Molecular Characterization of Pathogenic Fungi and Oomycetes Causing Soft Rot Disease of Ginger (Zingiber officinale) in Kaduna State, Nigeria

Abstract

Ginger (Zingiber officinale) is a globally cultivated spice crop with significant economic value. However, its production is severely hampered by soft rot diseases caused by a complex assemblage of pathogenic fungi and oomycetes, including Fusarium oxysporum, Phytophthora capsici, and Pythium spp. These pathogens not only cause substantial yield losses but also diminish the quality of ginger rhizomes, impacting both local livelihoods and international trade. Traditional morphological identification often falls short in distinguishing pathogen species and understanding their genetic diversity. Aims: To address this challenge, this study aimed to characterize the molecular features of ginger soft rot pathogens through comprehensive genetic analysis. Infected ginger samples were collected from major cultivation regions of the Gidan Tagwai district of Kachia as well as the Jaba Local Government Area of Kaduna State. Place and Duration of the Study: National Root Crop Research Institute, Maro Out-Station, Kaduna State, Nigeria, between May 2023 and November 2025. Methodology: The infected samples were isolated and purified. The samples were analyzed with molecular identification using Internal Transcribed Spacer (ITS) sequencing, multilocus sequence typing (MLST), and virulence gene profiling. Results: Phylogenetic analyses revealed high genetic variability among Fusarium oxysporum isolates, with evidence of multiple haplotypes indicating diverse origins and potential for differential virulence. Similarly, Phytophthora and Pythium isolates exhibited distinct genetic lineages, some closely related to known aggressive strains. The presence of key virulence genes such as pectinases and cellulases underscores their pathogenic potential. The findings provide critical insights into the molecular diversity and pathogenicity mechanisms of ginger soft rot pathogens, informing the development of targeted management strategies, resistant cultivars, and molecular diagnostics. This research advances our understanding of the genetic basis of soft rot disease and underscores the importance of molecular tools in plant disease epidemiology.