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

Ong-Abdullah, Meilina; Ordway, Jared M.; Jiang, Nan; Ooi, Siew-Eng; Kok, Sau-Yee; Sarpan, Norashikin; Azimi, Nuraziyan; Hashim, Ahmad Tarmizi; Ishak, Zamzuri; Rosli, Samsul Kamal; Malike, Fadila Ahmad; Bakar, Nor Azwani Abu; Marjuni, Marhalil; Abdullah, Norziha; Yaakub, Zulkifli; Amiruddin, Mohd Din; Nookiah, Rajanaidu; Singh, Rajinder; Low, Eng-Ti Leslie; Chan, Kuang-Lim; Azizi, Norazah; Smith, Steven W.; Bacher, Blaire; Budiman, Muhammad A.; Van Brunt, Andrew; Wischmeyer, Corey; Beil, Melissa; Hogan, Michael; Lakey, Nathan; Lim, Chin-Ching; Arulandoo, Xaviar; Wong, Choo-Kien; Choo, Chin-Nee; Wong, Wei-Chee; Kwan, Yen-Yen; Alwee, Sharifah Shahrul Rabiah Syed; Sambanthamurthi, Ravigadevi; Martienssen, Robert A.

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

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, 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, Steven W. Smith, Blaire Bacher, Muhammad A. Budiman, Andrew Van Brunt, Corey Wischmeyer, Melissa Beil, Michael Hogan, Nathan Lakey, Chin-Ching Lim, Xaviar Arulandoo, Choo-Kien Wong, Chin-Nee Choo, Wei-Chee Wong, Yen-Yen Kwan, Sharifah Shahrul Rabiah Syed Alwee, Ravigadevi Sambanthamurthi () and Robert A. Martienssen ()
Additional contact information
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
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

Nature, 2015, vol. 525, issue 7570, 533-537

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.

Date: 2015
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DOI: 10.1038/nature15365

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