By crossing Arabica plants that seem more resistant to rust for several generations, a heartier plant can be grown. It's a process that can take decades: In 1982, Cenicafe released its first coffee rust-resistant bean, called the Colombia Variety. In 2005, it released a second generation plant, called Castillo, which is even more resistant to the fungus.
Though Cenicafe is probably the world's most advanced coffee research center, with more than 60 researchers spread throughout Colombia, it's still fighting an uphill battle against coffee rust.
Due to an abnormally wet season in 2008 caused by La Nina, the country, which historically produces about 12 million 60 kilogram bags of coffee annually, produced just 7.5 million bags as its crop was devastated by rust.
Alvaro Gaitan, a lead researcher at Cenicafe, says the worldwide economic downturn increased the cost of fertilizers and fungicides to a point where coffee farmers in the country couldn't afford them. La Nina caused increased rain and cloudiness throughout the growing season.
"Under those conditions, coffee rust is very happy attacking plants," he says.
Creating a rust-resistant plant is one thing; getting it to Colombia's half million farmers—whose average farm is just 4 acres—and convincing them to use it is another.
Luis Fernando Samper, of the Colombian Coffee Federation, says the Colombian government has spent $1.4 billion over the past five years trying to replace coffee plants with rust-resistant varieties. It costs farmers $1,200 per acre to replace existing coffee plants with resistant strains, and often that money is fronted by the government. The government expects to offer nearly 200,000 loans of about $3,000 each by the time most farmers have replaced their plants with resistant strains.
Replacing the country's entire crop of coffee plants requires outreach to farmers, new banking services for the loans and researcher assistance in choosing which seeds are best to plant in certain regions.
"It's a huge challenge. It's like putting a little orchestra together," Samper says. "Certain farmers are skeptical until we can convince them that the quality is as good or better than what they had before."
Because creating a resistant Arabica plant often requires researchers to cross it with a Robusta plant that naturally has rust resistance, coffee purists have long alleged that rust-resistant coffee doesn't taste as good, a claim that Gaitan denies and says was born out of hastily produced rust-resistant varieties in Central America.
"That's a myth going on in the market. What happens sometimes is if you're not rigorous about quality, you end up with plants that have resistance, but don't taste good," he says.
Rhinehart, whose organization is responsible for setting specialty coffee standards, says that the idea that hybrid coffee plants generally produce worse-tasting beans is, more often than not, true.
"It's not fair to say that efforts to increase resistance to rust necessarily result in bad tasting coffee," he says. "But to date, the best-tasting coffees haven't been rust resistant."
One of the farmers who was eventually convinced to make the switch is Yoli Urresi, a 35-year-old farmer near the tiny southeastern town of Timbio. In 2008, "the seasons varied a lot," she says.
"When it was summer, it rained a lot, more than usual," leading to problems with coffee rust, she says, which led her to switch most of her plants to the Castillo variety three years ago. She is finally able to harvest the beans because it takes up to three years for newly planted coffee trees to bear fruit. In the meantime, she continued to grow some older varieties of the plant in order to keep production up.
"A month ago, there was hail and the Castillo plant has actually been resistant to it," she says. Older varieties of coffee were damaged by the hail.
Colombia's $1.4 billion plan to replace its old coffee plants has enabled the country's coffee production to slowly recover from the 2008 down year.
Corrected 03/28/13: An earlier version of this story misstated the total value of the worldwide coffee trade.