Introductory Chapter: Inevitable Cytogenetic, Genetic, and Epigenetic Changes Contributing to Phenotypic Plasticity for Plant Defence Mechanisms in Dynamic Environmental Conditions

1. Introduction

Plants are currently encountering many changes in the environment, which are being brought about by human activities due to increasing population demands and land fragmentations. Studies show that over 50% of the regions on the earth are expected to suffer from water scarcity by 2050 [1, 2]. These activities include pollutions, increase in temperature, lack of pollinators and dispersal mechanisms. The observed morphological changes in plants are due to changes in gene expressions [3]. These gene expression changes do not involve permanent changes in the DNA sequences; otherwise, the species would either become extinct or modified to be another. However, these changes have been identified in the functional genomics and names as mainly epigenetic. Epigenetic variations can be used to indicate the degree of plant responses due to environmental stresses. Plant adaptations in stress conditions can be induced by long-term or short-term stress exposures [4]. In stressful conditions, plants use three main strategies to survive. They either tolerate, resist, or escape but also employ stress recovery mechanisms after the stress challenging environmental conditions [5, 6, 7].

Climate change coupled with other environmental pressures is making the rate of formation of new plant gene combinations to seem quite slow compared with the occurrence of the environmental pressures [8]. Plants employ processes such as stress avoidance via regulating characteristics such as leaf structure, root growth, flowering patterns, seed development, so as to optimize prevailing morphological and physiological processes.

2. The relationship between environmental stress and epigenetic variability

Plants have to endure adverse environmental conditions at all times. This is because plants are sessile and do not physically escape stresses by changing locations. Plants defend themselves by employing epigenetic mechanisms [9]. Experiments have been done using plants of similar genetic compositions, which have grown in varied environmental conditions. For example, dandelion plants were grown in conditions of high salinity, low nutrients, and pathogenic induced by jasmonic acid or salicylic acid showed DNA methylation polymorphisms [10]. To confirm the results, the experimental control plants showed less epigenetic variations. Thus, epigenetic changes are important abiotic plant defense biomarkers in plant defense. Plants employ various mechanisms to sense environmental changes and then initiate epigenetic gene expression responses to enable adjustments in such situations [11]. More research should be done because, to date, only one transgenic maize cultivar has been commercialized among so many crop plants [6, 12].

3. The relationship between plant metabolism and epigenetic variability

Metabolism is defined as all chemical reactions in a cell that occur to maintain life. The level of acceptable rate of metabolism is determined by the number of environmental and cellular resources available for the plant. For example, water is a major plant resource that if there is water stress, much metabolism activity is shut down. This is done mainly via cytosine DNA hypermethylation. The mechanism that most plants use to respond to water stress is the expression of the abscisic acid (ABA) genes. For example, studies using repeated dehydration steps upregulated several ABA-induced genes in the model plant Arabidopsis thaliana [13, 14], while review studies by [4], suggested that changes in DNA methylation served as regulatory mechanisms affecting gene expression responses to drought stress. Previously, transposon mobility, activation of methyltransferase, and siRNA-mediated methylation have been implicated in phenotype variation in stress conditions [15].

4. The relationship between plant microbes, pests, abiotic stresses, and epigenetic variability

Plants establish biotic relationships, which are either beneficial or harmful. The beneficial relationships include those with the bacteria Rhizobia, mycorrhiza, with insect pollinators and seed dispersers. The harmful relationships involve viral, fungal, protozoan, bacterial pathogens and other competitors [16]. Thus, studies show that infection of plants by RNA viruses triggers epigenetic changes. For example, plants have been observed to recognize inserted viral double-strand RNA molecules and then inducing DCL2 and DCL4 for their degradation into siRNAs [17]. Other complex mechanisms to deal with single-stranded RNA (ssRNA) have also been observed. In this process, the genomes of ssRNA viruses are first converted into dsRNA molecules by RNA-dependent RNA polymerases and then the DCL family endoribonucleases act on the dsRNA,

Studies in Arabidopsis showed that an infection by a bacterial pathogen such as Pseudomonas syringae pv. tomato (Pst) elicited a defense response in plants that was suppressed by bacterial virulence factors. The data showed that cytosine DNA methylation pattern changes of some genes are associated with plant defense mechanisms. For example, de novo methylation can occur in a process where previously unmethylated DNA cytosine residues are methylated. This leads to new DNA methylation patterns being formed [18]. Other DNA expression related modifications include acetylation, phosphorylation, biotinylation, sumoylation, and ubiquitination at specific amino acid residues [19]. Furthermore, epigenetic changes were related to transcriptional changes of defense-related root genes [20, 21, 22].

