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Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

Author

Listed:
  • Meilina Ong-Abdullah

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Jared M. Ordway

    (Orion Genomics)

  • Nan Jiang

    (Orion Genomics)

  • Siew-Eng Ooi

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Sau-Yee Kok

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Norashikin Sarpan

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Nuraziyan Azimi

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Ahmad Tarmizi Hashim

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Zamzuri Ishak

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Samsul Kamal Rosli

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Fadila Ahmad Malike

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Nor Azwani Abu Bakar

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Marhalil Marjuni

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Norziha Abdullah

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Zulkifli Yaakub

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Mohd Din Amiruddin

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Rajanaidu Nookiah

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Rajinder Singh

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Eng-Ti Leslie Low

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Kuang-Lim Chan

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Norazah Azizi

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Steven W. Smith

    (Orion Genomics)

  • Blaire Bacher

    (Orion Genomics)

  • Muhammad A. Budiman

    (Orion Genomics)

  • Andrew Van Brunt

    (Orion Genomics)

  • Corey Wischmeyer

    (Orion Genomics)

  • Melissa Beil

    (Orion Genomics)

  • Michael Hogan

    (Orion Genomics
    †Present address: Thermo Fisher Scientific, 110 Miller Avenue, Ann Arbor, Michigan 48104, USA.)

  • Nathan Lakey

    (Orion Genomics)

  • Chin-Ching Lim

    (United Plantations Berhad, Jendarata Estate, 36009 Teluk Intan, Perak, Malaysia)

  • Xaviar Arulandoo

    (United Plantations Berhad, Jendarata Estate, 36009 Teluk Intan, Perak, Malaysia)

  • Choo-Kien Wong

    (Applied Agricultural Resources Sdn Bhd, No. 11, Jalan Teknologi 3/6, Taman Sains Selangor 1, 47810 Kota Damansara, Petaling Jaya, Selangor, Malaysia)

  • Chin-Nee Choo

    (Applied Agricultural Resources Sdn Bhd, No. 11, Jalan Teknologi 3/6, Taman Sains Selangor 1, 47810 Kota Damansara, Petaling Jaya, Selangor, Malaysia)

  • Wei-Chee Wong

    (Applied Agricultural Resources Sdn Bhd, No. 11, Jalan Teknologi 3/6, Taman Sains Selangor 1, 47810 Kota Damansara, Petaling Jaya, Selangor, Malaysia)

  • Yen-Yen Kwan

    (FELDA Global Ventures R&D Sdn Bhd, c/o FELDA Biotechnology Centre, PT 23417, Lengkuk Teknologi, 71760 Bandar Enstek, Negeri Sembilan, Malaysia)

  • Sharifah Shahrul Rabiah Syed Alwee

    (FELDA Global Ventures R&D Sdn Bhd, c/o FELDA Biotechnology Centre, PT 23417, Lengkuk Teknologi, 71760 Bandar Enstek, Negeri Sembilan, Malaysia)

  • Ravigadevi Sambanthamurthi

    (Malaysian Palm Oil Board, 6, Persiaran Institusi)

  • Robert A. Martienssen

    (Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory)

Abstract

The oil palm fruit ‘mantled’ abnormality is a somaclonal variant that markedly reduces yield; here, a genome-wide DNA methylation analysis finds that hypomethylation of a single Karma family retrotransposon embedded in a homeotic gene intron is common to all mantled clones and is associated with aberrant splicing and termination of the gene transcript, and that loss of methylation predicts a loss of oil palm yield.

Suggested Citation

  • Meilina Ong-Abdullah & Jared M. Ordway & Nan Jiang & Siew-Eng Ooi & Sau-Yee Kok & Norashikin Sarpan & Nuraziyan Azimi & Ahmad Tarmizi Hashim & Zamzuri Ishak & Samsul Kamal Rosli & Fadila Ahmad Malike , 2015. "Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm," Nature, Nature, vol. 525(7570), pages 533-537, September.
    • Handle: RePEc:nat:nature:v:525:y:2015:i:7570:d:10.1038_nature15365
    DOI: 10.1038/nature15365
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    Cited by:

    1. Jie Liu & Xuehua Zhong, 2024. "Epiallelic variation of non-coding RNA genes and their phenotypic consequences," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Yi-Wen Lim & Ben N. Mansfeld & Pascal Schläpfer & Kerrigan B. Gilbert & Narayanan N. Narayanan & Weihong Qi & Qi Wang & Zhenhui Zhong & Adam Boyher & Jackson Gehan & Getu Beyene & Zuh-Jyh Daniel Lin &, 2022. "Mutations in DNA polymerase δ subunit 1 co-segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. Yinwen Zhang & Hosung Jang & Rui Xiao & Ioanna Kakoulidou & Robert S. Piecyk & Frank Johannes & Robert J. Schmitz, 2021. "Heterochromatin is a quantitative trait associated with spontaneous epiallele formation," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    4. Xiaohe Lin & Junjie Yin & Yifan Wang & Jing Yao & Qingshun Q. Li & Vit Latzel & Oliver Bossdorf & Yuan-Ye Zhang, 2024. "Environment-induced heritable variations are common in Arabidopsis thaliana," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Najihah Ahmad Latif & Fatini Nadhirah Mohd Nain & Nurul Hashimah Ahamed Hassain Malim & Rosni Abdullah & Muhammad Farid Abdul Rahim & Mohd Nasruddin Mohamad & Nurul Syafika Mohamad Fauzi, 2021. "Predicting Heritability of Oil Palm Breeding Using Phenotypic Traits and Machine Learning," Sustainability, MDPI, vol. 13(22), pages 1-24, November.

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