Integrative Network Analysis Reveals OsGLK1 as a Central Regulator of Photosynthetic Efficiency and Yield in Rice (PRJCA050202)
Photosynthesis fuels crop growth and yield, yet the regulatory networks coordinating photosynthetic gene expression with carbon allocation remain incompletely understood. Here, we constructed a gene regulatory network (GRN) for rice photosynthesis by integrating time-resolved RNA-seq, ATAC-seq, and promoter cis-element analyses, capturing both diurnal and drought responses. We identified nine hub transcription factors (TFs), four of which (OsPIL13, OsbZIP72, OsCGA1, and OsGLK1) exhibited strong leaf-specific, light-inducible expression patterns. Overexpression of OsPIL13, OsbZIP72, or OsGLK1 using photosynthetic tissue-specific promoters significantly enhanced the light-saturated photosynthetic rate (Asat) across developmental stages, with OsPIL13 overexpression increasing Asat by up to 57% during grain filling. Multi-omics analyses via RNA-seq and CUT&Tag confirmed that these TFs directly bind to the promoters of core photosynthetic genes, validating GRN predictions. While multiple TFs activated photosynthetic genes, only OsGLK1 overexpression consistently improved grain yield across multiple growing seasons. Comparative transcriptomics indicated that OsGLK1 also upregulates brassinosteroid biosynthesis, sugar transporter, and lipid transporter genes, which are key pathways linking photosynthesis to growth. Our results demonstrate that enhancing photosynthesis alone is insufficient for yield gain; instead, coordinated regulation of photosynthesis and carbon allocation through master regulators such as OsGLK1 is essential for sustainable productivity improvement in rice.