Spermidine treatment promotes soybean germination under bicarbonate stress

Highlights 1 • Spermidine treatment alleviates bicarbonate stress in germinating soybean seeds. • Spermidine upregulates the phenylpropanoid and flavonoid pathways to enhance stress tolerance. • GmPAL1 . 1 -Hap1 and GmCCR1 -Hap3 are linked to adaptation to alkaline stress. Soil alkalization, driven by bicarbonate stress, severely inhibits soybean ( Glycine max L.) seed germination. While spermidine (Spd) is known to enhance plant tolerance to abiotic stress, whether and how it alleviates bicarbonate stress remains unclear. Here, we demonstrate that Spd treatment significantly alleviates bicarbonate stress experienced by in germinating soybeans, as evidenced by higher germination rates and greater root biomass. Physiological assays revealed that Spd diminishes accumulation of reactive oxygen species accumulation and malondialdehyde while promoting proline accumulation. Transcriptome and weighted gene co-expression network analysis (WGCNA) indicated that Spd continuously upregulates genes in the phenylpropanoid and flavonoid biosynthesis pathways in germinating seeds. Two key genes in these pathways, GmPAL1 . 1 ( Phenylalanine Ammonia-Lyase 1 . 1 ) and GmCCR1 ( Cinnamoyl-CoA Reductase 1 ), are associated with seed germination. Furthermore, natural variation in GmPAL1 . 1 and GmCCR1 is associated with adaptation to saline-alkaline soils: the elite haplotypes GmPAL1 . 1 -Hap1 and GmCCR1 -Hap3 are associated with favorable agronomic traits and improved adaptation to these soils. These findings reveal that Spd enhances bicarbonate tolerance by coordinating antioxidant defense mechanisms and activating the phenylpropanoid and flavonoid biosynthesis pathways. In addition, our results identify GmPAL1 . 1 and GmCCR1 as potential elite genes for breeding alkaline-tolerant soybean cultivars.