Disease management shapes genotype-by-environment interactions in European winter wheat

Genotype-by-environment interactions (GEI) remain a major challenge for plant breeding, limiting accurate prediction across target populations of environments (TPE). To determine how GEI are influenced by contrasting crop management, we analysed 227 winter wheat genotypes representing over 50 years of European breeding. The genotypes were previously evaluated across 25 environments in Germany under contrasting fungicide and nitrogen treatments. Genome-wide marker effects for grain yield were assessed using genotype data from genome-wide single-nucleotide polymorphism (SNP) markers. Across environments, correlations between marker effects remained high across treatments (r = 0.71–0.94), indicating a stable genetic basis despite stronger fungicide than nitrogen treatment effects. Localized reductions in marker-effect correlations were primarily observed in the A and D subgenomes. Subsequently, integrated factor analytic models (IFA) were used to partition additive GEI into components associated with environmental covariates and latent factors. The selected IFA4 model captured 91.5% of the additive GEI variance. Measured environmental covariates accounted for 10.3% of this variance. Temperature-related covariates showed the strongest associations with the latent factors, while precipitation explained comparatively little variation. While genotype performance generally improved with breeding progress over time, temporal trends in environmental stability through breeding depended on how stability was quantified. The IFA4 model linked part of the observed GEI to measured environmental covariates while enabling prediction of genotype performance across environments. Our results show that both environmental conditions and management treatments contribute to GEI in European winter wheat.