Abstract
Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.
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Acknowledgements
We are grateful to all farm owners in the Gera, Goma, and Mana districts to allow us to work in the different coffee production systems studied and to provide us with all the necessary information during the field work. Furthermore, we thankfully acknowledge Wendimu Bekele, Freweyni Michael, Dinkina Mijena, Nezif Yesuf, Miressa Raji, and Nasir Abba Macca for their help during sample collection and artificial fungal inoculation in the greenhouses at Jimma University College of Agriculture and Veterinary Medicine (JUCAVM). We also gratefully acknowledge Ethiopian Biodiversity Institute (EBI) for permitting material transfer of our coffee leaf rust spore samples with (Ref. No. EBI 71/300086/2018) for genetic diversity analysis at KU Leuven, Belgium
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This work was supported by VLIR-UOS, the Institutional University Cooperation program between Katholieke Universiteit Leuven and Jimma University.
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Gerba Daba, Gezahegn Berecha, Bart Lievens, and Olivier Honnay designed the study. Gerba Daba performed the field work. Gerba Daba, Bart Lievens, and Olivier Honnay led the writing of the manuscript. Robin Daelemans and Gerba Daba performed the statistical analyses. Margot W. J. Geerinck, Christel Verreth, and Sam Crauwels performed the molecular analysis, including data analysis. All authors contributed to the data interpretation and to the drafts of this manuscript and approved publication of the final manuscript.
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Daba, G., Daelemans, R., Berecha, G. et al. Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia. Int Microbiol 27, 525–534 (2024). https://doi.org/10.1007/s10123-023-00409-2
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DOI: https://doi.org/10.1007/s10123-023-00409-2