Light-defined cold acclimation reprograms organ-specific metabolic and transcriptional landscapes for salt stress responses in maize.

key messageCold acclimation of young maize plants induced a light-dependent, organ-specific reprogramming at the metabolomic and gene expression levels, which significantly altered responses to salinity. It has been shown that light plays a decisive role in cold acclimation in plants. The core objective of the present work was to elucidate how light conditions during cold acclimation affect subsequent salt stress responses by co-regulating various processes among organs maize (Zea mays L.). Plants were cold-acclimated under sufficient light or shade and subsequently exposed to severe cold or salinity. Organ-specific analyses of leaves, stems, and roots combined chlorophyll fluorescence measurements with targeted and untargeted metabolomics, hormone and polyamine profiling, and stress-related gene expression were studied. Cold acclimation under sufficient light established organ-specific metabolic and transcriptional reprogramming that substantially altered subsequent salt stress responses. Light-acclimated plants showed coordinated, pathway-level metabolic adjustments across organs and distinct regulation of key stress-responsive genes, particularly in leaves and roots. Analyses indicated systemic, rather than isolated, metabolic rearrangements. These findings demonstrate that cold acclimation, depending on light intensity, establishes an organ-coordinated acclimated state that modulates subsequent salinity responses, highlighting the importance of environmental history and inter-organ regulation in stress adaptation. This study is the first to systematically reveal the organ-specific and systemic regulatory network underlying the light-temperature-salt interaction in maize.