Genetic identification and characterization of putatively novel, stable, and validated loci for plant height in wheat (Triticum aestivum L.)

Plant height is a pivotal trait in wheat (Triticum aestivum L.), influencing both lodging resistance and yield potential. Understanding its genetic architecture is essential for developing semi-dwarf, high-yielding cultivars. In this study, 224 Sichuan wheat cultivars were evaluated for plant height across three environments and genotyped using a 120 K SNP array. A genome-wide association study identified four stable quantitative trait loci (QTL) on chromosomes 3D, 4D, 5A, and 7A. Among these, QPH.sau.4D and QPH.sau.7A are putatively novel, and their effects on reducing plant height were confirmed in an independent validation panel. Pleiotropy analysis revealed that these QTL are associated with plant architecture through distinct mechanisms. QPH.sau.3D coordinated increased plant height with longer spikes and higher grain number and grain weight. QPH.sau.5A increased plant height, tiller number, and grain weight. However, this gain was accompanied by a reduction in spikelet number, indicating a clear trade-off between vegetative growth and spikelet formation. In contrast, the novel QTL showed more specific effects, with QPH.sau.7A also associating with higher thousand-grain weight in the validation panel. Within the QTL intervals, we identified four candidate genes potentially involved in hormonal signaling and transcriptional regulation. Overall, this study identifies stable and putatively novel QTL and nominates promising putative candidate genes, providing genetic resources to advance marker-assisted selection and breeding for optimized architecture and yield.