Dynamic changes in the transcriptome of tropical region-originated king grasses in response to cold stress.

Introduction: Cold acclimatization in tropical region-originated plants involves complex gene expression reprogramming to adapt to fluctuating temperatures. However, the molecular mechanisms and gene networks regulating cold tolerance in king grass remain largely unknown. Methods: To address this, we established a full-length reference transcriptome of king grass to enhance assembly quality and performed multiple time-point transcriptomic analyses following cold treatment at 4°C. Differentially expressed genes (DEGs) and transcription factors (TFs) involved in cold stress response were identified and analyzed through clustering and co-expression network analysis. Results: A total of 13,056 DEGs were identified and classified into nine clusters via k-means analysis. The cold response exhibited three distinct phases: early (before 3 h), middle (6-24 h), and late (48-72 h). Early-responsive genes were enriched in glycolipid metabolism and photosynthesis, middle-stage genes in carbohydrate metabolism, and late-stage genes in cold stress, osmotic stress, and endogenous stimuli responses. Key regulators of the ICE-CBF-COR signaling module, including 13 positive and negative regulators, were identified. The co-expression network further revealed mutual regulatory interactions within this module, highlighting its role in cold stress adaptation. Discussion: Our findings provide insights into the cold tolerance mechanisms of king grass, offering a genetic basis for modifying cold stress regulators. This research contributes to the broader understanding of low-temperature adaptive mechanisms in tropical plants and supports future breeding strategies for improved cold tolerance.