Transcriptomic, proteomic, and physiological comparative analyses of foliar selenium application in flax

Abstract Background Flax ( Linum usitatissimum L.) is increasingly valued as a nutrient-rich oilseed crop because of its high content of unsaturated fatty acids and bioactive compounds. Foliar selenium (Se) application offers a promising strategy for crop Se biofortification, but its integrated effects on flax productivity, seed nutritional quality, and molecular regulation remain insufficiently characterized. This study evaluated the agronomic, physiological, biochemical, transcriptomic, and proteomic responses of flax to different foliar sodium selenite (Na 2 SeO 3 ) application rates. Results The 50 g ha −1 Na 2 SeO 3 treatment (T3) produced the highest seed yield in both years, with an 8.74–9.91% increase relative to the water-sprayed control (CK), mainly through higher capsules per plant and seeds per capsule. T3 improved photosynthetic performance by increasing net photosynthetic rate (Pn) and stomatal conductance (Gs) while reducing intercellular CO 2 concentration (Ci) by 24.54%. For seed antioxidant traits, T3 showed the highest superoxide dismutase (SOD) activity and the lowest malondialdehyde (MDA) content. Seed Se content increased with Na 2 SeO 3 application rate and peaked under T5, reaching 21.96-fold that of CK, whereas T3 increased seed Se content by 15.60-fold and increased linoleic and linolenic acid contents by 18.51% and 4.85%, respectively. Transcriptomic analysis of CK and T3 seeds identified 5,203 differentially expressed genes (DEGs), including 2,523 upregulated and 2,680 downregulated genes, with major enrichment in photosynthesis and carbon metabolism, redox-related processes, Se-associated metabolism, and lipid and fatty-acid metabolism. The 4D label-free proteomic analysis identified 76 differentially expressed proteins (DEPs), including 23 upregulated and 53 downregulated proteins, mainly associated with antioxidant and detoxification responses, photosynthesis and energy metabolism, and lipid metabolism. Integrated transcriptomic and proteomic analysis showed limited DEG-DEP overlap, with eight gene-protein pairs significantly altered at both transcript and protein levels. Conclusions Foliar Na 2 SeO 3 application improved flax yield, Se biofortification, seed antioxidant status, and fatty-acid quality in an application rate-dependent manner, with T3 showing the most favorable overall performance. Integrated transcriptomic and proteomic analyses associated this response with changes in carbon metabolism, redox regulation, Se-associated metabolism, lipid metabolism, and seed development. These findings inform the rational optimization of foliar Na 2 SeO 3 application to improve Se biofortification and seed nutritional quality in flax.