Scientists are raising awareness about the serious threat posed by coffee wilt disease to both arabica and robusta coffee varieties, which are essential to our daily coffee routine. Researchers from institutions such as Imperial College London, the University of Oxford, and CABI have highlighted that the fungal pathogen Fusarium xylarioides remains a critical danger to coffee harvests and the livelihoods of people in sub-Saharan Africa.
Researchers, including teams from Imperial College London, the University of Oxford, and CABI, have highlighted urgent concerns regarding the ongoing outbreaks of coffee wilt disease that threaten arabica and robusta varieties of our beloved coffee.
According to their findings published in the journal PLoS Biology, the fungal pathogen Fusarium xylarioides is still a significant risk to coffee farming and the economy in sub-Saharan Africa.
This research corroborates previous studies that indicated F. xylarioides consists of a complex of species with various populations adapted to specific host plants.
The study confirms the existence of genetically distinct lineages that show different host preferences for arabica and robusta coffee. It also indicates how the pathogen F. xylarioides has frequently acquired “horizontally transferred” DNA segments from a related fungus, contributing to repeated disease outbreaks.
Vital source of income for over 12 million households
Coffee serves as a crucial income source for more than 12 million families in Africa and is integral to tax revenues in various countries. For instance, Ethiopia records an impressive annual coffee export revenue of $762.8 million. However, chronic outbreaks of coffee wilt disease have devastated coffee farming in East and Central Africa since the 1920s, impacting both crop yields and farmers’ earnings.
In their study, scientists analyzed the genomes of 13 historical strains of F. xylarioides accumulated over six decades from CABI’s Culture Collection to trace the evolutionary history behind these continuous coffee wilt disease outbreaks.
Dr. Matthew Ryan, Senior Research Lead in Biological Resources at CABI, co-authored the research and worked alongside lead author Dr. Lily Peck from Imperial College London, with Professor Tim Barraclough from the University of Oxford also contributing.
Essential to grasp genetic structure and evolutionary potential
Dr. Peck emphasized, “To enhance our management strategies for fungal pathogens like Fusarium xylarioides, it’s crucial that we understand their genetic composition and evolutionary dynamics.”
“Our findings identified at least four separate lineages of F. xylarioides: one specific to arabica, one to robusta, and two older lineages from various coffee species.”
“The variation in large genomic sections among these lineages indicated that the exchange of effector genes—important for successful infections—helped establish host specificity.”
Dr. Peck noted that multiple gene transfers into F. xylarioides populations corresponded with different segments of the Fusarium oxysporum mobile pathogenicity chromosome, which were rich in effector genes and transposons.
Transposons, often referred to as “jumping genes,” are DNA sequences capable of relocating within genomes. They are present in a variety of organisms, including bacteria, yeast, humans, mice, fruit flies, and frogs.
Expressed significantly during infection based on transcriptomics
Transcriptomic analysis demonstrated that effector genes and other carbohydrate-active enzymes that aid in breaking down plant cell walls were highly activated during infections of arabica coffee by the specialized pathogenic strains.
Professor Barraclough stated, “The extensive sharing of certain transposons between F. xylarioides and F. oxysporum, along with the identification of mobile elements related to horizontal gene transfers, supports our belief in the occurrence of horizontal transfers.”
“This suggests that such genetic exchanges may account for the recurrent emergence of coffee wilt disease.”
Potential for profitable exports of diverse coffee varieties
Dr. Ryan highlighted that the implications of this research go beyond coffee and could provide insights into broader fungal interactions. He noted, “Understanding that horizontal gene exchanges between different Fusarium species have led to recurrent coffee wilt disease is essential for grasping wider fungal behaviors—though we still have much to learn.”
The researchers propose that these horizontal gene transfers might occur in shared environments since both F. xylarioides and F. oxysporum are soil-dwelling pathogens found in the roots and wood of coffee wilt-affected trees in Ethiopia and Central Africa, as well as in the roots of banana trees in the region.
Furthermore, understanding how horizontal transfers work could aid in developing intercropping strategies that lessen the risk of effector gene transfers between closely related Fusarium species.
