Karma-EgDEF1 methylation in Elaeis guineensis clonal mother palms that produced high mantling rates in the second clonal generation

The mantled phenotype in oil palm is a somaclonal variant that can only be visibly detected when the plant reaches reproductive maturity, which is typically 2 to 3 yr after planting in the field. This phenotype is linked to the Bad Karma epiallele, which involves reduced methylation of the Karma retrotransposon in the EgDEF1 gene. In this study, Karma - EgDEF1 methylation was examined in clonal mother palms (clonal ortets) that were phenotypically normal, but upon clonal propagation, produced high mantling rates in their reclones. These clonal ortets were clones of a seed-derived ortet. Single-nucleotide methylation analysis identified two hypomethylated regions located in the mid- Karma region of the high-mantling clonal ortets. One of these regions is located next to the RsaI methylation feature within Karma in mantled clones. This is the first report of such an event in oil palm clonal propagation, where almost all clonal ortets cloned from a seed-derived ortet produced high mantling rates in their reclones, representing a significant economic risk. The differentially methylated regions identified in this study could serve as potential methylation markers for screening high-risk clonal ortets, which merits further investigations.