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Key message <p><b>Differentially expressed genes involved in tension wood in ‘Shanxin’ poplar have been identified, and gene expression regulatory network has been established, laying the foundation for research on the molecular mechanisms.</b></p> Abstract <p>Tension wood (TW), a specialized wood structure, forms in woody angiosperms under mechanical force or gravity. Studying the transcriptional regulation of genes during TW formation is valuable for molecular biology research and the genetic improvement of wood properties. In this study, TW xylem cell walls in ‘Shanxin’ poplar (<i>Populus davidiana × P. alba var. pyramidalis</i>) exhibited a relatively higher cellulose content and a distinct gelatinous layer (G-layer), as identified by safranin-fast green staining, compared to opposite wood (OW) and normal wood (NW). Transcriptome analysis of TW, OW, and NW yielded 52,697 unigenes. Differential expression analysis identified 2,321, 462, and 2,683 differentially expressed genes(DEGs)in TW_NW, OW_NW, and TW_OW comparisons, respectively. GO enrichment analysis of DEGs highlighted their involvement in secondary processes including cell wall organization, response to stimulus, hormone-mediated signaling pathway, cell wall, transcription regulator activity and oxidoreductase activity. KEGG enrichment analysis revealed significant pathways including phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, plant hormone signal transduction, and starch and sucrose metabolism. Specifically, 13 out of 16 DEGs were noted in the glucose synthesis pathway within the starch and sucrose metabolism. A two-layer gene expression regulatory network (GRN) was constructed, involving 6 transcription factors (TFs) and 37 functional genes, totaling 181 interactions. Validation using ChIP-PCR and RT-qPCR for a total of 35 interactions involving <i>PdaMYB52</i>, <i>PdaERF6</i>, and <i>PdaERF17</i> demonstrated a 91% accuracy rate, with 57% direct interactions and 34% indirect interactions. These results lay the foundation for further exploration of the molecular mechanisms driving TW formation in ‘Shanxin’ poplar.</p>

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Transcriptome analysis and gene expression regulatory network construction of tension wood formation in Populus davidiana×P.alba var.pyramidalis

  • 期刊论文

  • 发表日期：

    2025年12月15日

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  • Xu Li,
  • Jiajia Shao,
  • Chichi Winarsih,
  • Youchao He,
  • Yiping Yang,
  • Meiqi Zhou,
  • Yan Gao,
  • Rina Su,
  • Caiqiu Gao,
  • Chao Wang

摘要

Key message

Differentially expressed genes involved in tension wood in ‘Shanxin’ poplar have been identified, and gene expression regulatory network has been established, laying the foundation for research on the molecular mechanisms.

Abstract

Tension wood (TW), a specialized wood structure, forms in woody angiosperms under mechanical force or gravity. Studying the transcriptional regulation of genes during TW formation is valuable for molecular biology research and the genetic improvement of wood properties. In this study, TW xylem cell walls in ‘Shanxin’ poplar (Populus davidiana × P. alba var. pyramidalis) exhibited a relatively higher cellulose content and a distinct gelatinous layer (G-layer), as identified by safranin-fast green staining, compared to opposite wood (OW) and normal wood (NW). Transcriptome analysis of TW, OW, and NW yielded 52,697 unigenes. Differential expression analysis identified 2,321, 462, and 2,683 differentially expressed genes(DEGs)in TW_NW, OW_NW, and TW_OW comparisons, respectively. GO enrichment analysis of DEGs highlighted their involvement in secondary processes including cell wall organization, response to stimulus, hormone-mediated signaling pathway, cell wall, transcription regulator activity and oxidoreductase activity. KEGG enrichment analysis revealed significant pathways including phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, plant hormone signal transduction, and starch and sucrose metabolism. Specifically, 13 out of 16 DEGs were noted in the glucose synthesis pathway within the starch and sucrose metabolism. A two-layer gene expression regulatory network (GRN) was constructed, involving 6 transcription factors (TFs) and 37 functional genes, totaling 181 interactions. Validation using ChIP-PCR and RT-qPCR for a total of 35 interactions involving PdaMYB52, PdaERF6, and PdaERF17 demonstrated a 91% accuracy rate, with 57% direct interactions and 34% indirect interactions. These results lay the foundation for further exploration of the molecular mechanisms driving TW formation in ‘Shanxin’ poplar.