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<p>Epigenetic modifications play crucial roles in regulating plant somatic embryogenesis (SE). However, the regulatory mechanisms of DNA methylation during SE process in <i>Hevea brasiliensis</i> remain unclear. This study investigated two <i>H. brasiliensis</i> genotypes with significantly different somatic embryogenic capacities: “Yunyan 73477” (Y, high-embryogenic) and “Reken 628” (R, low-embryogenic). Using Liquid Chromatography-Mass Spectrometry (LC-MS/MS), we quantitatively analyzed DNA modification levels at different developmental stages of SE and explored the relationship between DNA methylation and gene expression regulation through transcriptome sequencing data. The results showed that: (1) Among the four DNA modifications examined, 5-methyl- 2′-deoxycytidine (5-mdC) was the predominant form, while 5-hydroxymethyl- 2′-deoxycytidine (5-hmdC) and 5-formyl- 2′-deoxycytidine (5-fdC) were not detected, and N6-methyl- 2′-deoxyadenosine (6-mdA) was only detected at trace levels in the explant stage; (2) The genotype Y exhibited a dynamic pattern of 5-mdC levels during SE process, characterized by an initial decrease followed by an increase: 5-mdC content significantly decreased during callus induction (from 45.64 to 42.79%), then increased and maintained at a higher level (approximately 50%) during the differentiation phase. In contrast, the genotype R showed a continuous increase in DNA methylation levels; (3) Correlation analysis identified genes significantly associated with DNA methylation, predominantly showing negative correlations. Genotype-specific analysis revealed striking differences: only three genes with moderate correlation in genotype Y versus 147 genes with strong correlation in genotype R, suggesting distinct epigenetic regulatory mechanisms. Several key genes involved in embryonic development and hormone signaling pathways showed significant expression differences between genotypes. This study provides new insights into DNA methylation dynamics during SE in <i>H. brasiliensis</i> and identifies potential molecular markers for embryogenic capacity, offering theoretical basis for optimizing tissue culture systems for this economically important species.</p>

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Dynamic changes in DNA methylation and correlated expressing genes during somatic embryogenesis in Hevea brasiliensis

  • 期刊论文

  • 发表日期：

    2025年6月19日

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  • Ling Li,
  • Jia Miao,
  • Jin Liu,
  • Ming-Chun Gui,
  • Min Tang,
  • Hai Tian,
  • Wan-Yuan Shi,
  • Guo-Ping Liang,
  • Xiao-Long Sun

摘要

Epigenetic modifications play crucial roles in regulating plant somatic embryogenesis (SE). However, the regulatory mechanisms of DNA methylation during SE process in Hevea brasiliensis remain unclear. This study investigated two H. brasiliensis genotypes with significantly different somatic embryogenic capacities: “Yunyan 73477” (Y, high-embryogenic) and “Reken 628” (R, low-embryogenic). Using Liquid Chromatography-Mass Spectrometry (LC-MS/MS), we quantitatively analyzed DNA modification levels at different developmental stages of SE and explored the relationship between DNA methylation and gene expression regulation through transcriptome sequencing data. The results showed that: (1) Among the four DNA modifications examined, 5-methyl- 2′-deoxycytidine (5-mdC) was the predominant form, while 5-hydroxymethyl- 2′-deoxycytidine (5-hmdC) and 5-formyl- 2′-deoxycytidine (5-fdC) were not detected, and N6-methyl- 2′-deoxyadenosine (6-mdA) was only detected at trace levels in the explant stage; (2) The genotype Y exhibited a dynamic pattern of 5-mdC levels during SE process, characterized by an initial decrease followed by an increase: 5-mdC content significantly decreased during callus induction (from 45.64 to 42.79%), then increased and maintained at a higher level (approximately 50%) during the differentiation phase. In contrast, the genotype R showed a continuous increase in DNA methylation levels; (3) Correlation analysis identified genes significantly associated with DNA methylation, predominantly showing negative correlations. Genotype-specific analysis revealed striking differences: only three genes with moderate correlation in genotype Y versus 147 genes with strong correlation in genotype R, suggesting distinct epigenetic regulatory mechanisms. Several key genes involved in embryonic development and hormone signaling pathways showed significant expression differences between genotypes. This study provides new insights into DNA methylation dynamics during SE in H. brasiliensis and identifies potential molecular markers for embryogenic capacity, offering theoretical basis for optimizing tissue culture systems for this economically important species.