure for information and dissemination to farmers. Roasters continue to demand susceptible varieties because of their perceived sensory superiority, and a broken price discovery “C” Market that uses futures trading to set the price of our physical commodity remains the baseline figure for what a farmer is paid. These practices will doom our industry.

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The balcony at Cenicafé in Chinchiná, Colombia. Photo courtesy of Chris Kornman

Solutions for the future are multifaceted. First, dying farms must be renovated, and this takes time, energy and resources. Coffee farmers must be paid a fair wage, and that fair wage ought to include basic provisions that account for smallholder labor and the cost of materials. Farmers, to be sustainable, need to achieve a profit after the cost of production of coffee, or they will either abandon the farm or turn to a crop that is better suited for making a living. Many smallholders and subsistence farmers may also need some basic financial education to improve their ability to invest resourcefully in their farms and save for the future.

Second, ongoing research must continue and accelerate. New cultivars, faster development, and better treatments for trees are all part of a robust plan to combat changing climates and evolving rust fungi. But equally important is dissemination. If new technology emerges but is unavailable, then what use is it? The price of a WCR-developed F1 hybrid seed is orders of magnitude greater than a more common and less rust-resistant cultivar. With this barrier to entry, especially in a low market, growers will be unlikely to choose the best available option, especially if they don’t even know it exists.

Coffee quality specialists don’t have to give up SL-28 or Gesha micro-lot options. It’s not an either/or scenario, at least not yet. But the expectation shouldn’t be for the growth of Bourbons and Caturras to the exclusion of improved cultivars with proven yield and resistance, whose sensory quality is equally good.

Beating back rust requires strategy and investment from the entire supply chain; the farmer cannot bear the burden alone. Are you ready to join the resistance?