Genome-Wide Identification and Characterization of the Annexin (ANN) Gene Family in Potato (Solanum tuberosum L.) and Its Role in Salt Stress Response Revealed by Integrated Transcriptome and WGCNA Analysis

Background/Objectives: Soil salinization threatens global potato production, yet the molecular mechanisms underlying salt tolerance remain poorly understood. This study aimed to elucidate dynamic transcriptomic responses to salt stress, identify key regulatory genes, and characterize the corresponding gene family and its stress-responsive roles. Methods: Potato cv. Atlantic plantlets were subjected to 150 mM NaCl stress, with samples collected at 0, 3, 12, 24, and 48 h. Physiological and transcriptomic analyses were performed. WGCNA was employed to identify salt-responsive modules. Genome-wide identification, phylogenetic analysis, gene structure characterization, conserved motif analysis, and promoter cis-element prediction of the annexin gene family were conducted. Results: Transcriptome sequencing identified 1394 differentially expressed genes (DEGs) that were consistently responsive to salt stress, with functional enrichment highlighting stress signaling, hormone transduction, and phenylpropanoid biosynthesis pathways. Weighted gene co-expression network analysis (WGCNA) revealed the MEblack module as the key salt-responsive regulatory module, in which annexin genes exhibited high intramodular connectivity. Genome-wide identification uncovered nine annexin genes (StANN1–StANN9), characterized by uneven chromosomal distribution, conserved exon–intron structures and annexin repeat domains, and expansion through tandem, proximal and segmental duplication under purifying selection. Promoter analysis revealed abundant stress-responsive cis-elements, including ABRE and DRE/CRT motifs, in salt-inducible annexins. Expression profiling demonstrated that StANN5 and StANN6 were continuously upregulated under prolonged salt stress, whereas StANN2 and StANN3 showed transient early induction. Conclusions: These findings establish the central role of annexins in calcium signaling, redox homeostasis, and hormone-mediated stress adaptation, providing candidate targets for molecular breeding of salt-tolerant potato varieties.