Deciphering the molecular signatures of tropical Areca catechu L. under cold stress: an integrated physiological and transcriptomic analysis.

INTRODUCTION: Areca catechu is a widely cultivated palm species with significant economic and medicinal value. However, A. catechu is a tropical plant that is particularly susceptible to low temperatures. METHODS: This study integrates physiological profiling with transcriptomic sequencing to systematically investigate the cold-response mechanisms of A. catechu. RESULTS: Multivariate variance analysis revealed that peroxidase (POD) activity and chlorophyll content are significant biomarkers strongly correlated with cold tolerance. A comprehensive investigation into the temporal expression of genes in response to 24 hours of cold stress was conducted, using RNA-seq analysis. This analysis yielded a substantial number of differentially expressed genes (DEGs), amounting to 20,870, which were found to be subject to temporal regulation. KEGG pathway enrichment analysis revealed substantial activation in three metabolic pathways: phytohormone signaling, alkaloid biosynthesis (tropane/piperidine/pyridine), and flavonoid biosynthesis. The application of Weighted Gene Co-expression Network Analysis (WGCNA), in conjunction with a dynamic tree-cutting algorithm, resulted in the identification of 25 co-expression modules. Eigenvector centrality analysis identified six hub genes responsive to cold stress: ZMYND15, ABHD17B, ATL8, WNK5, XTH3 and TPS. The findings of this study delineate three key aspects: (1) temporal dynamics of cold-responsive physiological processes, (2) pathway-level characterization of DEG enrichment patterns, and (3) genetic determinants underlying cold stress adaptation. DISCUSSION: These findings clarify the time series and core physiological indicators of A. catechu during various physiological processes, identify pivotal genes associated with cold stress, and provide a gene-to-phenotype framework for optimizing cold-resilient cultivation protocols and molecular marker-assisted breeding strategies.