Sexual reproduction and the polygenic architecture of azole resistance in agricultural populations of Aspergillus fumigatus

Introduction Agricultural environments, particularly greenhouses, are recognized as hotspots for the evolution of azole resistance in the opportunistic pathogen Aspergillus fumigatus. This study aimed to investigate the role of sexual reproduction and its underlying genetic architecture in driving resistance in Yunnan Province, China. Methods We integrated large-scale sexual crossing experiments with hierarchical genetic association analysis. Sexual fitness was compared between greenhouse and outdoor populations. A genome-wide association study (GWAS) on greenhouse strains identified candidate SNPs, which were then analyzed via hierarchical association mapping in 300 sexual progeny strains to decipher the genetic architecture of resistance. Results Greenhouse populations exhibited significantly higher sexual fitness, evidenced by greater mating type diversity, mating success (28.36% vs. 12.38%), and ascospore viability. Resistance was shown to be a complex quantitative trait primarily governed by epistatic interactions, where the strength of genetic associations increased with SNP combination complexity. A key, previously uncharacterized locus (SNP6) consistently showed significant effects. Comparative analysis revealed divergent genetic architectures for itraconazole (ITR) and voriconazole (VOR) resistance. Functional annotations implicated SNPs in oxidative stress response (e.g., salicylate hydroxylase) and cell wall integrity (e.g., chitin synthase) pathways. Discussion We propose a synergistic model wherein high sexual competency provides a platform for recombination, acting upon a standing epistatic landscape to facilitate rapid adaptive evolution. Our findings highlight the potential for resistance allele spread via sexual reproduction and suggest that resistance surveillance may need to account for multi-locus genotypes.