Transcriptome analysis reveals Vernalization is independent of cold acclimation in Arabidopsis

BACKGROUND: Through vernalization, plants achieve flowering competence by sensing prolonged cold exposure (constant exposure approximately 2-5 °C). During this process, plants initiate defense responses to endure cold conditions. Here, we conducted transcriptome analysis of Arabidopsis plants subjected to prolonged cold exposure (6 weeks) to explore the physiological dynamics of vernalization and uncover the relationship between vernalization and cold stress. RESULTS: Time-lag initiation of the two pathways and weighted gene co-expression network analysis (WGCNA) revealed that vernalization is independent of cold acclimation. Moreover, WGCNA revealed three major networks involving ethylene and jasmonic acid response, cold acclimation, and chromatin modification in response to prolonged cold exposure. Finally, throughout vernalization, the cold stress response is regulated via an alternative splicing-mediated mechanism. CONCLUSION: These findings illustrate a comprehensive picture of cold stress- and vernalization-mediated global changes in Arabidopsis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-07763-3.