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<p>Seed germination is a complex developmental transition regulated by hormonal and metabolic pathways. To better understand the underlying molecular mechanisms in pecan, we conducted integrated transcriptomic and metabolomic analyses comparing germinated and non-germinated seeds. The results revealed substantial transcriptional changes and distinct metabolic reprogramming associated with hormone signaling, sugar mobilization, and reserve degradation. Key genes involved in ABA biosynthesis (<i>ZEP</i>, <i>NCED</i>, <i>AAO</i>) showed decreased expression, while those associated with catabolism (<i>CYP707A</i>) and signal transduction (<i>PYL</i>, <i>PP2C</i>, <i>SnRK2</i>) were differentially expressed, suggesting active modulation of ABA levels and responses during germination. Transcription factors from the MYB, bHLH, and ERF families were identified as potential upstream regulators of these pathways. Correlation analysis between DEGs and DEMs further highlighted metabolites such as L-glutamine, benzoic acid, and ferulic acid as potential hubs in germination-related metabolic networks. These findings indicate that pecan seed germination is tightly coordinated by transcriptional regulation and metabolic shifts, particularly involving ABA dynamics. Notably, our study reveals regulation of ABA conjugation and transcription factor associations in pecan, highlighting unique features of hormonal control in this woody species. This study provides new insights into the regulatory networks driving seed germination in woody species and offers a molecular basis for improving propagation efficiency in pecan.</p>

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Metabolome and transcriptome analyses unravel the potential mechanism of seed germination in pecan (Carya illinoinensis)

  • 期刊论文

  • 发表日期：

    2025年10月27日

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  • Guoming Wang,
  • Jiyu Zhang,
  • Zhanhui Jia,
  • Tao Wang,
  • Zhenghai Mo,
  • Min Zhai,
  • Wu Wang,
  • Jiping Xuan

摘要

Seed germination is a complex developmental transition regulated by hormonal and metabolic pathways. To better understand the underlying molecular mechanisms in pecan, we conducted integrated transcriptomic and metabolomic analyses comparing germinated and non-germinated seeds. The results revealed substantial transcriptional changes and distinct metabolic reprogramming associated with hormone signaling, sugar mobilization, and reserve degradation. Key genes involved in ABA biosynthesis (ZEP, NCED, AAO) showed decreased expression, while those associated with catabolism (CYP707A) and signal transduction (PYL, PP2C, SnRK2) were differentially expressed, suggesting active modulation of ABA levels and responses during germination. Transcription factors from the MYB, bHLH, and ERF families were identified as potential upstream regulators of these pathways. Correlation analysis between DEGs and DEMs further highlighted metabolites such as L-glutamine, benzoic acid, and ferulic acid as potential hubs in germination-related metabolic networks. These findings indicate that pecan seed germination is tightly coordinated by transcriptional regulation and metabolic shifts, particularly involving ABA dynamics. Notably, our study reveals regulation of ABA conjugation and transcription factor associations in pecan, highlighting unique features of hormonal control in this woody species. This study provides new insights into the regulatory networks driving seed germination in woody species and offers a molecular basis for improving propagation efficiency in pecan.