This study elucidated the molecular, morphological and anatomical mechanisms underlying differential cold tolerance between two cotton cultivars, cold-tolerant Xinluzhong 61 (C61) and cold-sensitive Tahe 2 (C2). Seedlings were subjected to 0 °C cold stress for 12 and 24 h, followed by comparative transcriptomic (RNA-Seq) and comprehensive anatomical analyses of cotyledons, true leaves and stems. Transcriptomic profiling identified 8834 and 14,664 differentially expressed genes (DEGs) in C2 and C61 at 12 h, and 14,399 and 16,791 DEGs at 24 h, respectively. KEGG enrichment revealed prominent involvement of phenylpropanoid biosynthesis, photosynthesis, and cutin/suberin/wax biosynthesis at 12 h, shifting to phagosome, cysteine and methionine metabolism at 24 h. Phenotypic and anatomical observations confirmed that C61 developed dense stem glandular trichomes absent in C2, maintained significantly greater leaf thickness, palisade tissue thickness and palisade-to-spongy ratio in true leaves after 24 h stress, and exhibited thicker stem xylem. These findings highlight core adaptive traits and provide valuable genetic targets for improving cold tolerance in cotton.

In the present study, an investigation was carried out on the molecular, morphological, and anatomical mechanisms underpinning the differential cold tolerance of two cotton cultivars, Xinluzhong 61 (C61) and Tahe 2 (C2). The seedlings of these cultivars were exposed to 0 °C treatments for 12 and 24 hours. Comparative transcriptomic analysis (RNA-Seq) was conducted to identify differentially expressed genes (DEGs). Simultaneously, comprehensive anatomical examinations of cotyledons, true leaves, and stems were carried out to evaluate morphological alterations.Transcriptomic analysis at the 24-hour time point, the transcriptional profile had changed, with trichome differentiation and phloem/xylem histogenesis were the most significantly enriched biological process in C61. This result was verified by phenotypic observations, as C61 developed dense glandular trichomes on its stems, a characteristic not observed in C2. Anatomical investigations demonstrated that although cold stress led to a reduction in tissue thickness in both cultivars, C61 maintained significantly greater leaf thickness, palisade tissue thickness, and a higher palisade-to-spongy tissue ratio in true leaves after stress. Moreover, C61 exhibited greater xylem thickness in the stem under cold conditions, implying superior structural integrity and water transport capacity. These findings highlight key adaptive traits and offer valuable targets for the genetic improvement of cold tolerance in cotton.