Methylation levels of a novel genetic element, EgNB3 as a candidate biomarker associated with the embryogenic competency of oil palm

Abstract

The association between DNA methylation status and embryogenic competency in oil palm tissue culture was examined through Representational Difference Analysis (RDA) approach, using methylation-sensitive restriction endonucleases. "Difference Products" (DPs) of RDA derived from palms of similar genetic backgrounds but exhibiting different embryogenesis rates during the regeneration process were isolated. The DPs were sequenced using a pyrosequencing platform. To our knowledge, this is the first study profiling partial HpaII methylation sites in oil palm young leaf tissues which are potentially associated with embryogenic amenability through a genomic subtractive approach. Quantitative real-time PCR analysis demonstrated that the methylation status of a novel fragment, EgNB3, was higher in highly embryogenic leaf explants compared to low embryogenesis rate materials. These differences are likely to be contributed by the 5′-mCCGG-3′ and/or 5′-mCmCGG-3′ methylation patterns. Our data suggest that the differentially methylated site in EgNB3 has potential as a molecular biomarker for the screening of oil palm leaf explants for their embryogenic potentials.

Progress in Tissue Culture and Genetic Transformation of Oil Palm: An Overview

“…The degree of methylation of a specific DNA sequence is directly associated with the embryogenesis rate of ex-plants obtained from ortets. Ho et al [47] assumed that this degree of methylation might be a powerful biomarker to identify and eliminate recalcitrant ortets regenerated through somatic embryogenesis. Somatic embryogenesis is a valuable and reliable tool for rapid propagation, genetic improvement, and synthetic seed production of oil palm [48].…”

Genetic diversity assessment and in vitro propagation of some date palm (Phoenix dactylifera L.) varieties

“…Several studies discussed the different methods for the assessment of the genetic variation of date palm, including proteomics (de Carvalho Silva et al, 2014;Tan et al, 2016); cytogenetics (Soliman et al, 2009); epigenetics (Ho et al, 2013); genomics (Ting et al, 2013;Tranbarger et al, 2012); and biochemical methods were used to distinguish between regenerants (Khierallah et al, 2014). Studies using peroxidase and isozyme analysis did not reveal genetic diversity among date palm varieties (Khierallah et al, 2014).…”