Structural and Transcriptional Adaptive Responses Contribute to Cold Tolerance Variation in Xinluzhong 61 and Tahe 2 Cotton Cultivars

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.