The problem

Coffee leaf rust is one of the most significant challenges faced by coffee farmers in many parts of the world. The disease has wreaked havoc on coffee production, particularly in Latin America, since an outbreak in 2012. But the fight against rust has been persistently hampered by one key fact: We know very little about the fungus.

Despite the fact that coffee producers have been living with rust for nearly 200 years, serious questions remain unanswered regarding the biology of coffee leaf rust, the answers to which could significantly influence approaches to fighting the disease.

This lack of understanding also means that the world has no method or tools for the rapid identification of potentially new emerging races of rust in a timely manner—a major problem given that the resistance to rust of many coffee varieties is being rapidly overcome by the emergence of new races and the movement of known races into new areas.

The solution

In 2018, WCR launched a major new research effort together with Purdue University, led by world-renowned rust expert Dr. M. Catherine Aime, to develop a comprehensive understanding of the biology of coffee leaf rust, from its reproductive processes to an annotated genome. The project is providing critical data about coffee leaf rust genetic diversity, reproductive strategy, and races, that will inform more effective CLR resistance breeding and mitigation of resistance breakdown programs. Key outputs of this program so far include:

1. Providing additional genomic coverage and assembly for genome of Hemileia vastatrix
2. Developing a variable marker set (SSRs) from the genome
3. Determining the population genetics of CLR populations on a global scale by indirect (SSR) and direct (MAT loci) analyses (ongoing)
4. Laying the groundwork for genotyping currently defined rust races and relating H. vastatrix genetic diversity to CLR race diversity

One of the most critical goals of the work is the development of molecular markers that would allow researchers to quickly and cheaply test rust that appears on coffee trees to figure out which race it is.

Impact

Understanding the genetic basis of coffee quality will assist coffee breeders to make quality improvement a primary target of breeding programs, and will produce knowledge that significantly shifts our understanding of the determinants of quality.