title: Epigenetic variation, inheritance, and parent-of-origin effects of cytosine methylation in maize (Zea mays).
abstract: Pure epigenetic variation, or epigenetic variation that is independent of genetic context, may provide a mechanism for phenotypic variation in the absence of DNA mutations. To estimate the extent of pure epigenetic variation within and across generations and to identify the DNA regions targeted, a group of eight plants derived from a highly inbred line of maize (Zea mays) was analyzed by the methylation-sensitive amplified polymorphism (MSAP) technique. We found that cytosine methylation (mC) differences among individuals accounted for up to 7.4% of CCGG sites investigated by MSAP. Of the differentially methylated fragments (DMFs) identified in the S0 generation, ∼12% were meiotically inherited for at least six generations. We show that meiotically heritable mC variation was consistently generated for an average of 0.5% CCGG sites per generation and that it largely occurred somatically. We provide evidence that mC variation can be established and inherited in a parent-of-origin manner, given that the paternal lineage is more prone to both forward and reverse mC changes. The molecular characterization of selected DMFs revealed that the variation was largely determined by CG methylation changes that map within gene regions. The expression analysis of genes overlapping with DMFs did not reveal an obvious correlation between mC variation and transcription, reinforcing the idea that the primary function of gene-body methylation is not to control gene expression. Because this study focuses on epigenetic variation in field-grown plants, the data presented herein pertain to spontaneous epigenetic changes of the maize genome in a natural context.
authors.affiliation: Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria, I-20133 Milano, Italy.
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Lauria
authors.forename: Sara
authors.initials: S
authors.lastname: Piccinini
authors.forename: Raul
authors.initials: R
authors.lastname: Pirona
authors.forename: Gertrud
authors.initials: G
authors.lastname: Lund
authors.forename: Angelo
authors.initials: A
authors.lastname: Viotti
authors.forename: Mario
authors.initials: M
authors.lastname: Motto
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis; D003596:Cytosine / Q000378:metabolism*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D018515:Plant Leaves / Q000235:genetics; D012150:Polymorphism, Restriction Fragment Length; D003313:Zea mays / Q000235:genetics*
chemical_list: D003596:Cytosine
keywords: DNA methylation; MSAP analysis; epigenetic inheritance; maize; parent-of-origin effects