Deciphering the molecular basis of maize cold tolerance via integrative regulatory network analysis

Maize (Zea mays L.) is a globally critical but cold-sensitive crop. Understanding the temporal organization of cold-responsive, circadian-associated, and hormone-associated transcriptional programs is essential for deciphering how plants balance growth and survival under cold stress to ensure food security. We performed high-resolution time-series RNA-seq on 108 maize seedling samples across 14 time points (0-36 h cold stress and 24 h recovery). Coronatine (COR) was utilized as a defined JA-associated chemical perturbation to probe hormone-associated transcriptional responses during cold stress. We identified 12 986 cold-responsive and 2259 recovery-responsive genes, revealing a recovery-associated transcriptional transition characterized by suppressed photosynthesis-related processes and enrichment of genes associated with lipid catabolism, accompanied by transient physiological stress during early recovery. Cold stress induced widespread phase shifts and reduced oscillation amplitudes among circadian-associated transcripts, while COR identified distinct hormone-associated transcriptional modules and candidate network-associated genes, including ZmWRKY71 and ZmHSP28, whose roles were further supported by molecular and genetic analyses. This study establishes a temporally resolved transcriptional framework for maize cold stress and recovery, integrating transcriptional dynamics, physiological responses, and experimentally supported regulatory nodes.