The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Plants regenerated from tissue culture contain stable epigenome changes in rice
Open accessAbstract
Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several regenerated rice lines. We found that all tested regenerated plants had significant losses of methylation compared to non-regenerated plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability.
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Conservation and divergence of methylation patterning in plants and animals
Feng, S., Cokus, S. J., Zhang, X., Chen, P.-Y., Bostick, M., Goll, M. G., Hetzel, J., Jain, J., Strauss, S. H., Halpern, M. E., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002720107 · Cited by 1,285
Self-citationEpigenetic aspects of somaclonal variation in plants
Kaeppler, S. M., Kaeppler, H. F., & Rhee, Y. (2000) · Plant Molecular Biology · doi:10.1023/a:1006423110134 · Cited by 743
Tissue Culture-Induced DNA Methylation Variation in Maize
Kaeppler, S. M., & Phillips, R. L. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.19.8773 · Cited by 225
Epigenomic consequences of immortalized plant cell suspension culture
Tanurdzic, M., Vaughn, M. W., Jiang, H., Lee, T.-J., Slotkin, R. K., Sosinski, B., Thompson, W. F., Doerge, R. W., & Martienssen, R. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060302 · Cited by 218
Cited by
The Role of Somaclonal Variation in Plant Genetic Improvement: A Systematic Review
Ferreira, M. D. S., Rocha, A. D. J., Nascimento, F. D. S., Oliveira, W. D. D. S., Soares, J. M. D. S., Rebouças, T. A., Morais Lino, L. S., Haddad, F., Ferreira, C. F., Santos-Serejo, J. A. D., et al. (2023) · Agronomy · doi:10.3390/agronomy13030730 · Cited by 95
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
Tissue Culture-Induced Heritable Genomic Variation in Rice, and Their Phenotypic Implications
Zhang, D., Wang, Z., Wang, N., Gao, Y., Liu, Y., Wu, Y., Bai, Y., Zhang, Z., Lin, X., Dong, Y., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096879 · Cited by 90
Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture
Han, Z., Crisp, P. A., Stelpflug, S., Kaeppler, S. M., Li, Q., & Springer, N. M. (2018) · Genetics · doi:10.1534/genetics.118.300987 · Cited by 78
Epigenomics of plant responses to environmental stress
Kumar, S. (2018) · Epigenomes · doi:10.3390/epigenomes2010006 · Cited by 73
Metadata
- Authors
- Stroud, H., Ding, B., Simon, S. A., Feng, S., Bellizzi, M., Pellegrini, M., Wang, G.-L., Meyers, B. C., & Jacobsen, S. E.
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2013-03-19
- Volume
- 2
- Pages
- e00354-e00354
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W2141275463
- Cited by
- 269
- References
- 5
- FWCI
- 8.47
- Type
- journal article
- Language
- en
- Open access
- gold
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- Stroud, H., Ding, B., Simon, S. A., Feng, S., Bellizzi, M., Pellegrini, M., Wang, G.-L., Meyers, B. C., & Jacobsen, S. E. (2013). Plants regenerated from tissue culture contain stable epigenome changes in rice. eLife. https://doi.org/10.7554/elife.00354
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
