DNA methylation changes in clonally propagated oil palm

Abstract

Key message

Several hypomethylated sites within the Karma region of EgDEF1 and hotspot regions in chromosomes 1, 2, 3, and 5 may be associated with mantling.

Abstract

One of the main challenges faced by the oil palm industry is fruit abnormalities, such as the “mantled” phenotype that can lead to reduced yields. This clonal abnormality is an epigenetic phenomenon and has been linked to the hypomethylation of a transposable element within the EgDEF1 gene. To understand the epigenome changes in clones, methylomes of clonal oil palms were compared to methylomes of seedling-derived oil palms. Whole-genome bisulfite sequencing data from seedlings, normal, and mantled clones were analyzed to determine and compare the context-specific DNA methylomes. In seedlings, coding and regulatory regions are generally hypomethylated while introns and repeats are extensively methylated. Genes with a low number of guanines and cytosines in the third position of codons (GC3-poor genes) were increasingly methylated towards their 3′ region, while GC3-rich genes remain demethylated, similar to patterns in other eukaryotic species. Predicted promoter regions were generally hypomethylated in seedlings. In clones, CG, CHG, and CHH methylation levels generally decreased in functionally important regions, such as promoters, 5′ UTRs, and coding regions. Although random regions were found to be hypomethylated in clonal genomes, hypomethylation of certain hotspot regions may be associated with the clonal mantling phenotype. Our findings, therefore, suggest other hypomethylated CHG sites within the Karma of EgDEF1 and hypomethylated hotspot regions in chromosomes 1, 2, 3 and 5, are associated with mantling.

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Abbreviations

WGBS:

Whole-genome bisulfite sequencing

TFBS:

Transcription factor binding site

TE:

Transposable element

mCG:

Methylation at CG context

mCHG:

Methylation at CHG context

mCHH:

Methylation at CHH context

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Acknowledgements

We would like to thank the Director-General of MPOB for permission to publish this study. Our appreciation goes to the Bioinformatics Unit, Breeding and Tissue Culture Unit of MPOB, especially Epigenetics Group and MPOB Bagan Datuk Research Station, Malaysia for their technical support throughout this study. We thank the University of La Verne for the support of this international collaboration.

Funding

The research was supported by the MPOB.

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Authors

Contributions

S-EO and NS performed the experiment, TT, AE, and ET analyzed the data, NS, S-EO, TT, E-TLL, and MO-A interpreted the findings. TT, E-TLL, and MO-A supervised the work. All authors participated in the preparation of the manuscript.

Corresponding authors

Correspondence to Tatiana V. Tatarinova or Meilina Ong-Abdullah.

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All authors agreed to the publication and approved the final version.

Availability of data and material

The central oil palm database is https://palmxplore.mpob.gov.my/palmXplore/. Whole-genome bisulfite sequence data can be assessed in the NCBI SRA under accession numbers SAMN03569063—SAMN03569077. The cDNA sequence of the kDEF1 transcript is available in GenBank under accession number KR347486. RNA-sequencing data can be accessed under GEO Accession No. GSE144079.

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Sarpan, N., Taranenko, E., Ooi, S. et al. DNA methylation changes in clonally propagated oil palm. Plant Cell Rep (2020). https://doi.org/10.1007/s00299-020-02561-9

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Keywords

  • Mantling
  • Epigenetics
  • Whole-genome bisulfite sequencing
  • Karma