Abstract: 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.

Key words: ABA, cold tolerance, natural variation, stress tolerance, vitamin B6