Transcriptome Analysis Coupled with Metabolome Profiling at a Key Time Point Reveals the Molecular Mechanism of Cold Stress Response in Oil Palm (Elaeis guineensis Jacq.)

Cold stress poses a major threat to global agricultural productivity. As a tropical woody oil crop, oil palm is highly susceptible to chilling damage; however, the molecular mechanisms underlying its cold response remain largely unknown. In this study, we profiled spear leaves of oil palm seedlings exposed to 8 °C for 0, 0.5, 1, 2, 4 and 8 h, using transcriptomic analysis across the full time course, complemented by metabolomic profiling at the 2 h time point. Physiological measurements showed cold stress-associated changes in chlorophyll and malondialdehyde (MDA) levels, as well as in the activities of antioxidant enzymes (SOD, POD, and CAT). Transcriptome analysis identified 31,576 expressed genes, including 9042 differentially expressed genes (DEGs). The highest number of specific DEGs was observed at the 2 h time point. Weighted gene co-expression network analysis (WGCNA) revealed nine co-expression modules with distinct temporal patterns. A total of 46 hub genes were identified, including WRKY, ERF, and seven genes encoding key enzymes involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan (LOC105041937, LOC105056784, LOC105048637, LOC105055093, LOC105038203, LOC105033050, and LOC105037948). Metabolomic analysis detected 98 differentially accumulated metabolites, which were enriched in the phenylalanine, tyrosine, and tryptophan pathway. qRT-PCR analysis showed that WRKY and ERF expression peaked at 2 h, coinciding with phenylalanine accumulation. In summary, this study describes the temporal dynamics of the cold stress response in oil palm, identifies the 2 h time point as a transition period, and provides a set of prioritized hub genes for further functional validation. These findings may support future breeding efforts aimed at improving cold tolerance in oil palm.