In oil palm, somatic-embryogenesis derived clonal plants have been found to display a small percentage of abnormal individuals showing a feminization of male parts in flowers of both sexes, called the mantled phenotype. Analysis of DNA methylation in mantled somaclonal variants showed both large-scale perturbations of global methylation rates and sequence-specific DNA methylation pattern changes when compared to their true-to-type counterparts. Several markers showing phenotype-specific transcription patterns have been identified at early stages of the SE-based process (calli, embryogenic suspensions, somatic embryos). Some of them are likely to be indicators of the altered physiological state of abnormal cultures (e.g. IAA gene homologues). Other putative markers have been isolated at the flower stage and they are possible targets of epigenetic changes in genes governing flower architecture (MADS-box). We are now exploring the possible links between the expression of these candidate marker genes, their methylation status and the expression of the "mantled" phenotype. This is achieved through the evaluation of transcription levels by real-time PCR and the determination of sequence-wide DNA methylation patterns on target sequences by bisulfite sequencing. Furthermore, changes in epigenetic prints on chromatin surrounding these genes are analysed by Chromatin Immuno-