Epigenetics is the study of heritable changes in gene expression that happen without any change in the DNA sequence. The main epigenetic mechanisms, including DNA methylation, histone modifications, and microRNA expression, can be caused by environmental reasons. The aim of this work explains that epigenetic modifications may be due to effects of environmental stress on plant growth and productivity. The study of epigenetic-based mechanisms in the plant is an emerging field; gene expressions are modulated and reprogrammed in response to environmental stress challenges. Due to increasing global population, in the same time the availability of arable lands is decreased regularly and the severe effects of climate change problem, therefore, it is essential to understand the mechanisms that plants have progressed to adapt with varied environments stress, and in particular how plant types adapt with various kinds of biotic and abiotic stress. The main role of epigenetics study is understanding the role of the epigenetic component in regulates plant gene expression and the plant phenotype, and how the epigenome workings as a great source of diversity for main agronomical characters and on how it could use, in crop breeding and implementation programs, it would be of benefit to humanity for next era, numerous papers have studied the effects of environmental exposures and epigenetic markers that modify epigenetic states of plants and refers those epigenetic modifications may be one of the mechanisms by which abiotic stress can have positive effects on plant growth.
Keywords: Epigenetics; DNA methylation; Histone modifications; Environmental stress and Plant crops.
For different centuries, scientists has been thought that DNA was the only source to determine the productivity, infection with pathogens or other changes in plants, but lately it has been found that epigenetic changes play important role could be at the same level of DNA changes, now researchers are observing the role of environmental conditions in epigenetic modifications to know if there is a change in gene expression and phenotype due to abiotic stresses condition, Plants are considered as the masters of epigenetic regulation due to their ability of rapid and reversible modification of their epigenetic state and also preserving a stable “memory” of it, in different conditions plants are grown under harsh environmental situations which decrease the total production, and may be survival, therefore, they have advanced complicated mechanisms at molecular level to survive under critical conditions to hastily obtain and resist environmental stress during their life cycle. Different kinds of stressors can induce transient, stable, and heritable change in gene expression that occurs without changes in DNA sequences, in general, plant response to external stress mostly temporary, whereas in some instances cases they persist longer.
Epigenetics has grown promptly over the last two decades as a contemporary field of biology; epigenetics regulation is the heritable meiotic or mitotic genetic change in gene expression that happens in the absence of modifications in DNA sequences.
There are different factors like stress signals, hormones, metabolites, free radicals are affecting genes encoding various epigenetic regulators such as histone variants, chromatin remodeling factors, transcription factors or DNA and histones modifying enzymes, all of these factors cause epigenetic changes in gene expression . Environmental stress has been shown to modulate epigenetic marks; there is more attention in estimating the modifications that environmental exposures may produce on epigenetic states, and whether such changes might activate pathways leading to detrimental effects on plant growth . Epigenetic is an important attribute to clarify the unknown changes in plants, with proper expression from new transgenic segments .
Epigenetics is the level of control that sits above the genes determine which genes are turned on and which genes are turned off. From another side, epigenetics means a variety of molecular mechanisms are involved in epigenetic regulation of gene expression and chromosomal stability, including histone modifications, non-coding RNA, and DNA methylation . The term epigenetic is often used to describe a variety of unexpected patterns of gene regulation.
II. Epigenetic trait: Is a stably heritable phenotype
resulting from changes in a chromosome without alterations
in the DNA sequence .
III. Epigenetics science
It is the study of chromosome changes that change the
expression of genes without any modification in the gene
sequences or Epigenetics is the study of heritable changes in gene
expression that occur without a change in the DNA sequence.
Remarkably, different stresses conditions may be activated
and stimulus epigenetic alters and changes genic expression
level by various mechanisms like DNA methylation, histone
modifications and miRNA therefore, Epigenetics considered
the most continuously progressing branch since the past two
IV. Why we need Epigenetic in crops?
Breeding techniques over the last several centuries have
led to the loss of genes that could be helpful to plant geneticists
looking for drought, tolerant, heat, withstanding varieties that
could be valuable for agricultural climate change adaptation.
This was a genetic bottleneck and led to limited diversity .
Epigenetic research could save scientists from going into the
wild to collect seeds to reclaim lost genetic material; we now
know that many new genetically engineered plants and animals
are as safe as conventionally grown alternatives. But the path to
approval for new GMOs remains lengthy and costly.
V. What’s the role of Epigenetics in Plant Processes?
Crop agriculture has two major problems, which are the
deficiency in nutrient and in water supply, also, many crop
species are clonally propagated, but, it doesn’t take into account
the epigenome. Epigenetics may play important roles to address
these challenges through various processes like:
a. Developmental regulation.
b. Responses to environmental stimuli.
c. Local adaptation.
d. Controls the time of flowering.
