In China, cotton is a significant cash crop, and cold stress negatively impacts the crop’s development, production, and quality formation. Recent studies have shown that melatonin (MT) can alleviate the damage to plants under cold stress and promote good growth and development. In this study, the morphological and physiological changes induced by exogenous melatonin pretreatment on ‘Xinluzao 33’ cotton seedlings under cold stress were examined to investigate its defensive effects. The results showed that 100 μM MT pretreatment improved the cold resistance of cotton most significantly. It also improved the wilting state of cotton under cold stress, greatly increased the photosynthetic rate (Pn), stomatal conductance (Gs), maximum photochemical efficiency (Fv/Fm), and photosynthetic performance index (PIabs) by 116.92%, 47.16%, 32.30%, and 50.22%, respectively, and mitigated the adverse effects of low-temperature. In addition, MT supplementation substantially reduced the accumulation of superoxide anion (O₂^•−) and hydrogen peroxide (H₂O₂) by 14.5% and 45.49%, respectively, in cold-stressed cotton leaves by modulating the antioxidant system, thereby mitigating oxidative damage. Furthermore, MT pretreatment increased the endogenous melatonin content (23.80%) and flavonoid content (21.44%) and considerably induced the expression of biosynthesis enzyme-related genes. The above results indicate that exogenous melatonin improves the low-temperature resistance of cotton seedlings by regulating photosynthetic performance, antioxidant enzyme activity, antioxidant content, endogenous melatonin and flavonoid content, and the expression levels of genes related to their synthesis.

Chitinase genes, as a class of cell wall hydrolases, are essential for the development and pathogenesis of Fusarium oxysporum f.sp. vasinfectum (F. ox) in cotton, but related research focused on chitinase genes are limited. This study explored two island cotton root secretions from the highly resistant cultivar Xinhai 41 and sensitive cultivar Xinhai 14 to investigate their interaction with F. ox by a weighted correlation network analysis (WGCNA). As a result, two modules that related to the fungal pathogenicity emerged. Additionally, a total of twenty-five chitinase genes were identified. Finally, host-induced gene silencing (HIGS) of FoChi20 was conducted, and the cotton plants showed noticeably milder disease with a significantly lower disease index than the control. This study illuminated that chitinase genes play crucial roles in the pathogenicity of cotton wilt fungi, and the FoChi20 gene could participate in the pathogenesis of F. ox and host–pathogen interactions, which establishes a theoretical framework for disease control in Sea Island cotton.