Elaeis guineensis cultivar:Jacq.

The oil palm fruit abnormality, mantled, is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for breeding and oil production. Widely regarded as epigenetic, mantling has defied explanation, and has become an icon of unsustainability in environmentally sensitive tropical plantation crops. We identified the MANTLED gene using Epigenome Wide Association analysis of genetically identical palms from multiple clonal lineages. Hypomethylation of a LINE retrotransposon related to rice Karma, found in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is correlated with alternative splicing and loss of small RNA. DNA methylation is regained in spontaneous revertants accounting for non-Mendelian inheritance of the Good Karma and Bad Karma epialleles. Thus epigenetic regulation of transposable elements results in somaclonal variation, and provides a means to cull mantled nursery palms before committing limiting plantation resources to clonal propagation.