Coffee Leaf Rust: A Genetic Solution

Leaft undersurface

The under surface of the infected leaves showing the rust uredospores

The coffee leaf rust has been in the news lately due to infection in Central American coffee growing regions in epidemic proportions. This recent outbreak of coffee rust in Central America has resulted in more than 60% of the trees exhibiting 80% defoliation in Mexico and crop devastation in Nicaragua, El Salvador, Guatemala and Honduras. According to the International Coffee Organization, this 2012/2013 outbreak of coffee rust in Central America is expected to cause crop losses of $500 million and cost 374,000 jobs.

Coffee leaf rust caused by the obligate parasitic fungus Hemileia vastatrix was first observed in 1861 near Lake Victoria. The fungus has now spread throughout coffee-growing countries, which led to significant economic impact in Sri Lanka in 1868. In India, crop losses due to coffee rust accounts for about 70% in susceptible Arabica coffee (Coffea arabica) cultivars.

Leaf upper surface

Symptoms seen on the upper leaf surface

I recently wrote a chapter for an upcoming book on marker assisted selection in coffee for crop improvement. Review of literature shows significant progress in breeding for varieties resistant to leaf rust.  Due to the long regeneration time of the coffee trees (i.e., approximately five years), conventional breeding of coffee has its limitations. It can take a minimum of 25 years after initial hybridization to ensure that the desirable trait for improved quality or disease or pest resistance has been transferred to the progeny. The development of marker-assisted selection (MAS) provides an alternative to overcome the limitations of conventional coffee breeding. The general principle of MAS is the use and selection of an identified molecular marker (a segment a DNA that can be easily identified) linked to the gene that confers the specific trait (such as resistance to leaf rust). This will eliminate the need to wait for the coffee trees to reach maturity in the field before they can express the desired traits. The presence (or absence) of the desired traits can be tested using MAS in the juvenile stage itself, thus leading to shorter breeding timeframes.

Nine resistance genes designated as SH1 – SH9, either singly or in combination confer leaf rust resistance in coffee plants. Of these resistance factors, SH1, SH2, SH4 and SH5 have been found in Arabica coffee and SH6, SH7, SH8 and SH9 have been have been found in robusta coffee (C. canephora). The SH3 gene originates from Liberian coffee (C. liberica). Various researchers have identified several markers linked to the resistant SH3 gene. Researchers in India have successfully applied the MAS technology to achieve durable rust resistance, which is one of the first successful applications in the field.

The present epidemic has resulted in various agencies (World Coffee Research, USAID, PROMECAFE, etc.) prioritizing coffee leaf rust research. Taking economics and minimization of chemical input for disease management into consideration, the most viable and effective option is the development and cultivation of resistant varieties. Hence, breeding for varieties resistant to coffee leaf rust should become one of the highest priorities.



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Posted in Genetics, Pests & Diseases, Production/Agronomy