Emerging insights into plant disease management: multi-omics approaches elucidate the molecular mechanisms underlying pathogen virulence differentiation in natural populations

A recent study by R. Cheng, T. Lv, P. Ji, B. Ma, et al. (Appl Environ Microbiol 91:e01685-25, 2025, https://doi.org/10.1128/aem.01685-25) used multi-omics analysis to reveal the molecular map of pathogen virulence differentiation driven by natural variation. Building on this work, this article examines how natural variation shapes pathogen virulence and disease prevalence and explores the use of multi-omics approaches to uncover associated molecular mechanisms. The opportunities and challenges of applying multi-omics technologies in plant disease management are also discussed in this article.