Transcriptomic analysis reveals the beneficial effects of salt priming on enhancing defense responses in upland cotton under successive salt stress

Priming-mediated stress tolerance in plants stimulates defense mechanisms and enables plants to cope with future stresses. Seed priming has been proven effective for tolerance against abiotic stresses; however, underlying genetic mechanisms are still unknown. We aimed to assess upland cotton genotypes and their transcriptional behaviors under salt priming and successive induced salt stress. We pre-selected 16 genotypes based on previous studies and performed morpho-physiological characterization, from which we selected three genotypes, representing different tolerance levels, for transcriptomic analysis. We subjected these genotypes to four different treatments: salt priming (P0), salt priming with salinity dose at 3-true-leaf stage (PD), salinity dose at 3-true-leaf stage without salt priming (0D), and control (CK). Although the three genotypes displayed distinct expression patterns, we identified common differentially expressed genes (DEGs) under PD enriched in pathways related to transferase activity, terpene synthase activity, lipid biosynthesis, and regulation of acquired resistance, indicating the beneficial role of salt priming in enhancing salt stress resistance. Moreover, the number of unique DEGs associated with G. hirsutum purpurascens was significantly higher compared to other genotypes. Coexpression network analysis identified 16 hub genes involved in cell wall biogenesis, glucan metabolic processes, and ribosomal RNA binding. Functional characterization of XTH6 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE) using virus-induced gene silencing revealed that suppressing its expression improves plant growth under salt stress. Overall, findings provide insights into the regulation of candidate genes in response to salt stress and the beneficial effects of salt priming on enhancing defense responses in upland cotton.