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 the micropropagation of elite hybrids and genetically modified crops, but the mechanism responsible remains unknown1. The oil palm fruit ‘mantled’ abnormality is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for oil production2,3,4. Widely regarded as an epigenetic phenomenon5, ‘mantling’ has defied explanation, but here we identify the MANTLED locus using epigenome-wide association studies of the African oil palm Elaeis guineensis. 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 (termed the Good Karma epiallele) predicts normal fruit set, whereas hypomethylation (the Bad Karma epiallele) predicts homeotic transformation, parthenocarpy and marked loss of yield. Loss of Karma methylation and of 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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Gene Expression Omnibus
Sequence Read Archive
Microarray data have been deposited in the NCBI Gene Expression Omnibus (GEO) and are accessible through GEO Series accession number GSE68410. Small RNA sequence data from the region of interest have been deposited in the NCBI Sequence Read Archive (SRA) database under the accession numbers SAMN03569290–SAMN03569351. Whole-genome bisulfite sequence data have been deposited in the NCBI SRA under accession numbers SAMN03569063–SAMN03569077. The cDNA sequence of the kDEF1 transcript has been deposited in GenBank under accession number KR347486.
We acknowledge the contributions of staff members of the Breeding and Tissue Culture Unit at MPOB for creating the valuable clonal lines, and for their extensive data collection and sampling efforts. We thank Genomics Unit at MPOB for conducting DNA fingerprinting to verify clonal lines. We thank The McDonnell Genome Institute at Washington University for genomic bisulfite sequencing and transcriptome sequencing support, and MOgene for microarray hybridizations. At Orion Genomics, we thank N. Sander, J. Reed, J. Brune, K. Soe, J. McDonald, C. Brown and B. Dove for technical support, and M.-F. Wu and M. Sachdeva for assistance with the manuscript and additional informatics support. We would also like to thank T. Dalmay for recommendations on sRNA library construction. We appreciate the constant support of the Director-General of MPOB, Datuk Dr. Yuen-May Choo, and the Ministry of Plantation Industries and Commodities, Malaysia.
Extended data figures
This file contains Supplementary Figure 1.