The molecular mechanisms by which multiple metabolic pathways regulate soybean responses to Mn stress

Manganese (Mn) is an essential micronutrient for plants. Soybean, a globally important food and feed crop, shows high sensitivity to Mn stress. This study applied an integrated multi-omics approach to elucidate the mechanisms underlying soybean responses to Mn toxicity stress.

The results showed that Mn toxicity significantly inhibited soybean growth, with a 35.68% decrease in leaf glutathione (GSH) content and a 53.54% decrease in hydrogen peroxide (H₂O₂) content, whereas phenylalanine ammonia-lyase (PAL) activity in roots increased by up to 83.15%. When soybean plants were treated with 100 µM Mn, it significantly affected phenotypic and physiological data and avoided lethality. Therefore, this concentration was selected as the Mn stress treatment concentration for subsequent ion content determination and omics studies. Under Mn toxicity stress (100 µM Mn), the Mn content in the roots and leaves of soybean plants increased by 7.4 times and 7.7 times respectively. Transcriptomic and metabolomic analyses were performed on soybean plants treated with 5 µM and 100 µM Mn. A total of 5045 differentially expressed genes (DEGs), including 3373 upregulated and 1672 downregulated genes, and 3259 differentially accumulated metabolites (DAMs), including 1505 upregulated and 1754 downregulated metabolites, were identified in leaves and roots. Integrated transcriptional and metabolomic analyses indicated that flavonoid biosynthesis and phenylalanine metabolism in leaves, and glycolysis/gluconeogenesis in roots, represent the core response pathways to Mn toxicity.

Coordinated regulation of genes and metabolites establishes a buffering system that mitigates Mn-induced toxicity. These findings provide a theoretical basis for breeding Mn-tolerant soybean cultivars and for strategies aimed at remediation of Mn-contaminated environments.