Leveraging genome and transcriptome sequencing to decipher fungicide resistance mechanisms in crop pathogenic fungi: current status and prospects

Fungicide resistance in crop‐pathogenic fungi presents a major threat to global agriculture, jeopardizing food security and sustainable crop production. This review thoroughly explores the use of genomic and transcriptomic sequencing technologies to uncover the molecular and genetic mechanisms underlying fungicide resistance in various phytopathogens. Resistance develops through both target‐site mutations, such as changes in CYP51 and β‐tubulin genes, and nontarget‐site mechanisms, including metabolic detoxification, efflux pump overexpression and stress response modulation. Advances in whole‐genome sequencing (WGS), genome‐wide association studies (GWAS) and RNA‐seq have led to the discovery of novel resistance alleles, differentially expressed genes (DEGs) and critical regulatory networks. Combining multi‐Omics approaches improves our understanding of resistance mechanisms and aids the development of targeted diagnostics, breeding of resistant crop varieties and precise application of fungicides. Furthermore, machine learning and bioinformatics tools offer predictive insights into the development of resistance and potential countermeasures. This review highlights the importance of using genomic and transcriptomic data to design sustainable and integrated strategies for managing crop diseases and combating fungicide resistance in agriculture. © 2025 Society of Chemical Industry.