Root genes reveal maize and soybean play different intercropping strategies

When maize and soybean grow side by side in the same field, each crop quietly rewrites the genetic script of its own roots, and the two species do so in strikingly different ways. A new study published in BMC Plant Biology used transcriptomic profiling to compare the root gene activity of intercropped maize and soybean against plants grown alone, and the results reveal two fundamentally different adaptive strategies operating beneath the soil surface. Maize, the cereal, responded with a focused genetic push toward nitrogen and carbon metabolism, while soybean, the legume, responded with a broad transcriptional retreat that paradoxically appears to strengthen the function of its nitrogen-fixing nodules.

The research team, led by Xinru Liu and corresponding author Caixia Sun of Northeastern University in Shenyang, together with colleagues from the Liaoning Academy of Agricultural Sciences, integrated phenotypic measurements with root transcriptomics to characterize how the two crops respond to intercropping at the molecular level. Maize and soybean intercropping is a well-established agroecosystem in sustainable agriculture, widely practiced because the cereal and legume complement each other in nutrient use, pest suppression, and yield stability. Yet the species-specific molecular mechanisms underlying their root adaptive strategies have remained unclear until now.

The scale of the transcriptional response differed dramatically between the two species. The researchers identified 3,544 differentially expressed genes, or DEGs, in soybean roots but only 422 DEGs in maize roots, meaning the legume reprogrammed nearly eight and a half times more genes than the cereal. Within the respective DEG sets, soybean also exhibited a higher proportion of downregulated genes, at 56.3 percent, than maize, at 46.7 percent. This asymmetry suggests that soybean roots undergo far more extensive transcriptional suppression in response to the presence of maize, while maize roots mount a comparatively restrained but highly targeted response.

Intercropped maize roots showed targeted upregulation of nitrogen metabolism and central carbon metabolism pathways. Among the genes switched on were nitrate transporter NRT2.1 and nitrate reductase, or NR, genes, which encode proteins that import nitrate into root cells and catalyze its reduction, the first committed step of the nitrate assimilation pathway. This genetic activation was accompanied by increased root biomass, indicating that maize invests in expanding its belowground foraging capacity when sharing a field with soybean. In effect, the cereal appears to accelerate its nitrogen uptake machinery and root growth to capitalize on the competitive environment.

In contrast, intercropped soybean roots displayed extensive transcriptional suppression, and the pattern was remarkably systematic. Phenylpropanoid, flavonoid, and isoflavonoid biosynthesis-related genes were nearly completely downregulated, with 99 of 107 DEGs in these categories repressed. All 18 genes encoding chalcone synthase, chalcone reductase, and isoflavone synthase, abbreviated CHS, CHR, and IFS, were repressed. These enzymes sit at the heart of the soybean specialized metabolism, producing flavonoid and isoflavonoid compounds that serve as defense molecules and as signals that recruit rhizobial bacteria for nodulation. The near-complete shutdown of this pathway in intercropped soybean roots is therefore one of the most striking molecular signatures in the dataset.

These transcriptional changes were paralleled by a distinct nodulation phenotype that challenges simple expectations. Nodule number and nodule dry weight did not differ significantly between intercropped and monocropped soybean, meaning the legume did not produce more or heavier nodules when sharing a field with maize. However, leghemoglobin content per nodule increased by 21 percent, a statistically significant change with a P value below 0.01. Leghemoglobin is the oxygen-binding pigment inside functional nodules, analogous to hemoglobin in animal blood, and it buffers free oxygen to protect the oxygen-sensitive nitrogenase enzyme that fixes atmospheric nitrogen into ammonia. More leghemoglobin per nodule therefore implies that individual nodules operate more efficiently.

The molecular evidence supports this interpretation. The researchers observed upregulation of ENOD93 and ENOD75, which encode early nodulin 93 and 75 respectively, and of CPX, which encodes coproporphyrinogen oxidase, an enzyme in the heme biosynthesis pathway. Early nodulins are proteins expressed during the early stages of nodule development, and coproporphyrinogen oxidase supplies the heme precursor required to build leghemoglobin itself. The coordinated upregulation of these genes coincided with the elevated leghemoglobin content, a pattern consistent with enhanced individual nodule function. In other words, soybean appears to shift from producing more nodules to making each existing nodule work harder.

The authors propose a hypothetical model in which species-specific transcriptional reprogramming is associated with altered phenotypic traits. Maize responds to intercropping by amplifying nitrogen and carbon metabolism and growing more root biomass, a strategy of competitive intensification. Soybean responds by suppressing a broad swath of its specialized metabolism while investing in the quality of its symbiotic machinery, a strategy of competitive accommodation through symbiotic optimization. These findings offer insights into the belowground competitive and symbiotic interactions that underpin cereal-legume intercropping, one of the most successful examples of sustainable intensification in global agriculture.

The study was funded by the National Key R&D Program of China under grant 2023YFD1501200 and by the National Natural Science Foundation of China under grant 32072667. The research was received on 17 June 2026, accepted on 9 September 2026, and published on 16 September 2026 in BMC Plant Biology under an open access Creative Commons Attribution 4.0 International License. The authors declare no competing interests. The work is citable under the permanent DOI 10.1186/s12870-026-09947-z.

For farmers and breeders, the molecular detail matters because it identifies the genetic levers that determine how each crop performs in a mixed stand. Understanding that maize ramps up nitrate transport and root growth while soybean restructures its specialized metabolism and nodule biochemistry provides breeders with candidate genes to select for improved intercropping performance. As global agriculture seeks to reduce fertilizer inputs while maintaining yields, the belowground genetic dialogue between cereals and legumes may prove to be one of the most important conversations in modern crop science.

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

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

Article References: Liu, X., Liu, B., Xu, X., Ma, Y., Xiang, W., Feng, C., & Sun, C. (2026). Transcriptomic profiling of roots reveals species-specific adaptive strategies in maize and soybean intercropping. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09947-z

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09947-z

Keywords: maize, soybean, intercropping, root transcriptomics, nitrogen fixation, sustainable agriculture, Transcriptomic, profiling, roots, reveals, species-specific, adaptive