Genome-Wide Characterization of SNAC Gene Family in Ten Cotton Species and Function Analysis of GhSNAC3D Under Cold Stress

The <i>SNAC</i> (Stress-responsive NAC) subfamily, a key branch of the conserved NAC transcription factor family, plays a central role in regulating plant stress response. However, systematic characterization of the <i>SNAC</i> family in cotton (<i>Gossypium</i> spp.) remains unclear. Employing a genome-wide screening approach, this study characterized 75 distinct <i>SNAC</i> transcription factor genes across ten <i>Gossypium</i> species, with tetraploid cottons harboring twice as many as their diploid progenitors. Phylogenetic analysis categorized the genes into three subgroups, with members of the same subgroup exhibiting conserved motif compositions and gene structures. Chromosomal localization revealed a conserved distribution pattern of <i>SNAC</i> genes between the Dt and At subgenomes in tetraploid cotton. Genomic collinearity analysis suggested that the primary driver of <i>SNAC</i> family expansion was segmental duplication. Promoter analysis predicted 2974 <i>cis</i>-regulatory elements, including cold- and hormone-responsive motifs, indicating their potential involvement in stress regulation. These <i>GhSNAC</i> genes indicated significant induced expressions under stress conditions, and <i>GhSNAC3D</i> exhibited the most significant up-regulated expression under low temperature stress. Genetic function studies displayed that VIGS-mediated <i>GhSNAC3D</i>-silencing significantly reduced the cold tolerance in cotton. This study systematically analyzed the genomic characteristics of the cotton <i>SNAC</i> family and functionally validated the molecular mechanism of <i>GhSNAC3D</i>-mediated cryogenic response, which lays a foundation for subsequent research on cold resistance in cotton and stress-resistant breeding.