Flag leaf chlorophyll content of wheat: genetic dissection, candidate genes prediction and its relationship with other agronomic traits

Chlorophyll is the primary pigment responsible for capturing light energy and driving photosynthetic conversion. As the key photosynthetic organ during grain filling, the flag leaf plays a critical role in carbon assimilation, consequently, its chlorophyll content (FLC) represents a promising target for enhancing wheat yield and ensuring food security. Dissecting the genetic basis underlying FLC and elucidating its relationships with other agronomic traits are essential for accelerating molecular breeding aiming at improving photosynthetic efficiency and yield in wheat varieties. In this study, a major and environmentally stable quantitative trait locus (QTL) for FLC was detected using a population of 197 recombinant inbred lines (RILs). This QTL, designated QFLC.scwl-4B , was consistently mapped to chromosome arm 4BS across multiple environments, explaining 9.36%–31.82% of the phenotypic variance (PVE). The effect of QFLC.scwl-4B was further validated in an additional RIL population under diverse environmental conditions. Correlation and effect analyses revealed that QFLC.scwl-4B exhibits pleiotropic, leading to increased FLC, spikelet number per spike (SNS), and flag leaf thickness (FLT), alongside reduced productive tiller number (PTN). Furthermore, a putative candidate gene for QFLC.scwl-4B , TraesCS4B03G0098300 , was identified as an ortholog of gene in BBX family, which is known to repress chlorophyll degradation and senescence, and likely involved in chlorophyll synthesis. Further, the promoter region of TraesCS4B03G0098300 harbors a single nucleotide polymorphism (G/C) between the two parents. Collectively, these findings provide valuable QTL resources and candidate gene targets for marker-assisted selection in breeding programs aiming at developing wheat varieties with high photosynthetic efficiency and yield.