Abstract
The mantled phenotype is an abnormal somaclonal variant arising from the oil palm cloning process and severe phenotypes lead to oil yield losses. Hypomethylation of the Karma retrotransposon within the B-type MADS-box EgDEF1 gene has been associated with this phenotype. While abnormal Karma-EgDEF1 hypomethylation was detected in mantled clones, we examined the methylation state of Karma in ortets that gave rise to high mantling rates in their clones. Small RNAs (sRNAs) were proposed to play a role in Karma hypomethylation as part of the RNA-directed DNA methylation process, hence differential expression analysis of sRNAs between the ortet groups was conducted. While no sRNA was differentially expressed at the Karma-EgDEF1 region, three sRNA clusters were differentially regulated in high-mantling ortets. The first two down-regulated clusters were possibly derived from long non-coding RNAs while the third up-regulated cluster was derived from the intron of a DnaJ chaperone gene. Several predicted mRNA targets for the first two sRNA clusters conversely displayed increased expression in high-mantling relative to low-mantling ortets. These predicted mRNA targets may be associated with defense or pathogenesis response. In addition, several differentially methylated regions (DMRs) were identified in Karma and its surrounding regions, mainly comprising subtle CHH hypomethylation in high-mantling ortets. Four of the 12 DMRs were located in a region corresponding to hypomethylated areas at the 3′end of Karma previously reported in mantled clones. Further investigations on these sRNAs and DMRs may indicate the predisposition of certain ortets towards mantled somaclonal variation.
Key message
Small RNA clusters derived from lncRNAs were differentially expressed in high mantling ortets, and hypomethylation of the 3′-end of Karma-EgDEF1 corresponded to previously identified hypomethylated regions in mantled clones.
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Data availability
The small RNA, 3′mRNA and BisPCR2sequencing data for this study have been deposited into NCBI database and is available via BioProject ID PRJNA837636, BioSample Accessions SAMN28226857-28226871.
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Acknowledgements
We thank the Director-General of the Malaysian Palm Oil Board for permission to publish this study. We also appreciate Professor Dr. Nathan Springer, University of Minnesota, USA, for his advice throughout this study. We are grateful to the head of ABBC, Dr. Mohamad Arif Abd Manaf, for his support, the staff from FGVR&D, and the Breeding & Tissue Culture Unit, MPOB, and our intern Sim Jie Ern, for their technical assistance.
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This study was supported by the Malaysian Palm Oil Board Internal Research funds.
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S-EO and MO-A conceived and designed the research. SHR, MNB and ARSR selected the samples and conducted sampling. IF and AN conducted the experiments. O-KT optimized the stem-loop qPCR procedure. S-EO, NS, ET, NJ and TT analyzed the data. S-EO drafted the manuscript and all authors commented and improved on previous versions of the manuscript. All authors read and approved the final manuscript.
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Ooi, SE., Sarpan, N., Taranenko, E. et al. Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling. Plant Mol Biol 111, 345–363 (2023). https://doi.org/10.1007/s11103-022-01330-4
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DOI: https://doi.org/10.1007/s11103-022-01330-4