Transcriptomic profiling of roots reveals species-specific adaptive strategies in maize and soybean intercropping

Abstract Maize/soybean intercropping is a well-established agroecosystem for sustainable agriculture, yet the species-specific molecular mechanisms underlying their root adaptive strategies remain unclear. Here, we integrated phenotypic measurements and root transcriptomics to characterize the transcriptional reprogramming of maize and soybean roots in response to intercropping. Transcriptomic profiling identified 3,544 differentially expressed genes (DEGs) in soybean roots and 422 DEGs in maize roots. Within the respective DEG sets, soybean exhibited a higher proportion of downregulated genes (56.3%) than maize (46.7%). Intercropped maize roots showed targeted upregulation of nitrogen metabolism and central carbon metabolism pathways, including nitrate transporter ( NRT2.1 ) and nitrate reductase ( NR ) genes, which was accompanied by increased root biomass. In contrast, intercropped soybean roots displayed extensive transcriptional suppression, encompassing near-complete downregulation of phenylpropanoid, flavonoid, and isoflavonoid biosynthesis–related genes (99 of 107 DEGs downregulated; all 18 CHS , CHR , and IFS genes repressed). These transcriptional changes were paralleled by a distinct nodulation phenotype: nodule number and dry weight did not differ significantly between treatments, whereas leghemoglobin content per nodule increased by 21% ( P < 0.01). The upregulation of ENOD93 and ENOD75 (encoding early nodulin 93 and 75, respectively) and CPX (encoding coproporphyrinogen oxidase) coincided with elevated leghemoglobin content, a pattern consistent with enhanced individual nodule function. These findings suggest a hypothetical model in which species-specific transcriptional reprogramming is associated with altered phenotypic traits, offering insights into the belowground competitive and symbiotic interactions in cereal–legume intercropping.