Genomic Characterization of TGA Transcription Factors in Gossypium Unravels WGD-Driven Functional Diversification in Development and Biotic Defense

Abstract TGA transcription factors, critical regulators of plant defense mechanisms, exhibit incompletely understood evolutionary dynamics and functional roles in the economically vital cotton genus (Gossypium). Genome-wide analysis of Gossypium hirsutum identified 32 GhTGA genes. Phylogenetic classification resolved four evolutionary clades, revealing significant lineage expansion primarily driven by whole-genome duplication (WGD), notably within Class IV. Conserved synteny analyses traced the polyploidization trajectory, while structural characterization detected ubiquitous DOG1 domains, bZIP domains in 16 members, clade-specific acquisitions (e.g., RVT_2 in GhTGA6), and conserved motifs. Promoter analysis revealed complex regulatory potential, featuring an abundance of light-responsive (GT1, G-box) and hormone-responsive cis-elements (predominantly ABREs), alongside extensive predicted transcription factor networks involving both conserved and lineage-specific regulators. Expression profiling indicated pronounced spatiotemporal specificity, with elevated transcript levels in developing vegetative organs and ovules (distinctly excluding Class II genes) but suppression in fibers and anthers. Crucially, key GhTGAs (e.g., GhTGA1, GhTGA4) exhibited marked upregulation under Verticillium dahliae stress, implicating their involvement in jasmonic acid/salicylic acid (JA/SA)-mediated defense. These findings provide valuable insights into the functions of GhTGAs and establish a foundation for cotton breeding programs.