Characterisation of mycotoxin-producing Fusarium species associated with maize ear rot and its pathogenomics and mycotoxin gene profile

Maize ear rot is a major constraint to maize production, causing yield losses, grain deterioration, and mycotoxin contamination. This study characterised the diversity, pathogenicity, mycotoxin-associated potential, and genomic features of Fusarium associated with maize ear rot in Karnataka, India. A total of 54 isolates were analysed using morphological, multilocus phylogenetic, pathogenicity, toxin-gene, and whole-genome approaches. Six Fusarium species were identified, with Fusarium verticillioides predominating (43 isolates; 79.63%). Most isolates exhibited high pathogenicity (> 75% disease severity), while tested representative isolates of F. verticillioides and F. graminearum reduced seed germination to 65% and 62%, respectively, and caused substantial stalk and ear rot symptoms. The predominance and pathogenicity of F. verticillioides were further associated with its fumonisin-related genetic potential, as FUM1 was detected in all 43 isolates, and LC–MS confirmed high fumonisin accumulation in kernels infected with the tested isolate. In contrast, the tested F. graminearum isolate contained trichothecene-associated genes, including NIV-associated TRI7 and TRI13 . Whole-genome sequencing of F. verticillioides PMER18 produced a ~ 40 Mb genome with 98.0% BUSCO completeness and identified putative pathogenicity-associated genes, CAZymes, transporters, and candidate effectors. Together, these findings integrate pathogen diversity, disease development, mycotoxin risk, and genomic features, providing a framework for risk assessment and integrated management of maize ear rot.