Genome-wide association study identifies variants of GhSAD1 conferring chilling tolerance in cotton

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 GhSAD1 HapB improved cold-stress resistance in cotton by increasing abscisic aldehyde (ABAld) and amino acid contents under chilling stress conditions. GhSAD1 HapB introduction considerably increased chilling tolerance in Arabidopsis transgenic plants, whereas GhSAD1 HapA plants exhibited chilling-sensitive phenotype. Additionally, we found that GhSAD1 HapB 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 GhSAD1 HapB 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.