Multi-omics insights into antioxidant defense, phenylpropanoid, and flavonoid pathways governing cold stress tolerance in cotton (Gossypium hirsutum).

Cold stress adversely affects cotton growth and development often causing morphological abnormalities during germination and seedling establishment. Nevertheless, the molecular and metabolic mechanisms conferring cold tolerance in cotton remain largely unclear. The study aimed to examine the morphological and physiological responses of two semi-wild Gossypium hirsutum accessions, the cold resistant Latifolium (CR-307) and cold susceptible Punctatum (CS-131) under cold stress. The experiment was conducted at two temperature regimes: 28-30 °C (control) and 4 °C for 96 h (cold stress). In comparison to the control, primary root length (PRL) decreased by 63% in CR-307 and by 73% in CS-131. Furthermore, biochemical analysis confirmed that CR-307 exhibited a stronger antioxidant defense system, showing higher SOD, POD, and CAT activities and reduced H2O2 accumulation under cold stress compared with CS-131. Transcriptome analysis identified 3135 differentially expressed genes (DEGs) associated with cold response regulation, mainly belonging to MYB, AP2/ERF, bHLH, WRKY, bZIP, and HSF transcription factor families. Cold stress also altered pathways related to phenylpropanoid, proline, flavonoid, and cofactor biosynthesis, reflecting adaptive molecular reprogramming. Moreover, 328 lipids, 105 organic acids, 87 phenylpropanoids and 39 flavonoids were detected as differentially expressed metabolites (DEMs) that contribute to cell wall reinforcement, antioxidant defense, transcriptional regulation and membrane stabilization under cold stress. Overall, the study provides comprehensive insights into the molecular and metabolic mechanisms underlying cold tolerance in cotton, offering potential targets for developing cold-resilient cultivars.