VI. Epigenetic mechanisms
In last decades, it has been revealed that epigenetic
mechanisms play an important role in the response of various
plant kinds to environmental stress. DNA methylation. Plants
are known for their complex gene silencing machinery, including
cytosine methylation, histone modifications and a wide variability
of small RNAs . There are numerous epigenetic mechanisms
identified and molecular mechanisms are involved in epigenetic
regulation of gene expression and chromosomal stability,
including DNA methylation, histone modifications, chromatin
remodeling, and non-coding RNA and DNA methylation. Alters
in gene expression suggested by stress signals follow posttranslational
histone modifications, DNA methylation, histone
variant incorporation, and the action of chromatin remodeling
Plants make varied use of DNA methylation as an
epigenetic mark and undergo histone modifications to
carry out transcriptional as well as posttranscriptional
gene silencing programs. Furthermore, current research
on epigenetic mechanisms indicates that DNA methylation,
histone posttranslational modifications, and small non-coding
RNAs are intricate in almost every trait of plant life including
important traits like flowering period, fruit growth, responses
to environmental conditions, and plant resistance. Epigenetic
alterations can be inherited during mitosis and meiosis phases,
through epigenetic memory, the plants can more efficiently
respond to future stressful conditions, thereby increasing their
potential for environmental adaptation, understanding of the
epigenetic mechanisms that take part in plants’ response to
changes in environmental conditions will enhance our realization
of adaptations of plants to stress conditions . Understanding
epigenetics mechanisms may help to improve plant productivity
and enhancement breeding practices in different plant kinds,
“the presence of stress memory keeps plants prepared for
DNA methylation targets the promoter region of the genes
transcriptional silencing when methyl groups added to DNA it
stop the gene from being “seen” by form 5-methylcytosine (5-
mC), the methyl groups basically block other proteins from
binding to the promoter region due to this areas contains a
high number of C (cytosine) and G (guanine) DNA bases, the
cytosine or C residues in these areas can receive methyl groups
added to them then the gene sequence cannot be read so genes
are switched off and no transcription after methylated [11,12].
Changes in DNA methylation in response to drought stress
cause differential expression of stress-responsive genes in the
drought-tolerant variety of rice . DNA methylation is one
of the most well-known epigenetic marks, it can be found in
the coding regions of genes in many organisms, ranging from
plants to humans, it targets the promoter region of the genes;
this process is catalyzed by an enzyme known as DNA methyl
Increasing evidence has shown that DNA methylation plays a
significant role as follow:
a. It plays a very important role in several key processes
as well as genomic imprinting, X-chromosome inactivation.
b. Suppression of repetitive element transcription and
c. Most DNA methylation is essential for normal
d. Removing methyl marks, known as DNA demethylation,
is carried out by a family of enzymes called TET enzymes
Demethylation of DNA is a significant epigenetic mark for
stress-induced gene expression, the loss of methylation may
also expose new phenotypes, including traits that could be
advantageous to crop species; therefore, if we can change the
methylation, we can create heritable phenotypic variation.
During 2015 growers of the African oil palm observed that there
are about 10 to 20 percent of trees weren’t producing oil, after
research, them found that this palm suffered from the activation
of a transposon that had lost its methylation and interrupted a
gene critical for oil production [CHH methylation] is changed
inefficiently and sometimes in the wrong place .
Post-translational histone modifications of lysine residues
at the N-terminal tails of histone proteins generate different
“histone code” that determine chromatin structure during
nuclear events . There is emerging evidence explained the
role of histone modifications in transcription regulation of stressresponsive
genes in plants [17,18]. Also, histone methylation has
an active role in the regulation of plant hormone biosynthesis in
common bean .
Epigenetic markers are chemical regulate genes that sit over
the DNA sequence, it explores the consequences of thermal and
ionic variation on the behavior of plant under stress conditions,
there are different epigenetic marks like DNA cytosine
methylation and histone variants as H2A.Z. Epigenetic markers
can be move from cell to cell and from generation to generation
The epigenome contains the chemical compounds that
express DNA what to do, where to do it and when to do it, all
of which can be functions undertaken by any one of organism
cells using the same identical DNA toolkit e.g. grow leaves vs.
flowering, grow a finger vs. grow a nose, in other words, if DNA is
hardware and epigenome as the software that controls hardware.
This refers to the genes with identical nucleotide sequence
but altered expression abilities due to epigenetic events .
Recent studies on abiotic stress signaling have explained the role
of the epigenome in adaptable stress-induced gene expression,
either by modulating chromatin structure through histone
modification and/or DNA methylation or through non-coding
Epigenetic modifications are relatively stable over time and
may be influenced by the environmental conditions; therefore,
exposure to abiotic stress could lead to epigenome modifications,
nowadays, it is now known that epigenetic modifications
control gene expression by modulating the access of regulatory
complexes to the genome. The previous researches refer that
abiotic stress can have positive effects on plant growth through
epigenetic modifications, and how the epigenome workings as a
great source of diversity for main agronomical characters and on
how it could use in crop breeding and implementation programs,
up to now many genetic pathways and regulatory mechanisms
have been elucidated, The major role of epigenetics science is
regulated plant gene expression and the plant phenotype; it
would be of benefit to humanity for next era. Further studies
obviously are required for a full understanding of different
epigenetics mechanisms in plants.