Genome-Wide Identification, Characterization, and Expression Analysis of VQ Gene Family in Salix suchowensis Under Abiotic Stresses and Hormone Treatments

The valine glutamine (VQ) proteins are transcription cofactors involved in various aspects of plant biology, including growth, development, and stress resistance, making them an attractive target for genetic engineering aimed at enhancing plant resilience and productivity. However, comprehensive reports or systematic studies on VQ cofactors in <i>Salix suchowensis</i> remain lacking. In this study, we analyzed <i>SsVQ</i> genes using bioinformatics methods based on the <i>Salix suchowensis</i> genome database. Expression profiles were further investigated through qRT-PCR under six treatments: PEG, NaCl, 40 °C, ABA, SA, and MeJA. A total of 39 <i>SsVQ</i> genes were identified, with phylogenetic analysis classifying them into seven groups. Collinearity analysis suggested that <i>SsVQ</i> gene amplification primarily resulted from whole genome duplication (WGD) or segmental duplication events. Ka/Ks ratios indicated that willow <i>VQ</i> genes have undergone predominantly purifying selection. Gene structure analysis revealed that <i>SsVQ</i> genes are intronless. Multiple sequence alignment showed that SsVQ19 shares similarity with PtVQ27, containing a hydrophilic threonine (T) residue preceding the VQ amino acid residues. Furthermore, genes within each group exhibited conserved structures and VQ motifs. Promoter and expression analyses suggested the potential roles of <i>SsVQ</i> genes in regulating willow responses to environmental stresses and hormonal signals. Most <i>SsVQ</i> genes displayed differential expression at specific time points, with six members (<i>SsVQ2</i>, <i>SsVQ9</i>, <i>SsVQ12</i>, <i>SsVQ23</i>, <i>SsVQ32</i>, and <i>SsVQ34</i>) showing sustained high-amplitude expression profiles across treatments. Notably, <i>SsVQ34</i> demonstrated pronounced transcriptional induction under PEG stress, with expression levels upregulated by 62.29-fold (1 h), 49.21-fold (6 h), 99.9-fold (12 h), and 201.50-fold (24 h). Certain <i>SsVQ</i> genes showed co-expression under abiotic/hormonal stresses, implying synergistic functions. Paralogous gene pairs exhibited stronger co-expression than non-paralogous pairs. This study provides novel insights into the structural and functional characteristics of the <i>VQ</i> gene family in <i>Salix suchowensis</i>, establishing a foundation for future research on the stress-resistance mechanisms of willow <i>VQ</i> genes.