Chlorophyll Deficiency by an OsCHLI Mutation Reprograms Metabolism and Alters Growth Trade-Offs in Rice Seedlings

Chlorophyll biosynthesis is essential for photosynthesis and plant development. Disruptions in this pathway often manifest as pigment-deficient phenotypes. This study characterizes the morphological, anatomical, and physiological consequences of a chlorophyll-deficient rice mutant (yellow seedling, YS) caused by a loss-of-function mutation in the OsCHLI gene, which encodes the ATPase subunit of magnesium chelatase. Comparative analyses between YSs and wild-type green seedlings (GSs) revealed that YSs exhibited severe growth retardation, altered mesophyll structure, reduced xylem and bulliform cell areas, and higher stomatal and papillae density. These phenotypes were strongly light-dependent, indicating that OsCHLI plays a crucial role in light-mediated chloroplast development and growth. Transcriptome analysis further revealed global down-regulation of photosynthesis-, TCA cycle-, and cell wall-related genes, alongside selective up-regulation of redox-related pathways. These results suggest that chlorophyll deficiency induces systemic metabolic reprogramming, prioritizing stress responses over growth. This study highlights the multifaceted role of OsCHLI in plastid maturation, retrograde signaling, and developmental regulation, providing new insights for improving photosynthetic efficiency and stress resilience in rice.