Epigenetic changes and their relationship to somaclonal variation: A need to monitor the micropropagation of plantation crops
Abstract
Chromatin modulation plays important roles in gene expression regulation and genome activities. In plants, epigenetic changes, including variations in histone modification and DNA methylation, are linked to alterations in gene expression. Despite the significance and potential of in vitro cell and tissue culture systems in fundamental research and marketable applications, these systems threaten the genetic and epigenetic networks of intact plant organs and tissues. Cell and tissue culture applications can lead to DNA variations, methylation alterations, transposon activation, and finally, somaclonal variations. In this review, we discuss the status of the current understanding of epigenomic changes that occur under in vitro conditions in plantation crops, including coconut, oil palm, rubber, cotton, coffee and tea. It is hoped that comprehensive knowledge of the molecular basis of these epigenomic variations will help researchers develop strategies to enhance the totipotent and embryogenic capabilities of tissue culture systems for plantation crops.
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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 [98]
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Somaclonal Variation—Advantage or Disadvantage in Micropropagation of the Medicinal Plants
Duta-Cornescu, G., Constantin, N., Pojoga, D.-M., Nicuta, D., & Simon-Gruita, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24010838 · Cited by 108 · see citing works
“Epigenetic variations in in vitro-regenerated plants, related to histone modifications, have been largely reviewed for model plants, such as Arabidopsis, rice, and maize [91,98,110,124], but not so much for medicinal plants.”
BackgroundChandana, B. S., Mahto, R. K., Singh, R. K., Ford, R., Vaghefi, N., Gupta, S. K., Yadav, H. K., Manohar, M., & Kumar, R. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.900253 · Cited by 23 · see citing works
Noncoding RNA-Mediated Regulation of DNA Methylation: Insights into Plant Epigenetic Mechanisms
Ali, S., & Tang, Y. (2025) · Journal of Plant Growth Regulation · doi:10.1007/s00344-024-11462-0 · Cited by 24 · see citing works
Somaclonal Variation for the Improvement of Tree Species
Joshi, A., Tripathi, A., Sharma, N., & Tailor, A. (2024) · Biotechnological Approaches for Sustaining Forest Trees and Their Products · doi:10.1007/978-981-97-4363-6_4 · Cited by 5 · see citing works
- Authors
- Azizi, P., Hanafi, M. M., Sahebi, M., Harikrishna, J. A., Taheri, S., Yassoralipour, A., & Nasehi, A.
- Affiliations
- Universiti Putra Malaysia (MY)
- University of Malaya (MY)
- Universiti Tunku Abdul Rahman (MY)
- Corresponding author
- Hanafi, Mohamed M.
- ORCID
- Venue
- Functional Plant Biology
- Publisher
- CSIRO Publishing
- Published
- 2020-04-30
- Volume
- 47
- Issue
- 6
- Pages
- 508-523
- ISSN
- 1445-4408 (ISSN-L)
- 1445-4416
- OpenAlex
- W3022602000
- Cited by
- 46
- References
- 8
- Citations by year
- 2026: 7 · 2025: 5 · 2024: 5 · 2023: 3 · 2022: 10 · 2021: 14 · 2020: 2
- FWCI
- 0.69
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Functional Plant Biology (publishedVersion)
- PubMed (publishedVersion)
- Universiti Putra Malaysia Institutional Repository (Universiti Putra Malaysia) (acceptedVersion)
- 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
- epigenetic modifications, somaclonal variation, micropropagation, histone modifications, DNA methylation, transposon activation, plantation crops, coconut, oil palm, rubber, cotton, coffee, tea, totipotency, embryogenic capacity, in vitro culture
- MeSH terms
- Chromatin, Crops, Agricultural, DNA Methylation, Epigenesis, Genetic, Epigenomics
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