Genome-Wide Identification of DnaJ Gene Family and VIGS Analysis Reveal the Function of GhDnaJ316 in Floral Development for Upland Cotton

DnaJ proteins are established regulators of multiple physiological processes in plants, but their systematic identification and functional characterization in cotton remains largely uncharacterized, particularly regarding their roles in floral developmental regulation. In this study, based on genome-wide analysis of <i>Gossypium hirsutum</i> L., 372 <i>DnaJ</i> genes were systematically identified and phylogenetically classified into four distinct clades (I-IV). These genes exhibited non-uniform chromosomal distribution. Structural analysis revealed clade-specific variations in intron numbers and conserved motifs. Cis-acting element profiling indicated the roles of <i>DnaJs</i> in modulating biosynthetic and metabolic regulation during both vegetative and reproductive development in cotton. Transcriptomic analysis highlighted tissue-specific expression patterns, with <i>GhDnaJ316</i> showing preferential expression in anthers and filaments. Functional validation via VIGS-mediated silencing confirmed <i>GhDnaJ316</i> as a negative regulator of floral transition, accelerating budding by 7.7 days and flowering by 9.7 days in silenced plants. This study elucidates the genomic architecture of <i>GhDnaJs</i>, demonstrates <i>GhDnaJ316</i>'s critical role in floral development and provides insights for molecular breeding in early-maturing cotton.