Genetic and epigenetic mechanisms underlying cadmium (Cd) stress responses in soybean cultivars

Multi-omics analysis reveals that isofl avonoid biosynthesis and gene-specifi c DNA methylation are key mechanisms underlying cadmiumtolerance in soybean. Cadmium (Cd) contamination poses a significant threat to crop productivity and food safety. Yet, the genetic and epigenetic mechanisms of Cd tolerance in soybean remain unclear. This study investigated the physiological, molecular, and epigenetic responses of 25 soybean germplasms grown hydroponically under Cd stress (20 µM). Tolerance coefficients and variability analyses revealed distinct responses among cultivars. Principal component and cluster analyses classified the germplasms into five groups, with ZH35 and ND257 identified as the most tolerant, while MRidge and JXD were the most susceptible cultivars. Tolerant lines maintained better growth and antioxidant defense, whereas susceptible cultivars accumulated higher levels of oxidative damage (hydrogen peroxide-H₂O₂ and malondialdehyde-MDA). Gene expression profiling and weighted gene co-expression network analysis (WGCNA) revealed stress-responsive modules, with the sensitive cultivar upregulating photosynthesis-related pathways under control conditions, while the tolerant cultivar under Cd stress exhibited upregulation of isoflavonoid biosynthesis, consistent with metabolomic patterns. DNA methylation profiling of selected germplasms uncovered differentially methylated promoter regions in genes linked to photosynthesis and isoflavonoid biosynthesis, validated by qPCR and McrBC-PCR. Together, the findings highlight key molecular and epigenetic features associated with Cd tolerance, offering valuable insights and potential targets for breeding stress-resilient soybean cultivars.