ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Bioinformatics
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1604186
This article is part of the Research TopicEvolutionary Adaptations of Plant Genes: A Comprehensive Study of Phylogenomics, Epigenetic Changes, and Protein DynamicsView all 4 articles
Transcriptomic Exploration Yields Novel Perspectives on the Regulatory Network Underlying Trichome Initiation in Gossypium arboreum Hypocotyl
Provisionally accepted
- Zhejiang Agriculture and Forestry University, Hangzhou, China
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Trichomes play a crucial role in plant stress tolerance and serve as an excellent model for studying epidermal cell differentiation. To elucidate the molecular mechanisms underlying trichome development in cotton stems, we investigated two Gossypium arboreum mutants that exhibit abnormal trichome patterns during hypocotyl growth. Based on morphological characteristics, we classified four developmental stages: preinitiation, initiation, elongation, and maturation. Comparative transcriptome profiling of epidermal cells across these stages identified differentially expressed genes (DEGs) through maSigPro analysis, which revealed that these DEGs were primarily associated with pathways involved in cell wall metabolism. Additionally, integrated weighted gene co-expression network analysis (WGCNA) and Cytoscape analyses identified 20 core regulatory genes from a total of 59 candidates linked to epidermal development. Utilizing three machine learning algorithms (SVM-RFE, Boruta, and LASSO), we consistently prioritized five key regulators: Ga02G1392 (TBR), Ga03G0474 (OMR1), Ga12G2860 (ACO1), Ga11G2117 (BBX19), and Ga12G2864 (CUE). RT-qPCR validation confirmed their stage-specific expression patterns, which were consistent with the RNA-Seq data. Our study establishes a comprehensive framework for research on cotton trichomes and identifies critical genetic components governing epidermal hair development, thereby providing new insights for the molecular breeding of stress-resistant cotton varieties.
Keywords: Gossypium arboreum, trichome initiation development, transcriptome analysis, WGCNA, machine learning
Received: 01 Apr 2025; Accepted: 30 May 2025.
Copyright: © 2025 Rong, Xie, 杨, Zhao, Ding, Cao and Hu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Junkang Rong, Zhejiang Agriculture and Forestry University, Hangzhou, China
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