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

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.