Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP)

DNA methylation in plants is related to a number of epigenetic (i.e. heritable, but potentially reversible) phenomena. Heavy methylation of cytosine residues plays an important role in gene expression, and significant differences in cytosine methylation levels have been observed among various tissue types, which can be explained as one of the regulatory mechanisms during development and differentiation. Here, we report on the analysis of cytosine methylation during pepper seed germination using an adaptation of the AFLP technique called methylation-sensitive amplified polymorphism (MSAP). Notable changes in MSAP profiles of genomic DNA obtained from embryo tissues of dry seeds and germinating seeds were detected. The changes were mainly: (i) fragments not detected in dry seeds were present after digestion with both EcoRI/HpaII and EcoRI/MspI at a certain stage during germination; (ii) fragments present after both digestions in dry seeds were no longer detected upon germination. Although changes in MSAP patterns during germination are not easily interpreted, our results can be mainly attributed to demethylation events, which appear to be necessary for transcriptional activation during germination. The potential and limits of MSAP in the analysis of DNA methylation status are discussed.