Proteomic Determinants of Fluctuating Light Sensitivity in Soybean: Comparative Analysis of Tolerant and Sensitive Cultivars

Fluctuating light (FL), caused by cloud movement, canopy dynamics, and intercropping, is a pervasive stress affecting crop productivity, yet the molecular basis of FL responses in different photosensitivity soybeans remains poorly understood. Here, we integrated physiological, transcriptomic, and proteomic analyses to compare the responses to FL between two contrasting soybean cultivars: ND12 (tolerant) and GX7 (sensitive). FL treatment increased plant height but reduced leaf area, leaf thickness, and net photosynthetic rate ( P n ) in soybean plants, also instigating structural changes in chloroplasts. Compared to ND12, GX7 was more severely affected under FL, exhibiting significant reductions in aboveground biomass, leaf area, stem diameter, and photosynthetic pigment content. Simultaneously, under fluctuating light conditions, ND12 maintained relatively stable performance in photosystem II (PSII). In contrast, the photochemical efficiency of PSII in GX7 was directly inhibited, along with obstruction in its downstream electron transport chain. Transcriptomic analysis revealed 1707 and 1836 differentially expressed genes (DEGs) in ND12 and GX7, respectively, while proteomic profiling identified 54 and 38 differentially expressed proteins (DEPs). Notably, GX7 showed significant downregulation of proteins involved in PSI, PSII, light‐harvesting complex II (LHCII), and the electron transport chain, with KEGG pathway analysis confirming suppression of “Photosynthesis—antenna proteins” and “Photosynthesis” pathways. In contrast, ND12 maintained stable expression of these photosynthetic components. These findings demonstrate that cultivar‐specific proteomic remodeling of the photosynthetic apparatus determines FL tolerance in soybean, providing molecular targets for breeding cultivars adapted to high‐density and intercropping systems.