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frojack writes:

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.

The rust, called roya in Spanish, is a fungus (Hemileia vastatrix) that is highly contagious due to airborne fungal spores. It affects different varieties, but the Arabica beans are especially susceptible. Rainy weather worsens the problem. The rust typically enters the coffee leaf via the stomata.

Their methods were traditional cross, breeding, planting, evaluating rust resistance, comparing taste and aroma. It was a long and arduous process, sometimes taking 25 years to develop a cultivar that was rust resistant. Still, Cenicafé succeeded with two cultivars, Colombia (in 1980) and Castillo (in 2005) that have been reasonably rust resistant.

Now ScienceMag is reporting that sequencing the genome of major Coffee families is shortening this development cycle by documenting those coffee genes that provide resistance. At the same time the sequencing of rust genes has identified those elements of its genome that are involved in gaining entry into the coffee leaf.

By selecting coffee for cross breeding with a map of the genome in hand, and analyzing the genome of the resultant plant, they can shorten the 25 year development cycle down to less than a year, without having to wait until the trees mature.

Unlike genetically modifying seed to tolerate pesticides, this method of selecting for the most resistant strains does not require the use of pesticides.

The US government will be offering a 5 million dollar aid package in partnership with Texas A&M Coffee Research Center to combat the fungus.