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Plants regenerated from tissue culture contain stable epigenome changes in rice

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 transgenic rice lines. We found that all tested transgenic plants had significant losses of methylation compared to untransformed 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.

ORGANISM(S): Oryza sativa

PROVIDER: GSE42410 | GEO | 2013/03/26

SECONDARY ACCESSION(S): PRJNA181348

REPOSITORIES: GEO

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Plants regenerated from tissue culture contain stable epigenome changes in rice

Project description: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 transgenic rice lines. We found that all tested transgenic plants had significant losses of methylation compared to untransformed 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. Whole genome methylation maps of rice were generated using BS-seq (Hume Stroud, Suhua Feng, Steve Jacobsen at UCLA). Whole genome expression maps of rice were generated using mRNA-seq and smRNA (Stacey Simon, Blake Meyers at Univ of Delaware).

2013-03-26 | E-GEOD-42410 | biostudies-arrayexpress

Vitis vinifera embryogenic callus epigenomics (small RNA data)

Project description:Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.

2021-08-27 | GSE164584 | GEO

Vitis vinifera embryogenic callus epigenomics (RNA-seq)

2021-08-27 | GSE164583 | GEO

Vitis vinifera embryogenic callus epigenomics (WGBS data)

2021-08-27 | GSE164582 | GEO

Consistent and Heritable Alterations of DNA Methylation are Induced by Tissue Culture in Maize

Project description:Plants regenerated from tissue culture and their progenies are expected to be identical clones, but often display heritable molecular and phenotypic variation. We characterized DNA methylation patterns in callus, primary regenerants, and regenerant-derived progenies using immunoprecipitation of methylated DNA (meDIP) to assess the genome-wide frequency, pattern, and heritability of DNA methylation changes. Although genome-wide DNA methylation levels remained similar following tissue culture, numerous regions exhibited altered DNA methylation levels. Hypomethylation events were observed more frequently than hypermethylation following tissue culture. Many of the hypomethylation events occur at the same genomic site across independent regenerants and cell lines. The DNA methylation changes were often heritable in progenies produced from self-pollination of primary regenerants. Methylation changes were enriched in regions upstream of genes and loss of DNA methylation at promoters was associated with altered expression at a subset of loci. Differentially methylated regions (DMRs) found in tissue culture regenerants overlap with the position of naturally occurring DMRs more often than expected by chance with 8% of tissue culture hypomethylated DMRs overlapping with DMRs identified by profiling natural variation, consistent with the hypotheses that genomic stresses similar to those causing somaclonal variation may also occur in nature, and that certain loci are particularly susceptible to epigenetic change in response to these stresses. The consistency of methylation changes across regenerants from independent cultures suggests a mechanistic response to the culture environment as opposed to an overall loss of fidelity in the maintenance of epigenetic states.

2015-03-24 | GSE56479 | GEO

Dynamics of the transcriptome and methylome during the regeneration of rice

Project description:Tissue culture is used to establish desired phenotypes in plants. Callus culture and regeneration are critical steps in this process. Calli of Oryza sativa japonica (cv. TNG67) and Oryza sativa indica (cv. IR64) have varying regeneration efficiencies. Genetic diversity could partly account for such differences but the epigenetic response to different cell culture environment could also play a role. We aimed to study the role of DNA methylation during the tissue culture process in determining its outcome.

2017-06-01 | GSE82138 | GEO

Integrative analysis of DNA methylation, mRNAs, and small RNAs during maize embryo dedifferentiation

Project description:Background: Maize (Zea Mays) is an important model crop for transgenic studies. However, genetic transformation of maize requires embryonic calli derived from immature embryo, and the impact of utilizing tissue culture methods on the maize epigenome is poorly understood. Here, we generated whole-genome MeDIP-seq data examining DNA methylation in dedifferentiated and normal immature maize embryos. Results: We observed that most of the dedifferentiated embryos exhibited a methylation increase compared to normal embryos. Increased methylation at promoters was associated with down-regulated protein-coding gene expression; however, the correlation was not strong. Analysis of the callus and immature embryos indicated that the methylation increase was induced during induction of embryonic callus, suggesting phenotypic consequences may be caused by perturbations in genomic DNA methylation levels. The correlation between the 21-24nt small RNAs and DNA methylation regions were investigated but only a statistically significant correlation for 24nt small RNAs was observed. Conclusions: These data extend the significance of epigenetic changes during maize embryo callus formation, and the methylation changes might explain some of the observed embryonic callus variation in callus formation.

2017-05-10 | GSE84455 | GEO

Loss of Karma transposon methylation underlies oil palm somaclonal mantling

Project description:The oil palm fruit abnormality, mantled, is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for breeding and oil production. Widely regarded as epigenetic, mantling had defied explanation, and has become an icon of unsustainability in environmentally sensitive tropical plantation crops. We identified the MANTLED gene using Epigenome Wide Association analysis of genetically identical palms from multiple clonal lineages. Hypomethylation of a LINE retrotransposon related to rice Karma, found in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is correlated with alternative splicing and loss of small RNA. DNA methylation is regained in spontaneous revertants accounting for non-Medelian inheritance of the Good Karma and Bad Karma epialleles. Thus epigenetic regulation of transposable elements results in somaclonal variation and provides a means to cull mantled nursery palms before committing limiting plantation resources to clonal propagation. DNA methylation profiling was performed using the McrBC DNA methylation dependent fractionation and microarray hybridization method as described in Lippman, Z., Gendrel, A. V., Colot, V. & Martienssen, R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods 2, 219-224 (2005). DNA methylation profiling was performed on 54 parthenocarpic mantled ramet, 43 normal ramet and 1 ortet adult leaf samples. For each sample, two independent fractionations of total genomic DNA and DNA methylation-depleted DNA were performed. Each total DNA/methylation-depleted DNA pair was differentially labeled and hydrized to a custon Nimblegen microarray in a dye-swapped design (4 array hybridizations per sample).

2015-09-09 | E-GEOD-68410 | biostudies-arrayexpress

Loss of Karma transposon methylation underlies oil palm somaclonal mantling

2015-09-09 | GSE68410 | GEO

Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean

Project description:Tissue culture is a major method for plant regeneration and for production of transgenic plants. Thus far, our knowledge of the dynamic epigenomic during tissue culture is limited. In this study, we generated epigenomes from nine different stages throughout the tissue culture process and found significant genome-wide increases of DNA methylation throughout the soybean genome. This change mostly happens in CHH (H = A, T, C) context and targets transposable elements (TEs). Subsequent analyses of corresponding transcriptomes and small RNA distributions indicate that it is associated with high activity of the RNA-directed DNA methylation (RdDM) pathway. These results provide important insights into the function of a dynamic epigenome throughout tissue culture and extends our understanding of epigenome-wide reprogramming of the DNA methylome in plants.

2019-10-01 | GSE94299 | GEO

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