The Complex Landscape of Multidrug Resistance in Zymoseptoria tritici: MFS1 Promoter Plasticity and beyond

Abstract

Multidrug resistance (MDR) in fungal pathogens poses a growing threat to fungicide efficacy and sustainable agriculture. In the wheat pathogen Zymoseptoria tritici, MDR is primarily linked to overexpression of the MFS1 transporter gene, driven by transposable element (TE) insertions in its promoter or their remnants. Here, we provide a comprehensive analysis of MFS1 promoter polymorphism and its phenotypic impact on MDR across 374 field isolates collected in Europe between 2020 and 2021. We identify six novel structural variants derived from diverse TE types, confirming that the MFS1 promoter undergoes recurrent and independent insertion events. While previously characterized inserts consistently confer resistance, other variants show limited or variable phenotypic effects. Genetic crosses and quantitative phenotyping further reveal that MDR behaves as a quantitative trait and genome-wide association study confirmed MFS1 as the major resistance locus but also identified additional candidate genes involved in xenobiotic detoxification and membrane transport, supporting a polygenic basis for MDR. Our findings highlight the interplay between TE-driven structural variation and background polygenic architecture in shaping resistance phenotypes. In parallel, this study highlights the need to improve MDR monitoring beyond single-locus genotyping and re-evaluate current resistance management strategies that may inadvertently select for broad-spectrum resistance.