Coffee wilt disease evolves new genetic weapons to target crops

Scientists reveal how coffee wilt fungi gained genes to better infect arabica and robusta crops.

A new study reveals how genetic interactions between fungal pathogens contributed to the repeated outbreaks of coffee wilt disease threatening arabica and robusta coffee. 

Coffee wilt disease is caused by Fusarium xylarioides, a soil-borne fungus that invades coffee plants through the roots, eventually blocking water uptake and causing the plants to wilt.

While arabica and robusta strains have long been its targets, scientists have now sequenced the pathogen’s genetic evolution across six decades using 13 historic fungal strains.

Their study, published in PLoS Biology, showed how F. xylarioides acquired critical genes from another fungus, Fusarium oxysporum, that allowed it to more effectively infect coffee plants by breaking down their cell walls. 

Genes on the move

The world drinks over 2.2 billion cups of coffee every day. Coffee exports serve as a vital income source for more than 12 million African, with Ethiopia alone exporting $762.8m worth of coffee every year.

However, since the 1920s, coffee wilt disease has decimated production, with devastating impacts on yields and farmer livelihoods.

Researchers from CABI, Imperial College London and the University of Oxford revealed how horizontal gene transfer – a process where genetic material is passed between organisms without reproduction – played a crucial role in the evolution of the coffee wilt fungi F. xylarioides. 

“We’ve found evidence for horizontal gene transfer in a disease that has had devastating impacts on real coffee crop production,” Dr Lily Peck from the Grantham Institute - Climate Change and the Environment at Imperial College London.

F. xylarioides evolved the ability to effectively infect coffee crops by breaking down tough plant tissues by exchanging genetic material from another fungi known as F. oxysporum. These genes may have been cargoed by large, mobile segments of DNA known as ‘starships’.

We found that the genes that are very useful in infection and are highly expressed are the same ones in horizontal transfers Dr Lily Peck Grantham Institute for Climate Change

These starships transfer clusters of genes between organisms in a shared environment, like soil. The study shows that F. xylarioides and F. oxysporum share highly similar genetic code, suggesting that the coffee wilt fungi picked up its tricks from its neighbours.

“We found that the genes that are very useful in infection and are highly expressed are the same ones in horizontal transfers,” said Dr Peck.

Protecting future brews

Outbreaks of coffee wilt disease have periodically slashed production, particularly in Ethiopia and central Africa. The team’s study not only explains the genetic origins of the pathogen’s repeated emergence but also offers insights into mitigating future risks.

The findings could shape future agricultural strategies, such as designing crop systems that minimise gene transfer between soil-borne pathogens. 

Understanding these genetic interactions may also help scientists develop resistant coffee varieties or targeted treatments.

The researchers used a sample of fungus that had been kept in cold storage for 70 years and was brought back to life for the study.

By understanding how these fungal pathogens have evolved in the past when we’ve tried to control them, we can try to manage outbreaks of new pathogens in the future Professor Timothy Barraclough University of Oxford

“By understanding how these fungal pathogens have evolved in the past when we’ve tried to control them, we can try to manage outbreaks of new pathogens in the future,” said co-author Professor Timothy Barraclough from the University of Oxford.

“This study is very much the tip of the iceberg. CABI has 30,000 strains in their culture collection and we’ve looked at just one species,” Dr Peck said, “Think of all the other questions that could be answered by studying other strains.”

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‘Horizontal transfers between fungal Fusarium species contributed to successive outbreaks of coffee wilt disease’ by Lily D. Peck et al., is published in PLoS Biology. DOI: 10.1371/journal.pbio.3002480.

Footnote: Dr Lily Peck carried out this research as part of her PhD at Imperial on the NERC Science and Solutions for a Changing Planet Doctoral Training Partnership. Professor Timothy Barraclough, who supervised the PhD, was formerly a member of the Department of Life Sciences at Imperial.