Population-scale evidence for the association of stem diameter with soybean yield in the maize–soybean intercropping system

Intercropping maize ( Zea mays ) and soybean ( Glycine max ) is an appealing strategy for improving land-use efficiency. However, the shade stress imposed by maize severely constrains soybean growth and yield. Most intercropping studies conducted to date have been based on artificial shading or relay intercropping, and neither the characteristics of the shade environment under simultaneous intercropping conditions nor the changes in soybean architectural traits have been systematically studied. Here, we evaluated 907 soybean accessions grown in a simultaneous maize–soybean intercropping system over two consecutive years to identify phenotypic traits associated with yield performance. Intercropping with maize produced a dynamic and heterogeneous shade environment within the soybean canopy, characterized by reductions in the red-to-far red light (R:FR) ratio, blue light fluence, and total photosynthetically active radiation. Shading began after the soybean stage V3 and persisted throughout reproductive development, triggering the shade avoidance response and resulting in substantial yield losses in soybean. Stem diameter showed the strongest positive correlation with yield per plant under intercropping conditions, outperforming the other architectural traits tested. In addition, general shade tolerance was positively associated with intercropping yield but negatively associated with monocropping yield. We compared a shade-tolerant soybean genotype (BX11) with a shade-sensitive genotype (72021). BX11 maintained upright growth under intercropping conditions and exhibited larger stem diameter with a well-developed vascular system while maintaining high expression levels of genes involved in radial growth and vascular development. By contrast, 72,021 showed excessively elongated thin stems and lodging under intercropping conditions, exhibiting extensive intercropping-induced transcriptional reprogramming consistent with the repression of secondary cell wall biosynthesis and the induction of auxin-responsive cell elongation pathways. We conclude that shade tolerance in simultaneous intercropping systems depends on the ability to sustain radial stem development and mechanical strength, providing important insights to guide the breeding of soybean varieties optimized for intercropping