Shade-induced transcriptional reprogramming and metabolic adaptation in contrasting soybean genotypes

Shade stress affects soybean yield in intercropping, but the molecular basis of cultivar-specific tolerance is unclear. We analyzed shade-tolerant (Guru) and sensitive (Heinong 53) soybeans under 30% and 70% shade using transcriptomic, physiological, and biochemical methods. Moderate shade (30%) initially promoted growth in Heinong 53, while 70% shade restricted growth in both. Guru maintained better physiology, with higher chlorophyll (2.8 vs. 2.1 mg/g), photosynthesis, and stable stomatal conductance. RNA-seq identified 2596-7841 differentially expressed genes (DEGs), with severe shade causing more changes. Down-regulated DEGs are linked to development and shade response; up-regulated DEGs are involved in metabolism, including glucosinolate biosynthesis and protein export. Core shade responses included 279 up- and 388 down-regulated DEGs across treatments. Shade tolerance involved metabolic reprogramming: Guru had higher sucrose content (30.2 vs. 13.8 mg/g) and sucrose synthase activity and increased nitrogen enzyme activity. Antioxidant enzymes showed cultivar-specific strategies, with Guru having higher peroxidase and lower oxidative stress markers. Gene-trait analysis linked 37 DEGs to photosynthesis and 28 to transpiration, indicating water use regulation. Key genes included calcium-dependent kinases and histone deacetylases. Overall, shade tolerance involves maintaining photosynthesis, metabolic shifts favoring carbs, and stress responses, guiding development of tolerant cultivars and understanding plant adaptation in intercropping systems.