Trehalose-6-phosphate phosphatase (TPP) modulates the Trehalose-6-phosphate–trehalose balance, a key regulatory node in plant carbon sensing and stress resilience. However, its functional roles in vegetative crops such as potato (Solanum tuberosum, St) remains poorly understood. Here, we conducted a genome-wide identification of the StTPP gene family and identified nine distinct loci distributed across five chromosomes. Phylogenetic analysis categorized these loci into three clades, supported by conserved HAD-box motifs and distinct exon–intron structures. Family expansion was driven by segmental duplication under purifying selection. In silico promoter analysis revealed cis-elements responsive to hormones, light, and stress, while network modeling identified 64 transcription factors potentially involved in regulating StTPP expression. A biphasic transcriptional response was observed in the salt-tolerant cultivar Xisen6: rapid induction of StTPP2/3/9 early in salt exposure, followed by late repression of most members. Subcellular localization assays indicated that StTPP3 is present in the nucleus and cytosol, suggesting multifunctional roles. These findings suggest that StTPPs integrate developmental and environmental signals, providing a molecular basis for improving potato stress tolerance and yield stability.

β-D-xylosidase (BXL) is a key enzyme involved in xylan degradation and plays crucial roles in plant development and stress responses. However, its functional roles in potato (Solanum tuberosum) remain poorly understood. In this study, we performed a genome-wide identification of the StBXL gene family and identified eight StBXL genes distributed across five chromosomes. A phylogenetic analysis classified these genes into four groups. Conserved motif and domain analyses indicated functional conservation among StBXL proteins. Analyses of cis-acting elements in the promoters and expression profiles of StBXL genes in various plant tissues under different stress treatments revealed their spatiotemporal expression patterns, as well as potential roles in phytohormone signaling and stress responses. Alkali stress significantly inhibited the expression of StBXL4 and StBXL5. The overexpression of StBXL4 enhanced the sensitivity of potato seedlings to alkali stress, whereas the overexpression of StBXL5 showed no significant phenotypic differences under the same conditions. These results suggest that StBXL4 acts as a negative regulator of the alkali stress response in potato. This study fills the research gap regarding the potato StBXL gene family and provides valuable insights for the molecular breeding of alkali-tolerant potato varieties.