Comparative transcriptome analysis reveals coordinated ABA, ROS, MAPK, and hormone-mediated regulatory networks...

Low-temperature stress severely limits the cultivation and geographical distribution of noni (Morinda citrifolia L.), a tropical medicinal plant with high economic and pharmaceutical values. However, the molecular mechanisms underlying cold tolerance in noni remain largely unknown. We conducted an integrated physiological, biochemical, and comparative transcriptomic analysis of a cold-susceptible genotype, Sanya (SY), and a cold-tolerant genotype, Kanghan-4 (KH-4), to elucidate the molecular mechanisms underlying differential cold tolerance. Relative to SY, KH-4 exhibited superior membrane stability, enhanced proline accumulation, and stronger antioxidant enzyme activities under cold stress. Transcriptome analysis revealed that KH-4 activated 1025 more differentially expressed genes (DEGs) than SY during the early cold exposure, reflecting a rapid transcriptional response. Comparative analysis across genotypes and time points identified 4286 candidate genes associated with cold tolerance, demonstrating that cold adaptation in noni involves coordinated activation of multiple stress-responsive pathways rather than a single dominant mechanism. Genes associated with ABA-dependent and ABA-independent signaling, ROS signaling, MAPK cascades, and other hormone pathways were preferentially induced in KH-4. Among the identified candidates, Contig_2712 exhibited the strongest genotype-specific induction, while NAC, AHP, GID2, ERF1, and PSαT were consistently downregulated in KH-4. Notably, the canonical ICE1-CBF cold signaling pathway was not prominently induced; instead, the data point to a MAPKKK, MKK, MPK, CAMTA3 module as a candidate alternative regulatory axis for cold tolerance in noni. These findings provide a molecular framework for cold tolerance in noni and identify candidate genes and pathways for functional studies and molecular breeding of cold-tolerant cultivars.