Plants trigger gene expressions to survive all kinds of biotic and abiotic stresses. However, if the stress occurs in a short term, the plant can trigger rapid epigenetic changes to survive. Cassava plants have been observed to rapidly produce hydrogen cyanide (HCN) in case of biotic environmental disturbance and also could mistake a long-term abiotic stress and continually produce HCN to defend itself [23, 24]. Plants such as Arabidopsis when subjected to several cycles of water stress were found to spring back to normal metabolism faster than plants that experienced the water stress for the first time [25]. This is because even the mechanisms employed by plants to overcome various kinds of stresses are metabolically expensive and can drain plant resources. Plants transmit the epigenetic changes to the next generation in a phenomenon called transgenerational inheritable epigenetic changes or epimutations [25, 26, 27]. Extremes of most essential substances for plant growth and development can trigger extensive DNA methylations. For example, water stress can interfere with almost all metabolic processes, and if not checked, the plant can die. Furthermore, studies have shown essential trace elements such as Cu²⁺ and Cr³⁺ caused gross changes in DNA methylation only at high concentrations. Studies on Laguncularia racemosa showed that same plant species can be in different environmental conditions and be genetically similar but be varied epigenetically [28]. The mechanisms underlying these epigenetic changes remain largely unknown.

Other questions that linger are, for example, if plant epigenetic plasticity could be the cause invasive plants to be established in new habitats or it is new habitats that caused epigenetic variability? [4, 29]. More information is still needed in deciphering the significance of epigenetic mechanisms in influencing activities of specific plant growth regulators (PGRs) in the regulation of plant drought resistance and plant-microbiome interactions [6]. Studies have already been done on various tolerance-enhancing PGRs such as agonists, polyamines, antioxidants, and osmoprotectants [30, 31, 32] while further studies on the model grass Brachypodium distachyon gave more light on the genetic, epigenetic, and cytogenetic polymorphism mechanisms in plants. This is because the plant has a small genome and has fully been sequenced. It has a fast growth and is also almost cosmopolitan. This makes it to portray a great deal of observable phenotypic plasticity [33]. Statistical modeling can be used to establish the relationship between genetic distance and epigenetic variability or phenotypic variance and additive genetic effects [4].

5. Conclusions and prospects

Recent studies have confirmed the perceived relationship between epigenetic variations and environmental adaptations. The phenomenon of phenotypic plasticity as guided by varied epigenetic expressions enables plants to survive in changing environments while maintaining DNA sequence integrity. An understanding of the correction between genetic distances, epigenetic variations, heritability, and stability in the face of climate change in future might be used as a measure of selectable features in environmentally induced adaptations (Figure 1). Plant stress driven changes can be either temporal or permanent and stable. These are carried to the next generations and make the plant adaptable to future higher levels of stresses [34].

Figure 1.

The impact on the plant cells, genetic and epigenetic constitution by various intensity levels and durations of biotic and abiotic environmental stresses. The short-term effects are mainly for survival strategies while the long-term effects drive a plant into dimensions of adaptive speciation. Most epigenetic changes occur more in short durations and are highly reversible unlike long-term genetic and mutational changes. However, epigenetic changes can be assimilated into phenotypes in long-term evolutionally durations.

Epigenetic changes can be observed in same species in different habitats and can provide raw materials for natural selection in climate change induced stresses. For example, changes in DNA methylation patterns were correlated to morphological modifications abundance of trichomes and spines in plants [35], modified leaf palatability [10], and later long-term differential vegetation browsing was observed [36]. This is because environmental stresses have been known to alter growth and productivity of even agricultural crop plants [15]. These epigenetic variations occur rapidly and can be used to predict the long-term effect of similar environmental stresses or hazards including heavy metals, air pollution, electromagnetic radiations, and high temperatures.

Epigenetic changes can affect genetic processes including DNA replication, DNA repair, transcription, transposon stability, and even cell differentiation [37]. These predictions can be simulated and studied in controlled laboratory environments, for example, recent analysis of plant mutations showed that epigenome-associated mutation bias could contribute to environmental effects on mutation [38, 39]. Studies in cosmopolitan plants can give an idea of the particular key mechanisms, which make them to survive and thrive in diverse environmental conditions. Species such as grasses can survive extreme temperature by shutting down entire metabolism and seem as if they are dead. They, however, rejuvenate rapidly at the onset of favorable conditions. The seeds of such plants can serve as study materials for such studies. They actually make all their processes to be in dormant state in adverse conditions.

Recent studies on plant microbiome show interactions that have symbiotic relationship, which reduce plant stress signaling [40]. Another epigenetic plant molecule of interest in abiotic stress that has been given recent attention is melatonin. The exogenous application of melatonin influences both physiological and molecular activities in a plant [41, 42, 43, 44]. Furthermore, chitosan has been found to have multifaceted effects in various plant crops such as maize, sun flower, and potato in adjusting in abiotic stresses and improving on crop productivity. Studies in the correlations between epigenetics and biotic interactions also are addressing morphological plasticity to identify epigenome markers to improve crop productivity [45]. The molecular basis of such effects is still yet to be fully understood [46, 47], although recent bioengineering predicts possibilities of more precision genome editing using the CRISPRCas9 system application in the generation of alleles to improve plant yields under various abiotic stresses [2]. This is future, which was predicted by [48].