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Coffee rust
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In Colombia, coffee scientists urge: Viva la resistencia!

Coffee scientists from around the world last week flew into Colombia's Eje Cafetero region, a verdant collage of deep gullies and mountainsides covered in thousands of small-scale coffee farms framed by banana trees. At the heart of the 25th International Conference on Coffee Science (ASIC) was a burning question: how to deal with coffee leaf rust, or roya. The world's most damaging coffee disease, leaf rust has torn through Latin America, costing farmers an estimated $1 billion and cutting some harvests by more than half in Central America. Between copious coffee breaks, scientists announced several new molecular techniques to help combat this continental epidemic.

Resistant coffee plants

Helping the coffee plant defend itself from the fungus is a top priority. Colombia leads the world in developing rust-resistant coffee breeds, also known as cultivars. When coffee leaf rust—which was first spotted in East Africa in the 1860s—made it to South America in the 1970s, Colombia's national coffee research center, Cenicafé, was already a decade into its rust resistance breeding program. Since then, it has released two major coffee cultivars—Colombia (in 1980) and Castillo (2005)—that have been effective since 1983 in tempering leaf rust while preserving the characteristics so important to world-class coffee: high yield, large grain size, great taste.

But, like a pharmaceutical pipeline, the problem has been the time and money required to take a new coffee plant from research to market. "It takes more than 25 years to develop a new variety," explains Pilar Moncada, a scientist at Cenicafé. "One of the ways we can reduce the amount of time is by using genetic markers to evaluate which genes are of interest to us."

At last week's ASIC conference, Moncada presented a database of Cenicafé's collection of coffee germplasm. It includes more than 600 characterized genetic resources, mostly Ethiopian in origin, that encode agronomically relevant characteristics like disease resistance and favorable aroma. When Moncada starts developing a new rust-resistant cultivar, she can now genetically screen her first-generation plants against this database to streamline the process. "If we have a marker that is associated with rust resistance, we don't have to take the plant out to the fields and wait until there is a rust outbreak to see if it's resistant." But budget cuts have limited these genetic experiments, Moncada says. "We still need to validate the rust-resistant genes. Once we are sure they are linked, we can start with the selection."

Moncada knows genetic insights will expedite crop improvement. She's not alone. The announcement of the sequencing of the Coffea canephora genome in Science this month was met with a buzz from coffee aficionados and researchers alike, namely because it provided new details on the chemical evolution of caffeine. But that project sequenced the C. robusta species of coffee, a large and low-quality bean that has lost its popularity in the last few decades. Sequencers have yet to completely map out the more prized C. arabica species, though they presented a draft last week in Colombia.

Characterizing the fungus

Another focus was understanding the biology of the rust fungus, Hemileia vastatrix. "Coffee rust is a hacker," explains Álvaro Gaitán, head of plant pathology at Cenicafé. "It's always looking for a new way to get inside the plant." Gaitán's team is trying to arrest the infiltration of coffee rust, which occurs when the fungus spore germinates and penetrates the plant's stomata. Researchers don’t yet know exactly what fungus is doing—or what proteins it's secreting—to infect the coffee plant. But research into other plant rusts has implicated several proteins in this pathogenic process, making them logical candidates for study by the Colombian team.

Using RNA sequencing, Gaitán's team identified 28 genes in H. vastatrix that are associated with breaking down the defenses of the coffee plant. These coded for a series of proteins which, as it turns out, are conserved across other species of fungal rusts. The pathogens seem to use some of the same tools to gain entry into a leaf.

Inhibiting this infiltration process could be key to stopping coffee leaf rust. But Gaitán warns that scientists need to be careful to target the entire range of coffee leaf rust, of which some races are more virulent than others. "We have to characterize the races of roya," Gaitán says. "You don't want to just target the weak rusts; you have to prove your materiel against strong rusts." The genetic screening of leaf rusts would also enable authorities to rapidly characterize—and more quickly mitigate—the next severe leaf rust outbreak.

Meanwhile, researchers say teasing apart the genetic machinery of coffee rust is relevant not only to coffee lovers but also to our global food supply. Coffee farms the world over are still planting susceptible cultivars that increasingly require pesticides to fend off disease. This heavy application of pesticides is irresponsible, Gaitán says, especially on small-holder farms like the ones dotting Colombia. "Every time you recommend the use of a pesticide you're exposing the family, too, because they live very close to these fields," he says. "And many of these coffee diseases are controlled by natural enemies of the fungus. You don't want to kill those off."

*Correction, 22 September, 12:25 p.m.: This article previously misattributed the quotes and work from Pilar Moncada.