Somaclonal variation arises in plants and animals when differentiated somatic cells are induced into a pluripotent state, but the resulting clones differ from each other and from their parents. In agriculture, somaclonal variation has hindered micropropagation of elite hybrids and genetically modified crops, but the mechanism remains a mystery1. 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 oil production2–4. Widely regarded as epigenetic5, mantling has defied explanation, but here we identify the MANTLED gene using Epigenome Wide Association Studies. DNA hypomethylation of a LINE retrotransposon related to rice Karma, in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is associated with alternative splicing and premature termination. Dense methylation near the Karma splice site (the Good Karma epiallele) predicts normal fruit set, while hypomethylation (the Bad Karma epiallele) predicts homeotic transformation, parthenocarpy and dramatic loss of yield. Loss of Karma methylation and small RNA in tissue culture contributes to the origin of mantled, while restoration in spontaneous revertants accounts for non-Mendelian inheritance. The ability to predict and cull mantling at the plantlet stage will facilitate the introduction of higher performing clones and optimize environmentally sensitive land resources.

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A long-term evaluation on fourteen D x P progenies of introgressed MPOB-Nigeria dura x AVROS pisifera were laid down in a randomized complete block design in two replicates with 371 palms in 2002. The aim was to evaluate the performance of fresh fruit bunch yield, bunch quality and vegetative traits among progenies. Analysis of variance revealed highly significant difference for all traits, indicating the existence of substantial variability within these population. In all cases, the phenotypic coefficient of variance was higher than the genotypic coefficients. Broad-sense heritability values estimated ranged from 8.85% to 100% for all the traits studied. The fresh fruit bunch also was found to be positively and highly correlated with bunch number, average bunch weight, oil yield ratio and kernel yield ratio. PK 3248 and PK 3166 were preferred as potential parental lines in breeding programmes and to be included in introgression with advanced breeding populations such as Deli dura.