Regulatory Roles of Seedling Shading and Strip Planting on Soybean Branching and Yield in Relay Intercropping Systems

The coordinated development of stems and branches, together with optimal strip spacing, is crucial for improving soybean yield in the soybean–maize relay strip intercropping system. Shading during the seedling stage often causes excessive stem elongation and reduced branching; however, the physiological mechanisms underlying stem–branch responses to changing light environments remain unclear. This study aimed to clarify how early-stage shading and subsequent light recovery regulate stem and branch development through changes in canopy light environment, phytohormones, and the expression of related genes. Shade-tolerant Nandou12 and shade-sensitive Nannong99-6 were used as experimental soybean cultivars. Six treatments were implemented: a non-shaded control with uniform strip spacing (T0: 40 cm); seedling shading (40% PAR-transmission nets for 35 days after emergence) combined with variable strip spacing (T1: 40 cm; T2: 70 cm; T3: 100 cm; T4: 130 cm; T5: 160 cm). Canopy light environment, main stem and branch traits, photosynthetic characteristics, phytohormones, related gene expression, and yield components were measured. The results indicated that shade at the seedling stage significantly upregulated auxin (IAA) biosynthesis gene GmYUCC and downregulated phytochrome gene GmPhyB in the main stem tips, corresponding to increased IAA and cytokinins (CKs). In branch tips, shading significantly downregulated GmYUCC and GmPhyB while upregulated GmMAX3B, which is consistent with reduced levels of IAA, CKs, and brassinosteroid (BR), and increased strigolactones (SLs). After light recovery, GmPhyB and GmYUCC were upregulated whereas GmMAX3B was downregulated, accompanied by higher IAA, GA, CKs, and BRs, lower SLs, and improved chlorophyll content, Rubisco content, photosynthesis, and the accumulation of soluble sugar and starch in branches. Nandou12 achieved up to 10% higher yield under shading, and a 100 cm strip spacing maintained 74–111% yield of the non-shaded soybean. These findings demonstrate that cultivars with strong shade tolerance and high branching potential, combined with a 100-cm strip spacing, effectively sustain yield in relay-intercropped soybean by enabling favorable physiological responses to early shading and subsequent light recovery.