title: Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize.
abstract: 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 of maize 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 sites 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.
authors.affiliation: Department of Agronomy, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706.
authors.forename: Scott C
authors.initials: SC
authors.lastname: Stelpflug
authors.affiliation: Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Eichten
authors.affiliation: Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Hermanson
authors.affiliation: Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Springer
authors.affiliation: Department of Agronomy, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53706 smkaeppl@wisc.edu.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Kaeppler
mesh_terms: D002478:Cells, Cultured; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018745:Genome, Plant; D018515:Plant Leaves / Q000166:cytology / Q000378:metabolism; D012639:Seeds / Q000166:cytology / Q000378:metabolism; D003313:Zea mays / Q000235:genetics*
keywords: DNA methylation; epigenetic; somaclonal variation; stress; tissue culture