Iron Chlorin e6 Improves Soybean Yield by Maintaining Chlorophyll Stability and Promoting Carbohydrate Accumulation Under Saline–Alkali Stress

Saline–alkali stress is a widespread abiotic stress that severely impairs crop growth and yield formation. Iron Chlorin e6 (ICe6), a novel plant growth regulator, is essentially a chlorophyll derivative, and possesses potential application value in regulating plant chlorophyll metabolism and improving plant stress resistance. In this study, the saline–alkali-sensitive soybean cultivar Henong 95 and saline–alkali-tolerant soybean cultivar Hefeng 50 were used as experimental materials, and foliar spraying with 120 nmol/L ICe6 was conducted at the R1 stage. The results indicated that relative to CK, SA treatment markedly inhibited soybean growth, accompanied by reduced antioxidant capacity, excessive reactive oxygen species (ROS) accumulation and significantly lowered photosynthetic pigment content. Carbohydrate accumulation was substantially suppressed, which ultimately resulted in yield reduction (HN95: −12.31%; HF50: −11.08%). ICe6 treatment mitigated saline–alkali-induced growth inhibition in soybean plants, as reflected by markedly restored antioxidant indices, sharply decreased malondialdehyde (MDA), H2O2, and O2− levels, and notably increased leaf area (HN95: +49.72%; HF50: +19.82%) and chlorophyll content (HN95: +36.06%; HF50: +90.75%). Combined transcriptomic and metabolomic profiling showed that, relative to the SA control, ICe6 treatment led to the identification of 2896 DEGs in HN95 and 3530 DEGs in HF50, with significant enrichment in photosynthesis- and chlorophyll metabolism-related pathways, e.g., GO:0009765 (photosynthesis, light harvesting). Differential metabolites were chiefly enriched in isoflavonoid biosynthesis—a source of antioxidants—and amino acid biosynthesis, which governs chlorophyll precursor synthesis. These findings suggest that ICe6 may enhance chlorophyll content by modulating the expression of genes involved in chlorophyll metabolism, contributing to light capture and chlorophyll biosynthesis, facilitating carbohydrate accumulation and ultimately contributing to increased yield under saline–alkali stress (HN95: +5.74%; HF50: +5.83%).