Morphological and molecular identification of Diaporthe eres, causing foliar blight on Chrysanthemum morifolium in Egypt: Integrated assessment of pathogen characterization, host genetic diversity and fungicide efficacy

Abstract Background Chrysanthemum morifolium is considered a vital export crop in Egypt, but its production is severely constrained by fungal foliar blights. While Alternaria species are known and well-addressed pathogens, identification of other fungal agents and their economical impact on crops remain poorly characterized in Egypt, leading to ineffective disease management. Methods Fungal agents from symptomatic chrysanthemum plants’ leaves, collected from Menofia governorate, were purified and identified, both morphologically and molecularly (ITS sequencing). Pathogenicity was confirmed via Koch's postulates. In vitro efficacy of five fungicides (Difinoconazole, Chlorothalonil, Azoxystrobin, Propamocarb and Thiophanate-methyl; at three concentrations: 1000–3000ppm) was assessed using poisoned food technique. Start Codon Targeted (SCoT) oligonucleotides were used on genetic matter (DNA) extracted from infected chrusanthemum plants to distinguish genetic diversity within forementioned fungal agents. Results Current study provides the first conclusive report of Diaporthe eres as a high virulence pathogen of chrysanthemum in Egypt, alongside infections by Alternaria sp ., confirmed by pathogenicity tests. Fungicide screening revealed superior efficacy of Difinoconazole, achieving up to 90% mycelial growth inhibition, against all pathogens. In contrast, Thiophanate-methyl was largely ineffective, indicating probable resistance due to the pathogen’s genetic background. SCoT analysis revealed genetic distinctness of D. eres from Alternaria isolates as well as moderate polymorphism (29.59%), providing insights into pathogen’s population structure. Conclusion The ineffectiveness of certain fungicides, due to emergence of D. eres , signifies a major shift chrysanthemums disease profile in Egyptian. Our findings advocate for an integrated disease management strategy that prioritizes application of an effective fungicide, Difinoconazole, combined with within rotation program. We highly recommend prohibiting distribution and application of ineffective chemicals, to reduce further emergence of pathogen mutants that overcome promising effective fungicides. Finally, pathogens’ and plants’ molecular characterization leverages genetic of great importance that can be utilized in developinmg disease-resisatnt cultivars.