Pathogen co-infections and disease complexes in cotton: Environmental drivers, diagnostics and research priorities for disease management

Cotton production has long faced multiple-pathogen disease scenarios. These include disease complexes where multiple pathogens are involved, accelerating disease progression, altering symptom expression, and reducing the effectiveness of disease management options. These complexes include cotton root rot, vascular wilt, leaf spot, and boll rot. This Feature Article explores plant-pathogen and pathogen-pathogen interactions in cotton disease complexes and the factors that influence them. It also discusses advances in molecular diagnostics, such as pathogen assemblage profiling, which enables more accurate detection and measurement of co-infections, thereby improving risk evaluation and informing targeted disease management practices. Drawing on evidence from cotton-growing regions worldwide, particular attention is given to the relevance and implications of pathogen co-infection and disease complexes for Australian cotton production systems. Recognizing and managing pathogen co-infections and disease complexes, rather than addressing individual pathogens in isolation, provides a framework for more sustainable cotton production systems and enhances the ability to anticipate and respond to evolving crop health challenges under changing conditions driven by climate change, global trade, and agricultural intensification.