Differential gene expression analysis in tissues during tobacco hairy root induction

Document Type

Article

Publication Date

4-30-2026

Abstract

[Background] Infection of plants by Agrobacterium rhizogenes can induce hairy root formation; however, the dynamic and systematic gene regulatory network underlying this process remains unclear. This study aims to elucidate the molecular mechanisms underlying hairy root formation. [Methods] This study aims to elucidate the temporal changes in gene expression during the infection of tobacco explants by Agrobacterium rhizogenes using RNA-seq combined with weighted gene co-expression network analysis (WGCNA) and transcription factor analysis. [Results] With prolonged infection time, the number of differentially expressed genes (DEGs) gradually increased. These DEGs were significantly enriched in processes such as oxidoreductase activity and metabolic reprogramming, and a total of 2,497 DEGs were shared among all comparison groups. WGCNA identified one module significantly positively correlated and one module significantly negatively correlated with Agrobacterium rhizogenes infection, each containing two hub genes. Auxin response factors (ARFs) were the most significantly enriched transcription factor family and showed strong evolutionary conservation. Integrated analysis identified a regulatory network for hairy root formation centered on a lateral organ boundary domain protein gene, including TCP family transcription factors, ethylene response transcription factors, and key ARF genes. [Conclusion] This study provides a theoretical basis and identifies key gene targets for both fundamental research in hairy root biology and its biotechnological applications.

Publication Title

Acta Tabacaria Sinica

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