ArticleeLife2013
Plants regenerated from tissue culture contain stable epigenome changes in rice.
Article in eLife, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 130 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
130 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea.Frontiers in genetics · 2022Pooled it
- Methylome and Transcriptome Analysis Reveals Differences in Callus Development and Plantlet Regeneration Capacity Between TwoPlants (Basel, Switzerland) · 2026Article
- Direct organogenesis and genetic fidelity of papaya 'Red Lady' with improved acclimatization using foliar silicon and salicylic acid.Journal, genetic engineering & biotechnology · 2026Article
- Morphogenetic Factors as a Tool for Enhancing Plant Regeneration Capacity During In Vitro Transformation.International journal of molecular sciences · 2025Review
- Maternal environmental effects and climate-smart seeds: unlocking epigenetic inheritance for crop innovation in the seed industry.The Plant journal : for cell and molecular biology · 2025Article
- Dynamic changes in DNA methylation play a regulatory role in gene expression during the formation of callus from immature barley embryos.BMC plant biology · 2025Article
- Multiple developmental pathways in organisms with developmentally complex life cycles.Frontiers in cell and developmental biology · 2025Review
- DEMETER DNA demethylase reshapes the global DNA methylation landscape and controls cell identity transition during plant regeneration.BMC genomics · 2024Article
- Synergistic induction of fertilization-independent embryogenesis in rice egg cells by paternal-genome-expressed transcription factors.Nature plants · 2024Article
- Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries.Genome research · 2024Article
- A Comparison of DNA-Methylation during Protoplast Culture of Ponkan Mandarin (Plants (Basel, Switzerland) · 2024Article
- Dynamic evolution of the heterochromatin sensing histone demethylase IBM1.PLoS genetics · 2024Article
- Insights into plant regeneration: cellular pathways and DNA methylation dynamics.Plant cell reports · 2024Review
- A Case Study from the Overexpression of OsTZF5, Encoding a CCCH Tandem Zinc Finger Protein, in Rice Plants Across Nineteen Yield Trials.Rice (New York, N.Y.) · 2024Article
- The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions.Plant physiology · 2024Review
- The lemon genome and DNA methylome unveil epigenetic regulation of citric acid biosynthesis during fruit development.Horticulture research · 2024Article
- Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce.GigaScience · 2024Article
- An efficientFrontiers in plant science · 2024Article
- Genomic consequences associated with Agrobacterium-mediated transformation of plants.The Plant journal : for cell and molecular biology · 2024Review
- Rice transformation treatments leave specific epigenome changes beyond tissue culture.Plant physiology · 2023Article
70 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. DOI:http://dx.doi.org/10.7554/eLife.00354.001.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.