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WGCNA analysis and identification of key genes in tobacco in response to different nitrogen levels

Xinwang Zhang, Shouhui Pan, Dong Chen, Yuqi Pan, Deepak Bhanot, Tianju Xu, Sachin Gupta, Jinling Zhang, Yin Huang

BMC Plant Biology, Vol 25, Iss 1, Pp 1-14 (2025)

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Bibliographic Details
Title WGCNA analysis and identification of key genes in tobacco in response to different nitrogen levels
Authors Xinwang Zhang, Shouhui Pan, Dong Chen, Yuqi Pan, Deepak Bhanot, Tianju Xu, Sachin Gupta, Jinling Zhang, Yin Huang
Publication Year
2025
Source
BMC Plant Biology, Vol 25, Iss 1, Pp 1-14 (2025)
Description
Abstract Background Nitrogen (N) supply directly impacts growth and quality in flue-cured tobacco. To decipher molecular responses to N gradients, we integrated transcriptomics and weighted gene co-expression network analysis (WGCNA) on leaves from four N treatments: 0 (inherent soil fertility), 60 (low), 105 (standard), and 150 kg/hm2 (high). Results Phenotypic analysis revealed dose-dependent increases in leaf nitrogen content with higher N application, accompanied by excessive vegetative growth and delayed maturity at 150 kg/hm2. Transcriptome sequencing identified 47,216 genes, with differentially expressed genes (DEGs) increasing linearly with N levels (1,458–2,147 DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment highlighted nitrogen metabolism pathways, yielding 14 DEGs (11 in assimilation, 3 in transport). Weighted gene co-expression network analysis (WGCNA) uncovered two modules (lightcyan1 and black) strongly associated with N responses, harboring transcription factors NtERF11 (AP2/ERF), NtWRKY3 (WRKY), and NtSRM1 (MYB). Sub-network analysis within these modules identified five hub genes: NtGLN1-1, two uncharacterized genes, NtDFC, and NtGDSL. NtGDSL may enhance nitrogen use efficiency (NUE) through stress-responsive mechanisms, while NtDFC could integrate N signaling with developmental processes. These findings provide novel insights into N regulatory networks in flue-cured tobacco. Conclusions This study reveals the effects of nitrogen application rates on flue-cured tobacco growth and gene expression. By identifying key transcription factors and genes regulating nitrogen metabolism, it provides a theoretical basis for dissecting nitrogen regulatory mechanisms, optimizing fertilization strategies, and improving nitrogen use efficiency in tobacco production.
Document Type
article
Language
English
Publisher Information
BMC, 2025.
Subject Terms
Tobacco(Nicotiana tabacum L.), Nitrogen Application, WGCNA, Botany, QK1-989
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