An epigenetic view of plant cells cultured in vitro: Somaclonal variation and beyond
Abstract
Epigenetic mechanisms are highly dynamic events that modulate gene expression. As more accurate and powerful tools for epigenetic analysis become available for application in a broader range of plant species, analysis of the epigenetic landscape of plant cell cultures may turn out to be crucial for understanding variant phenotypes. In vitro plant cell and tissue culture methodologies are important for many ongoing plant propagation and breeding programmes as well as for cutting-edge research in several plant model species. Although it has long been known that in vitro conditions induce variation at several levels, most studies using such conditions rely on the assumption that in vitro cultured plant cells/tissues mostly conform genotypically and phenotypically. However, when large-scale clonal propagation is the aim, there has been a concern in confirming true-to-typeness using molecular markers for evaluating stability. While in most reports genetic variation has been found to occur at relatively modest frequencies, variation in DNA methylation patterns seems to be much more frequent and in some cases it has been directly implicated in phenotypic variation. Recent advances in the field of epigenetics have uncovered highly dynamic mechanisms of chromatin remodelling occurring during cell dedifferentiation and differentiation processes on which in vitro adventitious plant regeneration systems are based. Here, an overview of recent findings related to developmental switches occ…
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In the Arabidopsis genome, histone modifications such as H2BK143 ubiquitination, H3K4/H3K36/H3 methylation, and H3/H4 lysine acetylation are associated with gene activation, while H3K9/H3K27/H4K20 methylation and H4R3 dimethylation are associated with gene inactivation.
“For example, it is well known that modifications such as the ubiquitination of H2BK143, mono-, di-, and trimethylation of H3K4, H3K36, and H3 and H4 lysine acetylation are associated, in Arabidopsis genome, with gene activation, while the mono-, di- and trimethylation of H3H9, H3K27, and H4K20, and the dimethylation of H4R3, are associated with gene inactivation [90,91,92,93]).”
From Somaclonal Variation—Advantage or Disadvantage in Micropropagation of the Medicinal Plants (2023) · cites this paper as [91]
Epigenetic variability observed at the phenotype level reflects adaptations of cellular processes to constraints of in vitro cultivation, which usually implies sequential dedifferentiation and re-differentiation.
“This epigenetic variability, which frequently is observed at phenotype level, reflects, in reality, the adaptations of the cellular processes to the various constraints of the in vitro cultivation technology, that usually implies sequential dedifferentiation (formation of callus) and re-differentiation (regeneration of plants) [91,95,96,97,98,99,100].”
From Somaclonal Variation—Advantage or Disadvantage in Micropropagation of the Medicinal Plants (2023) · cites this paper as [91]
Some genotypes possess greater genetic instability in tissue culture, mainly due to differences in genome size, ploidy levels, and genes involved in DNA repair and stress response.
“Some genotypes possess greater genetic instability in tissue culture, mainly due to differences in genome size, ploidy levels, and genes involved in DNA repair and stress response mechanisms [67].”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [67]
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- Authors
- Miguel, C., & Marum, L.
- Affiliations
- Instituto de Biologia Experimental e Tecnológica (PT)
- Corresponding author
- Miguel, C.
- Marum, L.
- ORCID
- Venue
- Journal of Experimental Botany
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-05-26
- Volume
- 62
- Issue
- 11
- Pages
- 3713-3725
- ISSN
- 0022-0957 (ISSN-L)
- 1460-2431
- OpenAlex
- W2170139296
- Cited by
- 395
- References
- 8
- Citations by year
- 2026: 20 · 2025: 19 · 2024: 25 · 2023: 22 · 2022: 28 · 2021: 38 · 2020: 28 · 2019: 21 · 2018: 20 · 2017: 20 · 2016: 30 · 2015: 46 · 2014: 29 · 2013: 22 · 2012: 26
- FWCI
- 2.26
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Experimental Botany (publishedVersion)
- 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
- somaclonal variation, epigenetics, plant cell culture, DNA methylation, chromatin remodeling, adventitious regeneration, developmental switching, clonal stability, gene expression regulation
- MeSH terms
- Cell Differentiation, Chromatin, Plants, Genetic Variation, Cell Culture Techniques, DNA Methylation, Epigenesis, Genetic, Epigenomics, Plant Cells, Plant Development
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