Epsilon Archive for Student Projects

Abstract

Maize is a key staple crop globally and plays a critical role in food security in Rwanda. However, its production is threatened by ear rot diseases caused by various fungal pathogens, many of which are known to produce harmful mycotoxins. This study aimed to determine the fungal isolates associated with ear rot in many maize-growing regions of Rwanda by multilocus phylogenetic analysis, and to investigate some of the selected fungal interactions using in vitro assays. The tef1-α, rpb2 and tub2 genes were sequenced to characterise the fungal isolates, and phylogenetic relationships were inferred via maximum likelihood analysis. Additionally, pathogenicity assays and PCR-based detection of species and toxin markers were performed to evaluate the selected isolates. Phylogenetic analysis revealed considerable fungal diversity associated with maize in Rwanda. Fusarium isolates were grouped within the following species complexes: Fusarium graminearum species complex (FGSC), Fusarium fujikuroi species complex (FFSC), Fusarium incarnatum-equiseti species complex (FIESC), and Fusarium oxysporum species complex (FOSC). β-tubulin analysis identified several Penicillium species, with Penicillium crustosum forming the predominant cluster. Phylogenetic analysis identified seven Trichoderma species that formed distinct groups.

Chi-square analyses showed that the distribution of fungal species differed significantly between provinces, districts, and maize varieties, suggesting that geographic location and host genotype affected the occurrence and distribution of maize ear rot pathogens. PCR amplification using Tri13DON and AFL primers produced inconsistent or non-specific results, whereas VER1 and Fg16N primers produced clear, specific amplicons. Successful amplification in all inoculated treatments confirmed fungal establishment in both single- and co-inoculation assays. Overall, this study highlights the diverse fungal community associated with maize ear rot in Rwanda, emphasising the effectiveness of multilocus phylogenetic analysis in fungal identification and characterization. These findings serve as a foundation for future research into fungal ecology, pathogen interactions, and mycotoxin challenges in maize production systems.