Multi-omics and anatomical insights into soybean stomatal adaptation and regulation under fluctuating light

Field crops are frequently exposed to fluctuating light (FL), which limits photosynthetic carbon assimilation and crop productivity. Mechanisms of soybean adaptation to FL remain largely unclear. This study investigated two soybean cultivars (ND12 and GX7) with contrasting responses to FL using integrated phenotypic, physiological, anatomical, transcriptomic and proteomic analyses. Under FL conditions, both cultivars showed consistent phenotypic and physiological changes: reduced specific leaf weight and leaf thickness, retarded vein development, a significant positive correlation between dynamic FL intensity and net photosynthetic rate, and asynchronous responses between stomatal movement and photosynthetic induction. Notably, ND12 enhanced CO 2 diffusion by optimizing mesophyll structure and exhibited demand-driven stomatal regulation tightly coordinated with photosynthetic activity. In contrast, GX7 showed greater structural sensitivity and adopted a preparatory stomatal opening pattern, maintaining partial aperture under low light to mitigate transient CO 2 limitation during light transitions. At the molecular level, both cultivars shared a conserved regulatory framework centered on the jasmonic acid (JA) signaling pathway and α-linolenic acid metabolism. Differential expression of JA biosynthetic and blue light-responsive genes contributed to cultivar divergence, with ND12 maintaining relatively stable JA-related gene expression, whereas GX7 displayed sustained downregulation and additional blue light-responsive differentially expressed genes. These findings clarify the coordinated physiological and molecular basis of soybean adaptation to FL and provide potential targets for breeding cultivars tolerant to FL environments.