Genetic identification and characterization of novel loci for flag leaf morphology traits in Chinese endemic wheat

Flag leaf morphology (FLM) is a critical determinant of wheat (Triticum aestivum L.) photosynthetic efficiency and grain yield. Chinese endemic wheat, a unique genetic reservoir formed by long-term adaptation to diverse and heterogeneous environments in China, harbors abundant, untapped allelic variation for traits related to environmental resilience and yield architecture. Mining this distinctive germplasm is therefore essential for identifying novel genetic determinants underlying complex traits like FLM. In this study, a genome-wide association study was conducted on 182 Chinese endemic wheat accessions using 38,490 single-nucleotide polymorphisms. We identified four stable quantitative trait loci (QTL) associated with FLM traits, three of which for flag leaf width (QFLW.sau.5A, QFLW.sau.5B, and QFLW.sau.5D) were intriguingly located on the homoeologous chromosomes of group 5, suggesting the action of a conserved, multi-subgenome genetic system. None of these QTLs overlapped with previously reported loci, highlighting their novelty and the value of this endemic gene pool. Pleiotropic analysis revealed that these loci also influence plant height and spike architecture. Their breeding value was further confirmed by validation in an independent population. Thirteen high-confidence candidate genes with elevated expression in flag leaf tissue were predicted, many involved in leaf development, photosynthesis, and stress responses. Collectively, by mining the unique genetic diversity of Chinese endemic wheat, we have uncovered a novel, homoeologous QTL system and candidate genes for FLM. These findings provide both a conceptual advance in understanding the polyploid genetic architecture of this key trait and valuable functional targets/molecular markers for improving photosynthetic efficiency and yield potential in wheat breeding.