Unveiling the genetic architecture of yield-related traits in spring wheat landraces: a region-specific genome-wide association study in the Qinghai-Tibet Plateau, China

Plant height is a key determinant of lodging resistance and yield potential in wheat. Although Green Revolution dwarfing genes have enhanced global production, their widespread use has reduced ·genetic diversity and imposed trade-offs in biomass and stress adaptation. This study explored the genetic architecture of plant height and yield-related traits in a panel of 273 spring wheat landraces collected from diverse high-altitude plateau regions. Multi-environment phenotyping revealed extensive variation and environment-dependent correlations among traits. Genome-wide association studies (GWAS) employing GLM, MLMM, and FarmCPU identified stable quantitative trait loci (QTL) for plant height on chromosomes 1B, 5B, 6B, and 6D. Importantly, these loci are genetically distinct from the widely deployed Rht-B1 and Rht-D1 genes, indicating that plateau landraces harbor alternative, underexploited height-regulating alleles. Co-localization analysis revealed QTL hotspots on chromosomes 1B and 5B with pleiotropic effects on spike morphology and tiller number, highlighting genomic regions with potential to optimize source–sink balance. Unlike modern semi-dwarf varieties, these landraces retain alleles that fine-tune plant architecture without severe biomass penalties, reflecting adaptation to the high-radiation, variable-temperature conditions of plateau environments. These findings highlight plateau wheat landraces as a reservoir of novel genetic variation, providing stable QTL targets for breeding climate-resilient cultivars with architectures suited to high-altitude and marginal environments.