Epigenetic inheritance and variation of DNA methylation level and pattern in maize intra-specific hybrids

Studies on transmission genetics of cytosine methylation in plants are important for elucidating the biological roles of this epigenetic modification. Using three sets of reciprocal maize hybrids and their inbred parents, we compared level and pattern of cytosine methylation in each of the hybrids and their corresponding parental inbred lines by the methylation-sensitive amplified polymorphism (MSAP) method. We found that whereas a great majority of cytosine methylation sites manifested faithful epigenetic inheritance, from 6.59% to 11.92% of the sites showed altered parental patterns in hybrids, with the extent of deviation being depending on both direction of the cross and parental combinations. DNA gel blot analysis demonstrated that the great majority of MSAP profiles in a hybrid, both inheritance and alteration, can be validated. The changes in cytosine methylation level and pattern were not caused by parental heterozygosity, and they could be either directed or stochastic among individual hybrid plants. Homology analysis of isolated MSAP profiles indicated that diverse sequences underlie methylation alterations, including known-function genes, ESTs and uncharacterized sequences. We discuss possible relevance of methylation-pattern remodeling to heterosis in a maize hybrid relative to its parental inbred lines.