Effects of shading on leaf structure, physiological characteristics, and transcriptome of different shade-tolerant varieties of soybeans

To investigate the response differences of soybean varieties with varying shade tolerance to shading environments, the study used the strong shade-tolerant variety ‘Changdou 33’ (cd33) and the weak shade-tolerant variety ‘Changdou 31’ (cd31) as materials. Agronomic traits, leaf tissue structure, mesophyll ultrastructure, physiological and biochemical indicators, endogenous hormone content, and transcriptomics of different varieties of soybean under natural light and shading conditions were analyzed. Under shading stress, both cd31 and cd33 exhibited increased plant height, reduced stem diameter, and decreased aboveground dry matter accumulation; and the changes in cd33 were less pronounced than those in cd31. Soybean improved light utilization efficiency by reducing leaf thickness and palisade tissue thickness, while increasing mesophyll cell area, perimeter, and chloroplast area. Cd33 plants exhibited a more intact cellular structure, which mitigated the effects of shading on photosynthesis. Physiological and biochemical results indicated that under shade conditions, superoxide dismutase and peroxidase activities increased; catalase activity significantly decreased; soluble sugar and proline contents increased; soluble protein content decreased; malondialdehyde content declined; and auxin, gibberellin, and abscisic acid levels decreased. This suggests that soybeans adapt to the environment by regulating their antioxidant systems, osmotic adjustment substances, and endogenous hormones. Additionally, the abscisic acid and gibberellin contents in cd33 leaves were lower than those in cd31 leaves, which may inhibit plant height and contribute to stronger lodging resistance. Transcriptomic analysis further revealed that the strong shade-tolerant variety had significantly more differentially expressed genes (5 783) under shade conditions than the weak shade-tolerant variety (2 319). These differentially expressed genes were mainly enriched in pathways such as the hydrogen peroxide response, protein kinase activity, plant hormone signal transduction, and phenylpropanoid biosynthesis. In conclusion, the strong shade-tolerant variety of soybean demonstrated greater shade tolerance by activating gene expression and metabolic pathways and maintaining cellular stability and light energy utilization efficiency.