Importance of DNA and histone methylation in in vitro plant propagation for crop improvement: a review
Abstract
Epigenetic changes including DNA and histone methylation may reorganise the nuclear architecture during in vitro culture. The states of methylation resulting from in vitro cultures are often related to control the somatic embryogenesis and regeneration process via modulating gene expression. By changing the methylation profile, it is possible to alter gene expression which may be applicable to produce large number of high quality planting materials or to improve agronomic traits leading to crop improvement. Understanding the molecular mechanisms of methylation alterations and acquisition of developmental cell fate during in vitro cultures can help in the development of strategies to enhance the embryogenic capability and totipotency in recalcitrant plant species and genotypes. Moreover, the methylation profile may also be useful to adapt crops under adverse environment as the plants undergo through various stresses during in vitro cultures. In this article, we review the literature on the role of DNA and histone methylation in plant variation and discuss the potential of targeted epigenetic variation for crop improvement.
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Hypermethylation is usually associated with promotion of somatic embryogenesis and silencing of repetitive elements, while hypomethylation suppresses somatic embryogenesis, but these processes are species-specific.
“Usually, hypermethylation is associated with the promotion of SE and silencing of repetitive elements, while hypomethylation suppresses SE, but these processes are species-specific.”
From Somaclonal Variation—Advantage or Disadvantage in Micropropagation of the Medicinal Plants (2023) · cites this paper as [110]
Direct somatic embryogenesis in in vitro micropropagation is characterized by either hypermethylation or hypomethylation of DNA.
“For example, many in vitro micropropagation strategies imply direct somatic embryogenesis (SE), and there are studies indicating that this process is characterized by either hypermethylation or hypomethylation of DNA [110].”
From Somaclonal Variation—Advantage or Disadvantage in Micropropagation of the Medicinal Plants (2023) · cites this paper as [110]
Cites
Somaclonal Variation in Plants: Causes and Detection Methods
Bairu, M. W., Aremu, A. O., & Van Staden, J. (2011) · Plant Growth Regulation · doi:10.1007/s10725-010-9554-x · Cited by 674 · see citing works
Bernatavichute, Y. V., Zhang, X., Cokus, S., Pellegrini, M., & Jacobsen, S. E. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003156 · Cited by 333 · see citing works
Nic-Can, G. I., López-Torres, A., Barredo-Pool, F., Wrobel, K., Loyola-Vargas, V. M., Rojas-Herrera, R., & De-la-Peña, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072160 · Cited by 164 · see citing works
Bobadilla Landey, R., Cenci, A., Georget, F., Bertrand, B., Camayo, G., Dechamp, E., Herrera, J. C., Santoni, S., Lashermes, P., Simpson, J., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056372 · Cited by 95 · see citing works
Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize
Stelpflug, S. C., Eichten, S. R., Hermanson, P. J., Springer, N. M., & Kaeppler, S. M. (2014) · Genetics · doi:10.1534/genetics.114.165480 · Cited by 90 · see citing works
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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.”
BackgroundMirani, A. A., Teo, C. H., Markhand, G. S., Abul-Soad, A. A., & Harikrishna, J. A. (2020) · Plant Cell, Tissue and Organ Culture (PCTOC) · doi:10.1007/s11240-020-01772-y · Cited by 39 · see citing works
Self-citationApplication of Somaclonal Variation in Crop Improvements
Dorani, E., Dehghanian, Z., Gougerdchi, V., & Hamedpour-Darabi, M. (2024) · Sustainable Landscape Planning and Natural Resources Management · doi:10.1007/978-3-031-50729-8_8 · Cited by 11 · see citing works
- Authors
- Karim, R., Nuruzzaman, M., Khalid, N., & Harikrishna, J. A.
- Affiliations
- University of Malaya (MY)
- Universiti Malaysia Terengganu (MY)
- Corresponding author
- Harikrishna, J.A.
- Venue
- Annals of Applied Biology
- Publisher
- Wiley
- Published
- 2016-03-02
- Volume
- 169
- Issue
- 1
- Pages
- 1-16
- ISSN
- 0003-4746 (ISSN-L)
- 1744-7348
- OpenAlex
- W2288496452
- Cited by
- 31
- References
- 5
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 5 · 2023: 3 · 2022: 5 · 2021: 6 · 2020: 4 · 2019: 2 · 2018: 4
- FWCI
- 1.04
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annals of Applied Biology (publishedVersion)
- Funders
- Bright Spark Program and High Impact Research Chancellory Grant (UM.S/P/628/3/HIR-MOHE-SC19)
- 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, histone methylation, epigenetics, in vitro plant propagation, somatic embryogenesis, plant regeneration, gene expression regulation, totipotency, recalcitrant genotypes, agronomic traits, crop improvement, plant stress adaptation
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