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Cited by 29Plant tissue culture and regenerationEpigenetics and DNA MethylationPlant Molecular Biology Research

The callus formation capacity of strawberry leaf explants is modulated by DNA methylation

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Liu, Decai, Mu, Qin, Li, Xianyang, Xu, Sheng, Li, Yi, Gu, Tingting·2022·Horticulture Research
DOI 10.1093/hr/uhab073PMC PMC8947209
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Abstract

Shoot regeneration from leaf tissue requires the de-differentiation of cells from a highly differentiated state into an actively dividing state, but it remains unclear how this physiological transition occurs and is regulated, especially at the epigenetic level. Here, we characterized the DNA methylome represented by 5-methylcytosine (5mC) in leaf and callus tissue derived from leaf explants of woodland strawberry, Fragaria vesca. We detected an overall increase in DNA methylation and distinct 5mC enrichment patterns in the CG, CHG, and CHH sequence contexts in genes and transposable elements. Our analyses revealed an intricate relationship between DNA methylation and gene expression level in leaves or leaf-derived callus. However, when considering the genes involved in callus formation and shoot regeneration, e.g. FvePLT3/7, FveWIND3, FveWIND4, FveLOG4 and FveIAA14, their dynamic transcription levels were associated with differentially methylated regions located in the promoters or gene bodies, indicating a regulatory role of DNA methylation in the transcriptional regulation of pluripotency acquisition in strawberry. Furthermore, application of the DNA methyltransferase inhibitor 5′-azacytidine (5′-Aza) hampered both callus formation and shoot regeneration from the leaf explants. We further showed that 5′-Aza downregulated the expression of genes involved in cell wall integrity, such as expansin, pectin lyase, and pectin methylesterase genes, suggesting an essential role of cell wall metabolism during callus formation. This study reveals the contribution of DNA methylation to callus formation capacity and will provide a basis for developing a strategy to improve shoot regeneration for basic and applied research applications.

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  • In strawberries' long-term in vitro shoot cultures, RNA sequencing detected increased DNA methylation in specific sequence contexts (CG, CHG, CHH), with changes linked to expression of regeneration-related genes.

    “The results showed increased DNA methylation in specific sequence contexts (CG, CHG, CHH), with changes linked to the expression of regeneration-related genes.”

    From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [155]

    The Results section on the methylation landscape reports increased overall methylation in strawberry leaf-derived callus, with increases in CG and CHG but a decrease in CHH relative to leaves. The Introduction and Methods describe leaf-to-callus formation studied by whole-genome bisulfite sequencing, not long-term shoot cultures with methylation detected by RNA sequencing. The Abstract and co-analysis Results do link methylation patterns to expression of regeneration-related genes. Page numbers are unavailable in our copy. (LLM, conf=0.90)

    Experimental — accuracy not yet measured

  • Inhibition of DNA methylation with 5′-azacytidine disrupted callus formation and regeneration, highlighting the critical role of DNA methylation in these processes.

    “Inhibition of DNA methylation with 5 ′ -azacytidine (5 ′ -Aza) disrupted callus formation and regeneration, highlighting the critical role of DNA methylation in these processes [155].”

    From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [155]

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Cited by

Sorted by citations

Authors
Liu, D., Mu, Q., Li, X., Xu, S., Li, Y., & Gu, T.
Affiliations
  • Nanjing Agricultural University (CN)
  • University of Connecticut (US)
Corresponding author
  • Li, Yi
  • Gu, Tingting
ORCID
Venue
Horticulture Research
Publisher
Oxford University Press (OUP)
Published
2022
Volume
9
Pages
uhab073-uhab073
ISSN
2052-7276 (ISSN-L)
DOI
10.1093/hr/uhab073
PMC
PMC8947209
OpenAlex
W4206758628
Cited by
29
References
0
Citations by year
2026: 6 · 2025: 6 · 2024: 6 · 2023: 8 · 2022: 3
FWCI
1.88
Type
journal article
Language
en
Open access
Licence
Locations
  • Horticulture Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant tissue culture and regeneration
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
Keywords
DNA methylation, callus formation, shoot regeneration, Fragaria vesca, leaf explants, 5-methylcytosine, differentially methylated regions, transposable elements, epigenetic regulation, azacitidine, cell wall metabolism, expansin, pectin lyase, pectin methylesterase, pluripotency genes

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