Hormones, particularly ABA-based signal transduction, play a pivotal role in alleviating photosynthetic inhibition in rice induced by NaHCO3 stress

• ABA signaling may contribute to photosynthetic stability and enhance NaHCO 3 tolerance. • Co-expression network identifies OsPP2C065 (Os07g0646100) as a highly connected for saline–alkaline tolerance. • Integrated physiology and transcriptomics reveal hormone–photosystem interplay. Soil salinization is a major constraint on global rice ( Oryza sativa L.) production, threatening both yield and grain quality. To clarify the molecular and physiological basis of rice tolerance to saline–alkaline stress, we compared two contrasting cultivars: the tolerant Qijing 10 (QJ10) and the sensitive Longjing 31 (LJ31). Plants were subjected to 250 mmol·L -1 NaHCO 3 stress, and their physiological responses and transcriptomic profiles were comprehensively analyzed. QJ10 exhibited markedly greater tolerance than LJ31, as indicated by higher photosynthetic efficiency (smaller decreases in F v / F m , PI total , PI ABS ), reduced oxidative damage (lower accumulation of hydrogen peroxide and malondialdehyde), and more stable expression of chlorophyll metabolism-related genes. RNA sequencing and weighted gene co-expression network analysis (WGCNA) revealed that differentially expressed genes (DEGs) under NaHCO 3 stress were enriched in photosynthesis and hormone signaling pathways. Activation of the abscisic acid (ABA) signaling pathway was strongly associated with stress responses, with PP2C065 (Os07g0646100) identified as a highly connected hub gene potentially associated with enhanced stress tolerance in QJ10. These findings reveal a crucial regulatory module linking photosynthetic stability and hormone-mediated signaling to saline–alkaline tolerance and provide candidate genes for breeding stress-resilient rice varieties.