Maize Genomics and Genetics 2025, Vol.16, No.6, 284-293 http://cropscipublisher.com/index.php/mgg 291 significant accumulation of these compounds. The metabolic adjustment of tolerant maize allowed it to maintain better water retention while keeping its photosynthetic processes active according to Liang et al. (2021), Brar et al. (2025) and Ren et al. (2025). Pathway enrichment analyses further highlighted activation of the glutamate–proline axis, suggesting a preferential allocation of nitrogen toward osmoprotectant biosynthesis as a key adaptive strategy (Brar et al., 2025; Ren et al., 2025). The research findings show that compatible solutes serve as vital metabolic markers which enable scientists to detect salt-resistant maize plants under salt stress conditions. 7.2 Differential accumulation of secondary metabolites contributes to genotype-specific adaptation The research investigated the impact of salinity stress on maize seedling secondary metabolite production through an individual case study. The UPLC-QTOF-MS results showed tolerant genotypes had elevated levels of flavonoids and phenolic acids and terpenoids but sensitive lines showed no or minimal induction. The antioxidant compounds quercetin and ferulic acid in tolerant maize showed strong links to enhanced antioxidant activity which protected cell membranes from peroxidation and improved survival rates under stress conditions (Brar et al., 2025; Ren et al., 2025). Network correlation analyses revealed that flavonoid accumulation was tightly linked to antioxidant enzyme activity, highlighting the synergy between metabolic and enzymatic defenses. The research demonstrates that particular genetic variations within secondary metabolism systems allow plants to build salt stress tolerance. 7.3 Translation of metabolite markers into breeding programs demonstrates practical feasibility The present translational research merges metabolomics with genetic mapping to identify metabolite markers which help detect salt tolerance in maize plants. The metabolome-wide association studies (mGWAS) of different maize panels revealed raffinose and linolenic acid as the most important metabolites which correlated with tolerance traits such as shoot biomass and ion exclusion capacity (Liang et al., 2021; Brar et al., 2025). The research team confirmed the candidate genes involved in raffinose family oligosaccharide biosynthesis and lipid desaturation through expression analysis. The researchers successfully added these metabolite markers to breeding programs through selection indices which helped discover new salt-resistant germplasm. The research shows that metabolomic markers serve as useful tools for breeding programs which link scientific research to agricultural development. 8 Future Perspectives and Conclusion Scientists need to study maize salt stress by tracking metabolic changes that occur at various times and locations. The majority of metabolomic research produces static views of biological systems although stress responses create dynamic changes in metabolism which affect various tissues at different developmental stages. The combination of imaging mass spectrometry and single-cell metabolomics techniques enables scientists to study how different plant tissues such as roots and leaves and reproductive organs distribute resources when exposed to salt stress. The research will examine short-term metabolic changes that lead to long-term adaptive responses through the analysis of their initial signaling pathways. The implementation of these methods will help us understand the mechanisms of salt tolerance development in maize. Future research needs to focus on combining metabolomics with other omics fields and sophisticated computational systems. The analysis of metabolite variation through transcriptome and proteome and ionome data requires advanced multi-omics methods which have successfully established mQTL and mGWAS to link proline and raffinose and flavonoids to their genetic origins (Liang et al., 2021; Brar et al., 2025). The scientific community continues to face a major challenge in determining cause-effect relationships between correlated events. The identification of salt tolerance drivers needs Mendelian randomization and structural equation modeling and machine learning-based causal inference methods to convert metabolomics from descriptive associations into predictive and mechanistic biology. Metabolomics provides scientists with an effective method to study the biochemical mechanisms that enable maize plants to adapt to salt stress conditions. The research reveals how tolerant and sensitive genotypes adapt through osmoprotectants and secondary metabolites and lipid remodeling pathways. Research studies have found metabolite biomarkers useful for breeding but genetic mapping and functional validation methods are needed to
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