Cold stress is a major environmental factor affecting plant growth and development. Although some plants have developed resistance to cold stress, the molecular mechanism underlying it is poorly understood. Here, we identified cold tolerance gene in cotton (Gossypium hirsutum L.) using genome-wide association study (GWAS) with 200 cotton accessions collected from different regions, and identified variations of a short chain alcohol dehydrogenase gene GhSAD1 that response to cold stress. The virus induced gene silencing (VIGS) and Arabidopsis overexpression experiments showed that GhSAD1 roles in cold-stress response.GhSAD1HapB introduction considerably increased cold tolerance in Arabidopsis transgenic plants, whereas GhSAD1HapA plants exhibited cold-sensitive phenotype. GhSAD1HapB silencing plants exhibited a decrease of abscisic acid (ABA) content and overexpression GhSAD1HapB in Arabidopsis increased ABA content. Additionally, we found that GhSAD1HapB regulated cold stress responses through the activity of c-repeat binding factor, which binds to the promoter region of the gene and regulates ABA signalling pathway under cold conditions. Overexpression of GhSAD1HapB induced cold-regulated (COR) genes expression and improved anti-cold metabolites under cold stress. Collectively, the findings of the study contribute to our understanding of the underlying mechanism of GhSAD1 in cold-stress response in cotton. Moreover, GhSAD1 could serve as candidate gene in improving crop stress

Cold stress is a major environmental factor affecting plant growth and development. Although some plants have developed resistance to cold stress, the molecular mechanism underlying it is poorly understood. Therefore, the aim of this study was to identify genes conferring cold resistance in cotton. Here, we identified cold tolerance gene in cotton (Gossypium hirsutum L.) using genome-wide association study (GWAS) with 200 cotton accessions collected from different regions. A variant of the gene was also identified. The results of the study showed that GhSAD1HapB improved cold-stress resistance in cotton by increasing abscisic aldehyde (ABAld) and amino acid contents under chilling stress conditions. GhSAD1HapB introduction considerably increased chilling tolerance in Arabidopsis transgenic plants, whereas GhSAD1HapA plants exhibited chilling-sensitive phenotype. Additionally, we found that GhSAD1HapB regulated chilling stress responses in cotton through the activity of c-repeat binding factor, which binds to the promoter region of the gene and regulates the ABA signalling pathway under chilling conditions. Overexpression of GhSAD1HapB induced COR genes expression and improved metabolic profile under cold stress. Collectively, the findings of the study contribute to our understanding of the underlying mechanism of GhSAD1 in cold-stress response in cotton. Moreover, GhSAD1 could serve as candidate gene in improving crop stress.