Summary: Salt stress negatively affects rice growth, development and yield. Metabolic adjustments contribute to the adaptation of rice under salt stress. Branched‐chain amino acids (BCAA) are three essential amino acids that cannot be synthesized by humans or animals. However, little is known about the role of BCAA in response to salt stress in plants. Here, we showed that BCAAs may function as scavengers of reactive oxygen species (ROS) to provide protection against damage caused by salinity. We determined that branched‐chain aminotransferase 2 (OsBCAT2), a protein responsible for the degradation of BCAA, positively regulates salt tolerance. Salt significantly induces the expression of OsBCAT2 rather than BCAA synthesis genes, which indicated that salt mainly promotes BCAA degradation and not de novo synthesis. Metabolomics analysis revealed that vitamin B5 (VB5) biosynthesis pathway intermediates were higher in the OsBCAT2‐overexpressing plants but lower in osbcat2 mutants under salt stress. The salt stress‐sensitive phenotypes of the osbcat2 mutants are rescued by exogenous VB5, indicating that OsBCAT2 affects rice salt tolerance by regulating VB5 synthesis. Our work provides new insights into the enzymes involved in BCAAs degradation and VB5 biosynthesis and sheds light on the molecular mechanism of BCAAs in response to salt stress.

Serotonin (5-hydroxytryptamine) plays an important role in many developmental processes and biotic/abiotic stress responses in plants. Although serotonin biosynthetic pathways in plants have been uncovered, knowledge of the mechanisms of serotonin accumulation is still limited, and no regulators have been identified to date. Here, we identified the basic leucine zipper transcription factor OsbZIP18 as a positive regulator of serotonin biosynthesis in rice. Overexpression of OsbZIP18 strongly induced the levels of serotonin and its early precursors (tryptophan and tryptamine), resulting in stunted growth and dark-brown phenotypes. A function analysis showed that OsbZIP18 activated serotonin biosynthesis genes (including tryptophan decarboxylase 1 (OsTDC1), tryptophan decarboxylase 3 (OsTDC3), and tryptamine 5-hydroxylase (OsT5H)) by directly binding to the ACE-containing or G-box cis-elements in their promoters. Furthermore, we demonstrated that OsbZIP18 is induced by UV-B stress, and experiments using UV-B radiation showed that transgenic plants overexpressing OsbZIP18 exhibited UV-B stress-sensitive phenotypes. Besides, exogenous serotonin significantly exacerbates UV-B stress of OsbZIP18_OE plants, suggesting that the excessive accumulation of serotonin may be responsible for the sensitivity of OsbZIP18_OE plants to UV-B stress. Overall, we identified a positive regulator of serotonin biosynthesis and demonstrated that UV-B-stress induced serotonin accumulation, partly in an OsbZIP18-dependent manner.

Salinity is an important environmental factor influencing crop growth and yield. Malate dehydrogenase (MDH) catalyses the reversible conversion of oxaloacetate (OAA) to malate. While many MDHs have been identified in various plants, the biochemical function of MDH in rice remains uncharacterised, and its role in growth and salt stress response is largely unexplored. In this study, the biochemical function of OsMDH12 was determined, revealing its involvement in regulating tiller number and salt tolerance in rice. OsMDH12 localises in the peroxisome and is expressed across various organs. In vitro analysis confirmed that OsMDH12 converts OAA to malate. Seedlings of OsMDH12-overexpressing (OE) plants had shorter shoot lengths and lower fresh weights than wild-type (WT) plants, while osmdh12 mutants displayed the opposite. At maturity, OsMDH12-OE plants had fewer tillers than WT, whereas osmdh12 mutants had more, suggesting OsMDH12’s role in tiller number regulation. Moreover, OsMDH12-OE plants were sensitive to salt stress, but osmdh12 mutants showed enhanced salt tolerance. The Na⁺/K⁺ content ratio increased in OsMDH12-OE plants and decreased in osmdh12 mutants, suggesting that OsMDH12 might negatively affect salt tolerance through influencing the Na⁺/K⁺ balance. These findings hint at OsMDH12’s potential as a genetic tool to enhance rice growth and salt tolerance.

Vitamin B6 (VB6) is an essential nutrient that must be obtained from the diet by humans and livestock, and plays an important role in response to various biotic and abiotic stresses in plants. Although the VB6 biosynthesis pathway has been uncovered in higher plants, understanding of its genetic control remains limited, and the role of VB6 in responding to cold stress is largely unknown. Here, we showed that variation in VB6 levels in rice is attributable to differential transcription of OsPDX1.2 , a pyridoxal phosphate synthase, due to polymorphisms in its promoter. Natural variations in the OsPDX1.2 promoter affect the binding affinity of OsbZIP18, a transcriptional factor repressing OsPDX1.2 transcription. Loss of function in OsPDX1.2 or overexpression of OsbZIP18 significantly reduces cold tolerance in rice. Further investigation revealed that both genes affect cold tolerance by regulating VB6 and abscisic acid (ABA) biosynthesis. Moreover, the frequency of the cold‐tolerant pOsPDX1.2 ^Hap2 increases at higher latitudes, whereas the cold‐sensitive pOsPDX1.2 ^Hap1 increases at lower latitudes, indicating that natural variation in OsPDX1.2 contributes to differential cold adaptation in rice. Overall, our results reveal a regulatory pathway controlling rice VB6 accumulation and cold tolerance via the OsbZIP18– OsPDX1.2 module, providing a potential target for improving rice quality and stress tolerance.

Seed germination rate is a key early trait that strongly influences rice yield. Although germination is known to be regulated by classical phytohormones and certain metabolites, the systematic metabolic regulatory network underlying natural variation, especially the key hub metabolites with causal function, still lacks in-depth analysis. In this study, we investigated 56 rice accessions showing pronounced differences in germination performance and systematically identified metabolic pathways associated with germination rate by integrating metabolomic and proteomic analyses. Pathways involved in amino acid metabolism, energy metabolism, and glutathione metabolism were coordinately activated in Rapid Germination (RG) seeds compared with Delayed Germination (DG) seeds. Among them, glutamine was significantly enriched in the RG group. Exogenous application of glutamine selectively and significantly promoted radicle and shoot elongation in a subset of DG varieties, providing direct evidence for a positive causal role of glutamine in seed germination. The variety-specific response further suggests that germination is controlled by a complex, genotype-dependent regulatory network. Together, our results highlight a glutamine-centered metabolic program as an important basis for rapid rice seed germination and provide potential targets for improving early vigor through metabolic engineering and molecular breeding.