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Background <p><i>Lycium ruthenicum</i> is an economically important shrub known for its resistance to drought and saline-alkali conditions. This study identified a particular <i>L. ruthenicum</i> clone whose leaf explants can undergo direct organogenesis on plant growth regulator (PGR)-free media, and both rooting and shooting abilities of the leaf-tip explants were significantly greater than those of the leaf-middle explants. However, the underlying mechanisms remain unclear.</p> Results <p>RNA-Seq analysis revealed that the differentially expressed genes (DEGs) associated with rooting and shooting in both leaf-tip and leaf-middle explants were enriched in the <i>Plant hormone signal transduction</i> KEGG pathway. For the first time, we identified 16 and nine differentially accumulated metabolites (DAMs) linked to direct root and shoot organogenesis from leaf explants, respectively. The stronger direct rooting ability observed in leaf-tip explants was associated with (i) up-regulation of sucrose synthase (SUS), scarecrow-like 21 (SCL21), transport inhibitor response 1 (TIR1), and auxin response factor (ARF) genes; (ii) up-regulation of IAA, IAA-Leu-Me, and BAP; (iii) down-regulation of eight DAMs. Moreover, the enhanced direct shooting ability in leaf-tip explants was correlated with (i) 13 DAMs including upregulated JA and JA-ILE, (ii) up-regulated <i>SUS</i> and (iii) down-regulated jasmonate ZIM domain 2 (JAZ2) gene. Notably, <i>JAZ2</i> and these 13 DAMs represent newly discovered factors associated with the stronger shooting ability of leaf explants. Additionally, this study conducted correlation analyses between DAMs and DEGs related to rooting and shooting in leaf explants, as well as the enhanced rooting and shooting capacities of leaf-tip explants.</p> Conclusions <p>This study identifies the key DEGs and DAMs correlated with the direct organogenesis of <i>L. ruthenicum</i> leaf explants. Building upon these findings, a mechanistic model for the stronger direct organogenesis observed in leaf-tip explants was established. These findings offer valuable theoretical guidance for optimizing direct organogenesis systems in plant leaves.</p>

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The mechanism of PGR-free direct organogenesis in Lycium ruthenicum leaf explants revealed by RNA-Seq and phytohormone metabolome co-analysis

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月2日

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  • Lujia Li,
  • Yucheng Wang,
  • Wenhui Liu,
  • Yue Gao,
  • Jiawen Wang,
  • Huifang Lu,
  • Weiman Xu,
  • Qin-Mei Wang

摘要

Background

Lycium ruthenicum is an economically important shrub known for its resistance to drought and saline-alkali conditions. This study identified a particular L. ruthenicum clone whose leaf explants can undergo direct organogenesis on plant growth regulator (PGR)-free media, and both rooting and shooting abilities of the leaf-tip explants were significantly greater than those of the leaf-middle explants. However, the underlying mechanisms remain unclear.

Results

RNA-Seq analysis revealed that the differentially expressed genes (DEGs) associated with rooting and shooting in both leaf-tip and leaf-middle explants were enriched in the Plant hormone signal transduction KEGG pathway. For the first time, we identified 16 and nine differentially accumulated metabolites (DAMs) linked to direct root and shoot organogenesis from leaf explants, respectively. The stronger direct rooting ability observed in leaf-tip explants was associated with (i) up-regulation of sucrose synthase (SUS), scarecrow-like 21 (SCL21), transport inhibitor response 1 (TIR1), and auxin response factor (ARF) genes; (ii) up-regulation of IAA, IAA-Leu-Me, and BAP; (iii) down-regulation of eight DAMs. Moreover, the enhanced direct shooting ability in leaf-tip explants was correlated with (i) 13 DAMs including upregulated JA and JA-ILE, (ii) up-regulated SUS and (iii) down-regulated jasmonate ZIM domain 2 (JAZ2) gene. Notably, JAZ2 and these 13 DAMs represent newly discovered factors associated with the stronger shooting ability of leaf explants. Additionally, this study conducted correlation analyses between DAMs and DEGs related to rooting and shooting in leaf explants, as well as the enhanced rooting and shooting capacities of leaf-tip explants.

Conclusions

This study identifies the key DEGs and DAMs correlated with the direct organogenesis of L. ruthenicum leaf explants. Building upon these findings, a mechanistic model for the stronger direct organogenesis observed in leaf-tip explants was established. These findings offer valuable theoretical guidance for optimizing direct organogenesis systems in plant leaves.