Genome Wide Association Study Identifies Novel Loci for Flag Leaf Morphology Traits in Chinese Endemic Wheat

Flag leaf morphology (FLM) is a critical determinant of wheat photosynthetic efficiency and grain yield. Understanding its genetic basis is essential for targeted breeding. In this study, 182 Chinese endemic wheat accessions were evaluated for FLM traits, revealing continuous variation with high heritability, indicative of polygenic control. Genome-wide association studies using 38,490 SNP and a mixed linear model with Q and K matrices identified four QTL: three for FLW on chromosomes 5A( QFLW.sau.5A ), 5B ( QFLW.sau.5B ), and 5D ( QFLW.sau.5D ), and one for flag leaf ratio (FLR) on chromosome 3D ( QFLR.sau.3D ). None overlapped with previously reported loci, indicating potential novelty. Effect analysis revealed pleiotropic influences on plant height (PH) and spike length (SL), and validation in an independent population confirmed their breeding relevance. Candidate gene analysis predicted 13 genes underlying the novel FLW QTL, including protein kinases, carbonic anhydrase, ATP synthase subunit C, SCO2, RING-finger/DEAD-box/PHD/SNF2 domain-containing proteins, transcription factors, and alpha/beta-hydrolases, many of which are involved in leaf development, photosynthesis, chloroplast function, and stress responses. These findings provide new insights into the genetic architecture of FLM and highlight potential targets for improving wheat leaf architecture and yield through molecular breeding.