Selenium-induced metabolic reprogramming in soybean activates nucleotide transport pathways and suppresses primary carbon metabolism

Selenium biofortification in soybean is one approach to addressing widespread selenium deficiency in human populations, yet the temporal dynamics of gene expression and antioxidant responses following selenium enrichment remain poorly characterized. Here, we examined the physiological and transcriptional responses of the HK88 soybean variety to selenium-enriched nutrient solution treatment, with seedlings sampled at 1, 24, and 48 h post-treatment. Total tissue selenium rose from 0.01 mg/kg at 1 h to 0.33 mg/kg at 48 h, with parallel increases in both inorganic and organic fractions, consistent with active biotransformation, though this interpretation remains to be confirmed experimentally. Antioxidant responses followed a distinct temporal pattern: superoxide dismutase (SOD) and peroxidase (POD) activities were initially lower in treated plants at 1 h relative to controls but were elevated at 24 and 48 h, while catalase (CAT) activity remained comparatively low across all time points. Malondialdehyde (MDA) levels were lower in selenium-treated plants at 1 h, suggesting early membrane stabilization, though this difference was no longer apparent by 48 h. RNA sequencing of 18 libraries identified 6,793 differentially expressed genes (DEGs) at 1 h, peaking at 13,196 (approximately 18% of the 72,513 annotated genes) at 24 h, then declining to 8,996 at 48 h. A Venn diagram analysis identified 565 DEGs shared across all three time points, comprising 196 consistently up-regulated and 369 consistently down-regulated genes. Up-regulated genes were enriched for nucleotide transmembrane transport functions, including ATP, ADP, and purine transport, with associated ABC transporter activity. Down-regulated genes were predominantly associated with primary carbon metabolism, including monosaccharide biosynthesis, gluconeogenesis, and the Calvin cycle. Gene Set Variation Analysis (GSVA) indicated positive enrichment scores for nucleotide transport pathways at 24 and 48 h in treated plants, contrasting with negative scores in controls. Mantel tests revealed significant associations between gene set activity profiles and measured physiological traits, particularly for gene sets related to molecular function and selenium accumulation. These findings suggest that selenium biofortification in HK88 is associated with a coordinated metabolic shift, in which primary carbon fixation is reduced while nucleotide transport capacity is enhanced, supporting antioxidant defense during selenium assimilation.