Abstract

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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Accessions

Primary accessions

GenBank/EMBL/DDBJ

Gene Expression Omnibus

Data deposits

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 SAMN03569290SAMN03569351. Whole-genome bisulfite sequence data have been deposited in the NCBI SRA under accession numbers SAMN03569063SAMN03569077. The cDNA sequence of the kDEF1 transcript has been deposited in GenBank under accession number KR347486.

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Acknowledgements

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.

Author information

Author notes

    • Michael Hogan

    Present address: Thermo Fisher Scientific, 110 Miller Avenue, Ann Arbor, Michigan 48104, USA.

Affiliations

  1. Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia

    • Meilina Ong-Abdullah
    • , Siew-Eng Ooi
    • , Sau-Yee Kok
    • , Norashikin Sarpan
    • , Nuraziyan Azimi
    • , Ahmad Tarmizi Hashim
    • , Zamzuri Ishak
    • , Samsul Kamal Rosli
    • , Fadila Ahmad Malike
    • , Nor Azwani Abu Bakar
    • , Marhalil Marjuni
    • , Norziha Abdullah
    • , Zulkifli Yaakub
    • , Mohd Din Amiruddin
    • , Rajanaidu Nookiah
    • , Rajinder Singh
    • , Eng-Ti Leslie Low
    • , Kuang-Lim Chan
    • , Norazah Azizi
    •  & Ravigadevi Sambanthamurthi
  2. Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA

    • Jared M. Ordway
    • , Nan Jiang
    • , Steven W. Smith
    • , Blaire Bacher
    • , Muhammad A. Budiman
    • , Andrew Van Brunt
    • , Corey Wischmeyer
    • , Melissa Beil
    • , Michael Hogan
    •  & Nathan Lakey
  3. United Plantations Berhad, Jendarata Estate, 36009 Teluk Intan, Perak, Malaysia

    • Chin-Ching Lim
    •  & Xaviar Arulandoo
  4. Applied Agricultural Resources Sdn Bhd, No. 11, Jalan Teknologi 3/6, Taman Sains Selangor 1, 47810 Kota Damansara, Petaling Jaya, Selangor, Malaysia

    • Choo-Kien Wong
    • , Chin-Nee Choo
    •  & Wei-Chee Wong
  5. FELDA Global Ventures R&D Sdn Bhd, c/o FELDA Biotechnology Centre, PT 23417, Lengkuk Teknologi, 71760 Bandar Enstek, Negeri Sembilan, Malaysia

    • Yen-Yen Kwan
    •  & Sharifah Shahrul Rabiah Syed Alwee
  6. Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA

    • Robert A. Martienssen

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Contributions

M.O.-A. led the work on the MANTLED marker/gene. M.O.-A., R.Si., E.-T.L.L. and R.Sa. conceptualized the research programme. M.O.-A., R.Si., E.-T.L.L., R.N., N.L., S.W.S., J.M.O., R.Sa. and R.A.M. developed the overall strategy, designed experiments and coordinated the project. A.T.H., Z.I. and S.K.R. performed tissue culture on selected ortets and field-planted the ramets. Field data collection and fruit bunch census were conducted at various research stations by F.A.M., N.A.A.B., M.M., N.A., Z.Y. and M.D.A. M.O.-A., C.-C.L., X.A., C.-N.C., W.-C.W., S.S.R.S.A. and Y.-Y.K. identified samples for discovery and validation panels. M.O.-A., C.-C.L. and X.A. identified materials used in the mosaic experiments. M.O.-A., S.-E.O., S.-Y.K., N.S. and N.A. conducted laboratory experiments, histological staging of inflorescences and data analyses. N.J. and S.W.S performed microarray analyses. B.B. and M.A.B. prepared fractions for microarray hybridizations. B.B. designed and analysed qPCR experiments. B.B. and M.B. performed qPCR assays. A.V.B. designed and analysed clone-based bisulfite sequencing experiments, and A.V.B. and M.B. performed bisulfite sequencing assays. M.B. designed and performed qRT–PCR experiments. C.W. and J.M.O. analysed transcriptome data. K.-L.C., N.A., S.W.S., M.H., C.W. and A.V.B. provided bioinformatics support. M.O.-A., R.Si., E.-T.L.L., R.N., N.L., S.W.S., J.M.O., R.Sa. and R.A.M. prepared and revised the manuscript.

Competing interests

R.A.M. is a former consultant of Orion Genomics, LLC.

Corresponding authors

Correspondence to Ravigadevi Sambanthamurthi or Robert A. Martienssen.

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https://doi.org/10.1038/nature15365

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