Temporal Transcriptomic and Metabolomic Reprogramming Unveils a Two-Phase Salt Tolerance Mechanism in Apocynum venetum

Soil salinization poses a major constraint to global agriculture. <i>Apocynum venetum</i>, a salt-tolerant halophyte, provides an effective model for investigating salt-adaptive strategies; however, the temporal dynamics of its tolerance-associated genes and metabolites remain unclear. In this study, integrated transcriptomics, metabolomics (UHPLC-MS), physiological assays, and weighted gene co-expression network analysis (WGCNA) were conducted to characterize early (7-day) and late (18-day) responses to 200 mM NaCl stress. NaCl stress significantly reduced chlorophyll content while increasing Na⁺ accumulation, MDA levels, antioxidant enzyme activities (SOD and CAT), and total flavonoid content. Early responses (NaCl7) were marked by accumulation of ferulic acid, rhamnetin, and 3,4-dihydrocoumarin, with activation of plant hormone (ABA, auxin, zeatin) and MAPK signaling pathways. Late responses (NaCl18) exhibited increased accumulation of scopoletin, formononetin, and caffeyl-alcohol, with enrichment of phenylpropanoid biosynthesis, glutathione metabolism, and photosynthesis-related pathways. WGCNA identified early-response hub genes, including <i>AOC</i>, <i>MAPKKK17/18</i>, <i>CYP98A</i>, and <i>CCoAOMT</i>, coordinating stress signaling and antioxidant metabolism. Late stress responses involved genes like <i>CPK</i>, <i>GST</i>, <i>CYCD3</i>, and <i>ARF</i>, modulating calcium signaling and ROS detoxification. Genes shared across phases included <i>CYP90C1</i>, <i>HD-ZIP</i>, <i>HSP20</i>, and <i>PP2C</i>, regulating protein stabilization and stress signaling. These findings reveal a two-phase salt tolerance strategy in <i>A. venetum</i>, integrating early signaling and late metabolic adaptation.