An Epigenetic Alphabet of Crop Adaptation to Climate Change

Abstract

Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the "epigenetic alphabet" that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.

Keywords: abiotic stresses; adaptation; climate change; environmental stresses; epigenetic code; epigenetics.

FIGURE 1

Deciphering the alphabet of epigenetic responses to the environmental stresses in plants. Different types of epigenetic modifications in response to different abiotic and biotic stresses. A-O—Histone modifications; P-R—Cytosine methylation; S—Adenine methylation.

FIGURE 2

Roles of DNA-methylation in environmental stress responses and memories in plants. Changes in DNA-methylation landscape are part of the response of plants to environmental stresses. De novo methylation, which is targeted at specific loci by small-RNAs, is established by the RNA-dependent-DNA-Methylation pathway (RdDM) whereas, DNA demethylation at specific loci requires functional DNA Glycosylase Lyase also called DNA demethylase such as Repressor of Silencing 1 (ROS1). Modification of DNA methylation patterns at genes may result in changes in gene expression level leading to gene induction or repression. In addition, stress induced DNA methylation variations may occur at transposable elements (TEs) and determine their inactive or active state. When hypomethylated and transcriptionally active, TEs may indirectly influence the expression of genes located in their vicinity, whereas their hypermethylation has the reverse effect. Additionally, the mobility of TEs may generate new regulatory patterns or mutations leading to loss of gene function when their insertion occurs in genes. Maintenance of stress induced patterns of DNA methylation through cell division (Mitosis or meiosis), results in an epigenetic memory. This memory requires the context-specific DNA-methyltransferases METHYLTRANSFERASE-1 (MET1), CHROMOMETHYLASE-3 (CMT3) for CG and CHG sequence context, respectively. Methylation in the CHH sequence context is maintained by CMT2 or by the RdDM pathway in heterochromatic and euchromatic regions, respectively.

FIGURE 3

Histone modifications in response to environmental stresses. HAT, histone acetyltransferase; HDA, histone deacetylase; HMT, histone methyltransferase; ROS, reactive oxygen species; ABA, abscisic acid.

FIGURE 4

Epigenetic mechanisms involved in plant response to stress. Histone modifications (A) include acetylation/deacetyaltion and methylation/demethylation, while DNA methylation (B) includes cytosine methylation and adenine methylation processes.