Ginger rhizome rot first emerged as a problem in Australian ginger crops in the 1930’s, likely introduced through infected imported rhizomes. Today, rhizome rot remains a major challenge for ginger growers, with Fusarium oxysporum f. sp. zingiberi (Foz) being the primary causal agent of Fusarium yellows. Despite its significance as a pathogen of ginger, much remains unknown about Foz’s pathogenicity and diversity. Even less is known about other Fusarium oxysporum strains that colonise ginger and their possible role in causing disease symptoms in ginger crops. To better understand the overall role of F. oxysporum in ginger, we obtained 60 isolates of F. oxysporum from ginger rhizomes that were either healthy or symptomatic for Fusarium yellows. A phylogenetic tree was constructed based on TEF1α sequences and at the same time, the isolates were screened for the presence of pathogenicity-associated, secreted in xylem (SIX) genes. Four-month-old ‘Canton’ ginger plants, propagated from rhizome pieces and grown under greenhouse conditions, were inoculated with 15 of these isolates, ten of which were putatively identified as Foz and five as non-pathogenic endophytes based on their SIX gene profile. Leaf discolouration, considered the first symptoms of Fusarium yellows, first appeared at 5 weeks post inoculation (wpi) in plants inoculated with two of the putative Foz isolates. All plants were harvested at 8 wpi. Plants inoculated with the putative endophyte, or the mock inoculated controls remained asymptomatic, displaying healthy leaves, tall tillers and rhizomes free from internal discolouration. In contrast, all plants inoculated with the ten putative Foz isolates exhibited significant leaf discolouration and rhizome rot at harvest. Despite significant rhizome discolouration and rot, the final rhizome weight did not significantly differ between plants inoculated with Foz and those inoculated with the putative non-pathogenic isolates. This suggests that ginger plants continue to grow and develop rhizome tissue despite pathogen presence. However, as infection progressed, the pathogen likely transitioned from a biotrophic to a necrotrophic phase, leading to tissue decay and appearance of external ‘yellows’ symptoms at 5 wpi.
Notably, the putative non-pathogenic isolates did not cause any disease symptoms in ginger. This aligns with our phylogenetic analysis, which showed that the Foz isolates formed a distinct cluster separate from the other F. oxysporum isolates. These findings are critical for improving Fusarium yellows diagnostics and management and for the development of disease-free Foz resistant cultivars.