Integrated Transcriptomics and Metabolomics Analyses Revealed that Phenylpropanoid Metabolism Regulates the Complex Salt-alkali Tolerance in Allium mongolicum

Allium mongolicum, a xerophytic industrial plant native to the Mongolian Plateau, demonstrates notable stress resistance, though its salt-alkali tolerance mechanisms remain poorly understood. This study integrates physiological assessments, transcriptomics, metabolomics, and full-length transcriptome analyses to uncover its adaptive mechanisms under salt-alkali stress.A comprehensive full-length transcriptome was constructed under these conditions, comprising 30,117 non-redundant genes, alongside significant trends observed in the activities of antioxidant enzymes and key enzymes in the phenylpropanoid pathway. Combined transcriptomic and metabolomic analyses identified key genes and metabolites in the phenylpropanoid pathway as central to salt-alkali tolerance. WGCNA further highlighted critical genes, such as AmCOMT1, AmHSP18, and AmPPL7, with functional validation of AmCOMT1 and AmHSP18 confirming transcriptome reliability. The salt tolerance function of AmCOMT1 has been validated through overexpression in plants, and the binding interaction with AmERF4 has also been confirmed.A proposed model suggests A. mongolicum mitigates salt-alkali stress via reactive oxygen species scavenging, osmotic regulation, and structural support, providing valuable insights for breeding salt-tolerant crops and enhancing its agricultural applications. Overall design: In this study, plump and similarly sized seeds of Allium mongolicum were used for germination on paper. The germination conditions were set at 20°C in the dark for 7 days, after which seeds with good germination status were selected and transplanted into pots filled with substrate soil. The cultivation conditions were established at 25°C with 12 hours of light and 12 hours of darkness, maintaining a humidity of 70%. After 45 days of seedling growth, the seedlings were transferred to 1/2 Hoagland nutrient solution for an additional 7 days, followed by exposure to composite saline-alkali stress treatment. The composition of the saline-alkali solution was NaCl:Na2SO4:NaHCO3:Na2CO3 = 1:9:9:1, the total salinity concentration is 150 mmol/L, with treatment durations of 0 hours (control group CK), 24 hours (T24), 48 hours (T48), and 72 hours (T72). Under this salinity composition(Hou et al., 2023), the expression of salt-related genes significantly increased. For each treatment group, 20 seedlings were randomly selected to obtain root samples, which were immediately frozen in liquid nitrogen for further experiments.