Haplotype-based genetic dissection of baking quality in the MAGIC winter wheat population WM-800 under contrasting nitrogen treatments

Improved wheat baking quality under reduced nitrogen (N) inputs is an essential requirement for climate smart and environmentally sustainable agriculture. To enhance wheat nitrogen use efficiency, a detailed understanding of the underlying quantitative genetic architecture is required. The MAGIC (Multi-parent Advanced Generation Inter-Cross) population WM-800, derived from intercrossing eight diverse German elite winter wheat cultivars, provides a powerful resource for high-resolution trait dissection. Here, Zeleny sedimentation volume (SED) and grain protein content (GPC) were assessed across seven environments under low and high N supply. The multi-parental design of WM-800 enabled the detection of highly resolved haplotype effects. Under N limited conditions, the haplotype-based GWAS revealed significant associations at three Glu-1 loci, which encode the high-molecular-weight glutenin subunits. Beyond this, a previously unreported QTL on chromosome 3 A with large, additive effects on both GPC (increased by 0.46%) and SED (increased by 2.49 mL) was identified. Additional QTL with stable, N independent effects across environments were detected. The predominantly additive contributions across all QTL highlight the suitability of WM-800 for dissecting quality traits and provide effective targets for breeding more resource-efficient and environmentally sustainable wheat cultivars. These findings expand the known genetic determinants of wheat baking quality. Moreover, they show that the targeted accumulation of favourable haplotypes may enable a wheat quality improvement under reduced N fertilization, contributing directly to lower N fertilizer demand and a reduced carbon footprint. • A wheat MAGIC population was characterized by SNP haplotypes and multi-field baking trials. • Haplotype-based GWAS identified 47 marker-trait-associations for baking quality traits GPC and SED. • Several QTL could be assigned to known HMW-GS glutenin loci under both tested N treatments. • Novel QTL showed genetic effects of increasing GPC and SED by up to 0.46% and 4.35 mL, respectively. • N independent quality QTL may promote selection for baking quality under reduced N fertilization.