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

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 modifi...

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Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857894/
https://www.ncbi.nlm.nih.gov/pubmed/26352475
http://dx.doi.org/10.1038/nature15365
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author 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.
author_facet 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.
author_sort Ong-Abdullah, Meilina
collection PubMed
description 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 mystery(1). 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 production(2–4). Widely regarded as epigenetic(5), 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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spelling pubmed-48578942016-05-05 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. Nature Article 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 mystery(1). 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 production(2–4). Widely regarded as epigenetic(5), 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. 2015-09-09 2015-09-24 /pmc/articles/PMC4857894/ /pubmed/26352475 http://dx.doi.org/10.1038/nature15365 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
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
title Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
title_full Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
title_fullStr Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
title_full_unstemmed Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
title_short Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
title_sort loss of karma transposon methylation underlies the mantled somaclonal variant of oil palm
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4857894/
https://www.ncbi.nlm.nih.gov/pubmed/26352475
http://dx.doi.org/10.1038/nature15365
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