The implementation of in vitro tissue culture propagation methods, such as somatic embryogenesis (SE), rely on the amenability of plant cells to undergoing induced reprogrammation (de-differentiation followed by re-differentiation) after treatment by growth regulators. It has been well documented in various species that these processes involve epigenetic regulation pathways that are similar to those associated with responses to abiotic stresses, which makes in vitro-derived material a great system for studying them within (theoretically) genetically homogeneous populations. Originally, our work on SE-derived oil palms stems from the practical necessity of understanding and preventing the emergence of a pervasive somaclonal variation (the mantled floral phenotype) with negative impact on oil production. In doing so, we also aim to leverage the knowledge acquired from this case study to address broader scientific questions related to stress memory and acclimation in perennial species. With this dual objective in mind, we are currently assessing the expression of small non-coding RNAs (sncRNAs) in embryogenic suspensions and their possible roles in the regulation of genome expression and structure. We are using high-throughput transcriptome, small RNAome and degradome datasets to identify both source and target sequences of sncRNA-mediated regulations, and annotate the biological pathways that are affected by these regulations. As our analyses are still under way, we will present a global outline of our project and report on both our progress and a few lessons learned.