Abstract
DNA methylation and histone modifications allow for distinct cell identities to emerge from the same set of genomic instructions within multicellular organisms. Though the basis of epigenetic regulation is similar for all eukaryotes, the multiple contexts in which cytosine methylation occur in plants adds to the complexity. Maintaining proper epigenetic marks is vital to appropriate plant development and survival, and crop propagation methods can disrupt these marks, leading to phenotypic alterations. A better understanding of the effects of epigenetic changes may continue to allow for further improvement, while avoiding undesirable effects, in agriculturally important species, such as oil palm.
Though it is the most consumed vegetable oil and utilizes land resources the most efficiently of all major vegetable oils, oil palm has substantial environmental and socioeconomic impacts. While breeding programs have increased oil yields, further improvements backed by better understanding the genome and epigenome can be made. Micropropagation of elite palms intended to further this goal have introduced a major negative somaclonal variant, mantling, which dramatically reduces oil yields in affected ramets. The cause of mantling was determined to be caused by disturbed cytosine methylation within Karma, a LINE retrotransposon, located within an intron of the MADS-box gene, EgDEF1. Hypomethylation induces an altered form of this transcription factor, leading to aberrant flower and fruit formation. This study investigated the Karma DMR to determine if measurements of cytosine methylation within leaf samples can accurately predict risk of mantling. The assay designed to measure cytosine methylation within the DMR can identify risk of mantling with 90% sensitivity 84% specificity. This research also gave insight into the mechanics of cytosine methylation reversion and the resulting epigenetic mosaicism in oil palm ramets.