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 the micropropagation of elite hybrids and genetically modified crops, but the mechanism responsible remains unknown. 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 production. Widely regarded as an epigenetic phenomenon, '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.
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Meilina
M
Ong-Abdullah
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Jared M
JM
Ordway
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Nan
N
Jiang
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Siew-Eng
SE
Ooi
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Sau-Yee
SY
Kok
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Norashikin
N
Sarpan
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Nuraziyan
N
Azimi
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Ahmad Tarmizi
AT
Hashim
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Zamzuri
Z
Ishak
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Samsul Kamal
SK
Rosli
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Fadila Ahmad
FA
Malike
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Nor Azwani Abu
NA
Bakar
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Marhalil
M
Marjuni
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Norziha
N
Abdullah
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Zulkifli
Z
Yaakub
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Mohd Din
MD
Amiruddin
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Rajanaidu
R
Nookiah
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Rajinder
R
Singh
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Eng-Ti Leslie
ET
Low
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Kuang-Lim
KL
Chan
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Norazah
N
Azizi
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Steven W
SW
Smith
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Blaire
B
Bacher
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Muhammad A
MA
Budiman
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Andrew
A
Van Brunt
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Corey
C
Wischmeyer
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Melissa
M
Beil
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Michael
M
Hogan
Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA.
Nathan
N
Lakey
United Plantations Berhad, Jendarata Estate, 36009 Teluk Intan, Perak, Malaysia.
Chin-Ching
CC
Lim
United Plantations Berhad, Jendarata Estate, 36009 Teluk Intan, Perak, Malaysia.
Xaviar
X
Arulandoo
Applied Agricultural Resources Sdn Bhd, No. 11, Jalan Teknologi 3/6, Taman Sains Selangor 1, 47810 Kota Damansara, Petaling Jaya, Selangor, Malaysia.
Choo-Kien
CK
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
CN
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
WC
Wong
FELDA Global Ventures R&D Sdn Bhd, c/o FELDA Biotechnology Centre, PT 23417, Lengkuk Teknologi, 71760 Bandar Enstek, Negeri Sembilan, Malaysia.
Yen-Yen
YY
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
SS
Alwee
Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
Ravigadevi
R
Sambanthamurthi
Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Robert A
RA
Martienssen
D000483:Alleles; D017398:Alternative Splicing / Q000235:genetics; D028023:Arecaceae / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic / Q000235:genetics*; D057890:Epigenomics; D005638:Fruit / Q000235:genetics; D005801:Genes, Homeobox / Q000235:genetics; D056726:Genetic Association Studies; D018745:Genome, Plant / Q000235:genetics*; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D000073878:Palm Oil; D010641:Phenotype; D010938:Plant Oils / Q000032:analysis / Q000378:metabolism; D022821:RNA Splice Sites / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D018626:Retroelements / Q000235:genetics*
D010938:Plant Oils; D022821:RNA Splice Sites; D034741:RNA, Small Interfering; D018626:Retroelements; D000073878:Palm Oil