High Resolution Epigenome Assay for Clonal Conformity in Oil Palm

The failure to detect genetic changes in the abnormal (mantled) phenotype observed in tissue culture-derived oil palms has led to a concerted effort channelled towards dissecting the possible epigenetic mechanisms surrounding this phenomenon. With the availability of the oil palm genome information, MPOB is now in a better position to survey the epigenome landscape at a higher resolution with the use of genome tiling arrays. This novel proprietary genome-wide microarray approach has to date been successfully applied to detect DNA methylation alterations in human tumours.  Screening through several ortet-ramet sample sets has enabled the detection of consistently differentially methylated loci based on comparative assessment of normal and abnormal palms.  Subsequently, specific primers were designed at these loci for independent analysis via a quantitative real-time PCR based method. Due to the strong influence of genotype on the analyses, we have increased the range of samples used in the discovery stage. Somaclonal variation has been shown to involve a multipartite mechanism, namely DNA methylation, histone modification and small RNA directed methylation.  We will briefly highlight some our efforts in mapping the epigenome of the oil palm towards understanding somaclonal variation and clonal abnormality.