Future directions

Gaps in current method and empirical knowledge: the transition from model to non-model plants

Deciphering the role of epigenetics for plant stress response has started with model species and only recently included species with different life-history. This is a challenging step that requires continuous improvement of molecular tools and collaboration among molecular geneticists, ecologists, and bioinformaticians. Experimental studies in plants with distinctive genomic and ecological features could contribute to understanding epigenetic responses to stress in terms of molecular and phenotypic changes. We need to extend the study by associating the role of stress-relevant features towards the stability of epigenetic marks for both priming and transgenerational defense using suitable tools. In order to get an approximate overview, I screened the literature studies for epigenetic contribution for explaining biotic and abiotic stress response of plants without attempting to cover all literature available. In ISI Web of Science (www.webofknowledge.com), I conducted a search for the articles published in English between 1990 and 2020 (last accessed 17th January 2020) using the following keywords combination [(plant stress) AND (epigenet*)] that gave us 1281 results on abiotic and biotic stress studies. Adding the keyword [AND (abiotic)/ AND (biotic)], the search retained 377 abiotic studies and 164 biotic studies, respectively, that also contained the keyword epigenetics, which does not mean that these studies identified correlating or causative epigenetic mechanisms for plant defense. Although the numbers of studies are increasing for the two types of stress events, there is also huge inadequacy of these studies with non-model plants due to several experimental shortcomings. In the following, I outline the most important gaps which are still understudied and where we still need to establish the proper relation of epigenetic contribution to plant defense strategies.

Representation of plant species:

First and foremost, the representation of diverse plant species in epigenetic studies of plant stress responses is important as most of the existing knowledge is based on studies conducted using model systems or cultivated plants that tend to be plants with a fast life-cycle. To gain generality in ecological settings, we need to study more non-model species with different life histories that can explain the phenotypic consequences and the epigenetic contribution to different stress responses.

Porper toolkit & statistical relevance:

The most studied epigenetic mechanism in plants is DNA methylation, though others like SmallRNA and histones are increasing in frequency. However, while for DNA methylation, reduced representation methods like provide the means to conduct large-scale ecological studies, such methods are mostly non-existent in other epigenetic contexts. This makes it often difficult to study more than DNA methylation in such projects or in plants with large and polyploid genomes.

Distinguish genetic and epigenetic contribution

A prevailing gap includes the lack of measures to untangle genetic and epigenetic contribution as ecological studies are often focused on collections from natural populations in situ. Ecological relationships should be evaluated across environmental gradients to gain an overview of the stress response, paired with an analysis of spatial genetic and epigenetic structure in the wild populations to understand the respective contribution (Herrera, Medrano, et al. 2012).

Understanding the cross-talk of epigentic regulators:

The link between epigenetic regulators (e.g., DNA methylation, histone modifications, and small RNAs) is often missing in current projects. However, it is often indispensable to understand the mechanisms of both the biotic and the abiotic stress response. This is because the cross-talks between epigenetic regulators themselves may have a role in gene expression (Grativol et al. 2012). More synthesis studies are needed to connect the dots in plant stress response by understanding the cross-talk of significant epigenetic regulators.