Decoding nitrogen uptake efficiency in maize and sorghum: insights from comparative gene regulatory networks

Braynen, Janeen, Zhang, Lifang, Kumari, Sunita, Olson, Andrew, Kumar, Vivek, Regulski, Michael, Liseron-Monfils, Christophe, Gaudinier, Allison, Bågman, Anne-Maarit, Abbitt, Shane, Frank, Mary J, Shen, Bo, Kochian, Leon, Brady, Siobhan M, Ware, Doreen (December 2025) Decoding nitrogen uptake efficiency in maize and sorghum: insights from comparative gene regulatory networks. The Plant Journal, 124 (6). e70631. ISSN 0960-7412

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Abstract

Nitrogen (N) is an essential macronutrient for plant growth and yield, yet optimizing nitrogen use efficiency remains a challenge in agriculture. To better understand the regulatory basis of plant responses to N availability, we constructed a maize-specific nitrogen uptake efficiency gene regulatory network (mNUEGRN) comprising 1625 protein-DNA interactions (PDI) between 70 promoters and 301 transcription factors using enhanced yeast one-hybrid assays. We also projected a sorghum NUE GRN (spNUEGRN) based on maize orthologs and analyzed N-responsive subnetworks in both species using transcriptome profiling under N stress of early deprivation and recovery. Cross-species comparison with an existing Arabidopsis GRN revealed about 18% conserved interaction, corresponding to 11% of the mNUEGRN, particularly within the nitrate assimilation pathways. Notably, bZIP18 and bZIP30 emerged as central regulators in mNUEGRN, forming highly connected feed-forward loops (FFLs). From our time series data, we identified 19 236 and 23 864 differentially expressed genes in maize and sorghum, respectively. Gini correlation analysis uncovered 764 and 638 FFLs in mNUEGRN and spNUEGRN, respectively, of which 22 FFLs in maize and 35 in sorghum were identified in both leaf and root for each species. These FFLs may represent candidate regulatory motifs that contribute to modulating transcriptional responses under fluctuating N conditions, but their potential roles require further investigation. Together, our findings reveal evolutionarily conserved and species-specific regulatory strategies that mediate early N responsiveness, offering a foundation for engineering crops with improved NUE.

Item Type: Paper
Subjects: organism description > plant
organism description > plant > sorghum
CSHL Authors:
Communities: CSHL labs > Ware lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: December 2025
Date Deposited: 22 Dec 2025 13:11
Last Modified: 22 Dec 2025 13:11
PMCID: PMC12714369
Related URLs:
URI: https://repository.cshl.edu/id/eprint/42046

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