Genome-wide characterization of the cotton E2F/DP gene family and a negative role of GhDEL1_D08 in salt tolerance

Abstract Background E2F/DP is a transcription factor family essential for regulating the cell cycle during plant growth, development, and stress response. However, its role in cotton, a crop of significant economic importance, particularly concerning salt tolerance, remains unexplored. Results We systematically identified 70 E2F/DP genes across four cotton species, including the allopolyploids Gossypium hirsutum and G. barbadense, as well as the parental diploids A-genome G. arboreum and D-genome G. raimondii. Phylogenetic analysis classified these genes into three subfamilies (E2F, DP, and DEL), with notable expansion of the E2F subfamily in tetraploid cotton through local duplication events rather than tandem duplication. Promoter analysis revealed enrichment of stress- and hormone-responsive cis-elements, suggesting functional roles in environmental adaptation. Tissue-specific and salt stress expression profiling highlighted GhDEL1_D08 as a key candidate, exhibiting rapid induction under salt stress. Functional validation using virus- induced gene silencing in cotton and overexpression in Arabidopsis thaliana demonstrated that GhDEL1_D08 negatively regulates salt tolerance by modulating antioxidant enzyme activities and membrane lipid peroxidation. Conclusions These findings provide a comprehensive view of the E2F/DP gene family in cotton and identify GhDEL1_D08 as a critical regulator of salt stress response, offering potential targets for breeding stress-resilient cotton varieties.