## 5 Conclusions  
This study systematically compared the salt tolerance of _Astragalus__mongholicus_ germplasms from different regions of China and analyzed their responses to salt stress through phenotypic and physiological biochemical data. The salt-tolerant germplasm LQ demonstrated notable advantages in physiological traits such as antioxidant capacity and osmoregulatory ability. Subsequently, integrated transcriptomic and metabolomic analyses further confirmed that the salt-tolerant germplasm LQ alleviates the negative impacts of salt stress by regulating key metabolic pathways, including flavonoid biosynthesis, phenylalanine metabolism, and isoquinoline alkaloid synthesis, and modulating the expression of related genes, thus influencing metabolite accumulation. Notably, the accumulation of metabolites such as apigenin, neohesperidin, L-phenylalanine, and dopamine significantly enhanced LQ's antioxidant and osmoregulatory abilities, thereby reducing the damage to plant growth and development caused by salt stress. This study also identified that the isoquinoline alkaloid and phenylalanine metabolism pathways play a role in _A.__mongholicus_ response to salt stress--mechanisms that have been relatively underexplored in previous studies on salt-alkali mixed stress in _A.__mongholicus_. These findings not only provide novel insights into the molecular mechanisms of salt tolerance but also establish a theoretical foundation and practical basis for future strategies in metabolic regulation and gene editing aimed at improving salt tolerance in _A.__mongholicus_ and other crops.  
**Supplementary Materials:** The following supporting information can be downloaded at [[https://www.mdpi.com/article/10.3390/app15052575/s1](https://www.mdpi.com/article/10.3390/app15052575/s1)]([https://www.mdpi.com/article/10.3390/app15052575/s1](https://www.mdpi.com/article/10.3390/app15052575/s1)), Table S1: Distribution and classification of _A.__mongholicus_ varieties across different provinces in China; Table S2: Results of principal component analysis of various indicators of _A.__mongholicus_ germplasm at the seedling stage; Table S3: Loading and weight of each index of _A.__mongholicus_ germplasm at the seedling stage; Table S4: Membership values and comprehensive evaluation indexes of _A.__mongholicus_ germplasm seedling indicators.  
**Author Contributions:** Conceptualization, methodology, investigation, data curation, formal analysis, project administration, and writing--original draft preparation, Y.L. and J.S.; resources, software, data curation, and validation, X.L. and J.Y.; supervision, funding acquisition, and writing--review and editing, J.S. All authors have read and agreed to the published version of the manuscript.  
**Funding:** This work was financially supported by the China Agriculture Research System-Chinese Materia Medica (No. CARS-21), the Science and Technology Program of Inner Mongolia Autonomous Region (No. 2023 YFFH0069), the Science and Technology Program of Inner Mongolia Autonomous Region (No. 2021 GG0358), the Natural Science Foundation of Inner Mongolia Autonomous Region(No. 2024 MS03032), and the Double First-Class Construction Funds--Discipline Construction Quality Improvement Project (No. DC2400000900).  
**Institutional Review Board Statement**: Not applicable.  
**Informed Consent Statement**: Not applicable.  
**Data Availability Statement**: The transcriptome datasets in this study were stored in NCBI under the accession number PRJNA1197969.  
**Acknowledgments**: We would like to express our heartfelt gratitude to [PERSON] and [PERSON] for their valuable assistance during the research and manuscript preparation process. Their constructive feedback and technical support greatly contributed to the refinement of this work.  
**Conflicts of Interest**: The authors declare no conflicts of interest.