title: 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 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.
authors.affiliation: Department of Molecular, Cell and Developmental Biology , University of California, Los Angeles , Los Angeles , United States.
authors.forename: Hume
authors.initials: H
authors.lastname: Stroud
authors.forename: Bo
authors.initials: B
authors.lastname: Ding
authors.forename: Stacey A
authors.initials: SA
authors.lastname: Simon
authors.forename: Suhua
authors.initials: S
authors.lastname: Feng
authors.forename: Maria
authors.initials: M
authors.lastname: Bellizzi
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Wang
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
mesh_terms: D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D018506:Gene Expression Regulation, Plant; D005838:Genotype; D012275:Oryza / Q000235:genetics* / Q000254:growth & development*; D010641:Phenotype; D030821:Plants, Genetically Modified / Q000235:genetics* / Q000254:growth & development*; D011401:Promoter Regions, Genetic; D012038:Regeneration; D013269:Stochastic Processes; D013997:Time Factors; D046509:Tissue Culture Techniques
keywords: DNA methylation; Other; Rice; regeneration; small RNA; tissue culture
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