Genetic dynamics of fusarium xylarioides: key to the management of coffee wilt disease in Uganda

Abstract

Fusarium xylarioides (F. xylarioides) is a vascular fungal pathogen that causes Coffee Wilt Disease (tracheomycosis). The pathogen is only endemic to Robusta coffee in Uganda while Arabica coffee is immune to it, yet Robusta coffee contributes 80% of the Uganda traded coffee. Currently, the pathogen is estimated at 3% incidence with economic losses of $17m annually. The pathogen is present in all traditional Robusta coffee growing regions and is spreading to non-traditional areas like Kabale. Despite the importance of F. xylarioides, there is limited information on the contribution of environmental factors and its genetic diversity to the spread of the pathogen. The aim of this study was to determine the genetic dynamics of F. xylarioides and the environmental factors that contribute to its spread to new places in Uganda. Environmental data comprising rainfall, relative humidity, speed of wind, and temperature for 2000 to 2005 and 2020 was obtained from the POWER project. Historical pathogen incidence data was obtained from UCDA reports while the primary incidence data was obtained from the coffee fields during specimen collection in 2020. The environmental data was then correlated to the pathogen incidence data in SPSS. Pathogen isolates that had been stored for a period of ten years (2009 to 2019) were used to study the genetic dynamics of the pathogen over a 10-year period by subjecting their DNA to PCR analysis using SSR primers. Twenty-three (23) F. xylarioides isolates obtained from 3 coffee growing regions in Uganda were used to study the genetic dynamics of the pathogen as of 2020 using SSR markers. The results revealed that all the environmental factors studied were significant to the spread of the disease. However, it was revealed that rainfall (R= 0.8680, R=1), temperature (R= 0.8680, R=1, R=-1) and humidity (R=0.76, R=1, R=-1) were key in the spread of the pathogen. The study observed 0.00% genetic variation in the F. xylarioides population in Uganda over a 10-year period. The study also observed 0.00% genetic variation in the pathogen populations from the 3 coffee growing regions of Uganda as of 2020. This implies the spread of the pathogen in Uganda is mainly due to the environmental factors and not the pathogen genetic diversity. However, there is need of consistent annual data collection and storage, and use of a variety of molecular markers in a diverse study.