Transcriptome analysis of OsNCED3 transgenic rice reveals the response mechanism to alkaline stress

Soil alkalinization is a major environmental stress that severely limits plant growth and development. Rice (Oryza sativa) is a globally important food crop, and to improve its yield and quality in saline-alkaline environments, its molecular responses to alkaline stress must be better understood. Here, we cloned and overexpressed the abscisic acid (ABA)-synthesizing gene 9-cis-epoxycarotenoid dioxygenase 3 (OsNCED3) in the alkaline-resistant rice cultivar Dongdao-4 to generate three transgenic lines (OE-1, -2, and -3). These transgenic lines exhibited enhanced root phenotypes and increased tolerance to alkaline stress compared to wild-type (WT) plants. The content of ABA and activity of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX), were significantly higher in the transgenic lines, whereas the levels of reactive oxygen species (ROS) (O₂·^- and H₂O₂) and malondialdehyde (MDA) were reduced in the transgenic lines under hydroponic alkaline stress conditions. Transcriptome analysis of the roots under 15 mmol L^-1 Na₂CO₃ stress identified 2915 upregulated and 2070 downregulated differentially expressed genes (DEGs) between the WT and transgenic lines. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses of the DEGs revealed enrichment in plant hormone signal transduction and MAPK signalling pathways, suggesting a role in stress response regulation. Additionally, agronomic surveys indicated that the grain yield of OsNCED3-overexpressing lines was significantly higher than that of the WT. These findings provide a theoretical and practical foundation for improving rice alkaline tolerance and productivity in saline-alkaline soils.