Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture
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Abstract
DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. To investigate heritable epigenetic changes as a consequence of tissue culture, a sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ∼15 Mb of the maize genome for a population of plants that had been regenerated from tissue culture. Plants that have been regenerated from tissue culture exhibit gains and losses of DNA methylation at a subset of genomic regions. There was evidence for a high rate of homozygous changes to DNA methylation levels that occur consistently in multiple independent tissue culture lines, suggesting that some loci are either targeted or hotspots for epigenetic variation. The consistent changes inherited following tissue culture include both gains and losses of DNA methylation and can affect CG, CHG, or both contexts within a region. Only a subset of the tissue culture changes observed in callus plants are observed in the primary regenerants, but the majority of DNA methylation changes present in primary regenerants are passed onto offspring. This study provides insights into the susceptibility of some loci and potential mechanisms that could contribute to altered DNA methylation and epigenetic state that occur during tissue culture in plant species.
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In Zea mays embryogenic callus culture, DNA methylation variation was observed.
“Variation observed”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [92]
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Additional file 6 of Chromosome-level genome assembly of a regenerable maize inbred line A188
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Self-citationAdditional file 10 of Chromosome-level genome assembly of a regenerable maize inbred line A188
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Self-citationAdditional file 8 of Chromosome-level genome assembly of a regenerable maize inbred line A188
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Self-citationAdditional file 2 of Chromosome-level genome assembly of a regenerable maize inbred line A188
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Self-citationAdditional file 7 of Chromosome-level genome assembly of a regenerable maize inbred line A188
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Self-citationAdditional file 9 of Chromosome-level genome assembly of a regenerable maize inbred line A188
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Self-citationAdditional file 4 of Chromosome-level genome assembly of a regenerable maize inbred line A188
Lin, G., He, C., Zheng, J., Koo, D., Le, H., Zheng, H., Tamang, T. M., Lin, J., Liu, Y., Zhao, M., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14759661
Self-citationAdditional file 5 of Chromosome-level genome assembly of a regenerable maize inbred line A188
Lin, G., He, C., Zheng, J., Koo, D., Le, H., Zheng, H., Tamang, T. M., Lin, J., Liú, Y., Zhao, M., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14759664
Self-citationAdditional file 3 of Chromosome-level genome assembly of a regenerable maize inbred line A188
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Self-citationAdditional file 11 of Chromosome-level genome assembly of a regenerable maize inbred line A188
Lin, G., He, C., Zheng, J., Koo, D., Le, H., Zheng, H., Tamang, T. M., Lin, J., Liu, Y., Zhao, M., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14759643
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Additional file 12 of Chromosome-level genome assembly of a regenerable maize inbred line A188
Lin, G., He, C., Zheng, J., Koo, D.-H., Le, H., Zheng, H., Tamang, T. M., Lin, J., Liu, Y., Zhao, M., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14759646
Self-citationAdditional file 1 of Chromosome-level genome assembly of a regenerable maize inbred line A188
Lin, G., He, C., Zheng, J., Koo, D.-H., Le, H., Zheng, H., Tamang, T. M., Lin, J., Liu, Y., Zhao, M., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14759652
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- Authors
- Han, Z., Crisp, P. A., Stelpflug, S., Kaeppler, S. M., Li, Q., & Springer, N. M.
- Affiliations
- University of Minnesota (US)
- University of Wisconsin–Madison (US)
- Corresponding author
- Springer, Nathan M
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-05-30
- Volume
- 209
- Issue
- 4
- Pages
- 983-995
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- PMC
- PMC6063226
- OpenAlex
- W2787468300
- Cited by
- 78
- References
- 56
- Citations by year
- 2026: 7 · 2025: 6 · 2024: 6 · 2023: 9 · 2022: 10 · 2021: 17 · 2020: 12 · 2019: 9 · 2018: 2
- FWCI
- 4.45
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (1237931)
- University of Minnesota
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Plant tissue culture and regeneration
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetically Modified Organisms Research
- Keywords
- DNA methylation, maize, somaclonal variation, tissue culture, epigenetic inheritance, CG and CHG methylation, callus, plant regeneration
- MeSH terms
- Zea mays, Sequence Analysis, DNA, Sequence Analysis, RNA, Gene Expression Regulation, Plant, Plant Leaves, DNA Methylation, Quantitative Trait, Heritable, Epigenesis, Genetic, Tissue Culture Techniques, Epigenomics
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