Epigenetics and its roles in plants biotechnology

What is Epigenetics?

• Epigenetics is a process involving changes in the function and expression of the genes.
• The basis for epigenetics is changes in chromosomal structures and not the alterations in DNA sequence of the chromosomes.
• Hence, epigenetics refers to any heritable phenotypic changes.
• Over all, these are not due to genome sequence changes, such as mutations, etc.
• These changes are affected and controlled by a variety of external influences, such as environmental stresses or internal ones, such as the cell’s own innate developmental program.
• It tends to occur in all Eukaryotes.
• The study of the epigenetics of the cell helps to clarify how newly developed cells of an organism that possess identical genome or DNA sequence goes through differentiation to give various cell types and maintain a particular physiology and morphology.
• For instance, it clarifies why and how leaf epidermis cells and root cells, vary so much even if they possess same DNA sequence in their genome.
• Thus, epigenetics serves as a bridge between the phenotype and genotype of a cell.
•  Like all other eukaryotes plants also rely on the action of epigenetic regulatory mechanisms for their ability to function.
• The study of epigenetics and its benefits may allow breeders to not only recognize the nature of plants they are breeding but also to develop strategies that would inculcate desirable characteristics in their plants such as; exhibit resistance towards environmental stresses or to adapt to some particular conditions.

Modes of epigenetic variations in plants:

• There are set of mechanisms and factors responsible for regulating the process of epigenetics and are listed below.
• They affect the functioning of the genome but not of the DNA sequence.
• When these regulatory changes take place, they are often inherited from generation to generation.
  • DNA methylation
  • Histone modifications
  • RNA interference

1. DNA methylation in plants:

• DNA methylation is one of the covalent modifications found in DNA.
• In methylation, the incorporation of methyl (-CH3) groups takes place at 5C’ position of cytosine dNTP ring that yields 5 methyl-cytosine.
• The addition of methyl groups is performed by two enzymes namely methyltransferases and demethylases.
• Three types of methylations are found in plants on the basis of nature of the plant i.e. CG, CHH, CHG.
• The most common methylation is CG methylation whereas CHG methylation is the least frequent.
• The requirement of methylation of transposons sequences by plants is necessary as it might result in lethal phenotypes when not limited by methylation.
• Their exons also manifest higher level of methylation, however, promoter regions of genes exhibit less methylation and hence they are easily acted upon by transcription factors.
• This process also ensures the presence of a methylated sequence of CpG genes, which is responsible for maintaining chromosomal stability by controlling chromatin content condensation and also maintaining gene silencing patterns.
• This mechanism and that of histone modification together decide which portion of chromatin is to be condensed and rendered inaccessible as a heterochromatin segment of chromosome.

2. Histone modifications in plants:

• In DNA packaging, histone proteins play a very significant role.
• In order to obtain condensed chromosomal configuration, the DNA segments wound around these octamer proteins to yield nucleosomes.
• As histones can stabilize the negative charge of DNA molecule, they are essential for DNA binding.
• The His-DNA interactions are affected by the post translational modifications like phosphorylation, acetylation, biotinylation, ubiquitation and methylation of specific amino acids at histone tails and these are responsible for determining the extent of condensation at that region.
•  Hence, the chromatin state differs along with a particular modification and with the aid of certain particular internal or external signaling factors, it goes through transcriptional activity.
• For instance, upon the methylation of histone H3K4, transcription factors are expressed whereas methylation of H3K9 suppresses it.

3. RNA interference in plants:

• In a number of processes, such as transgene silencing, post-transcriptional processing of mRNAs, combating viral invasions, development of unexpressive heterochromatin, silencing of transposable components, etc., small interference RNAs (siRNA) play a crucial role.
• Research carried out on the Arabidopsis plant shows how these siRNAs serve as mobile markers that cause epigenetic variations.
• By inducing epigenetic variations, they not only affect the normal plant development system but also aid those plants to adapt to invitro conditions and the changing environments.
• Several transcriptional factors, repressor proteins, mRNAs and microRNAs have also been found to function and assist in the display of these epigenetic processes and cause phenotypic variation to occur in the plant.
• Together, they all allow greater polymorphism to occur, which generally brings new phenotypes.

Role of epigenetics in plants:

• In order to function, plants depend on epigenetics.
• This was first observed by Gassner, who found that it was important to provide the plant with a cold phase for its growth.
• After this, some others found that photo-periodism is also very important for the growth of plants.
• They also illustrated how some epigenetic modifications trigger flowering during the vernalization process.
• Biotechnology progress has helped scientists to illustrate the underlying epigenetic mechanisms that govern flowering, germination, fruit ripening, vernalization of fruiting and photoperiodism etc, as well as to research the configurational changes that genome undergoes during cell differentiation.
• By conducting epigenetic research on all aspects of plant development, such as identification of complex characteristics of novel crops through DNA methylation, processes controlling plant flower timing, plant resistance to certain microbes, their activity of virus resistance through gene silencing, etc., gaining an understanding of all this, applicable to a particular type of plant, will help us optimize genomic activity of this crop in a field or cultured in vitro.
• Researchers have also been assisted in the study of the processes of natural selection and other adaptive responses of plants to their environment by assessing the heritable epigenetic marks of a plant.

Environment induced epigenetics:

• Physiological changes in plants are also brought about by the external factors such as the stresses of the environment and its conditions and permit them to respond to these conditions.
• In response to external stimuli, plants exhibit modification in their chromatin material.
• For example, in response to several environmental stress, DNA methylation takes place.
• In order to introduce stable epigenetic modifications, this stress stimuli must be perpetuated by cell divisions.
• The alterations are brought by abiotic stresses such as draught, UV radiation, high saline concentrations, excessive heat.
• The alterations include silencing of reporter transgenes and endogenous loci in specific plant types.
• However, these alterations are short-lived in their expression.
• The previously suppressed silencing process are restored by the return of optimal conditions.
• The other examples are listed as follows:
  • In tobacco plant, the exposure to stresses of cold, and aluminum salts results in DNA methylation.
  • The hypomethylation occurs in Cannabis sativa upon exposure to heavy metal stress.
  • To the rice varieties that ae sensitive to draught, the hyper and hypo-methylation of DNA takes place.

Application of Epigenetics in plant biotechnology:

1. Somaclonal variations:
   • For researchers who want to implement soma clonal variations through in vitro plant culture, research on epigenetic modifications has proved to be of high importance.
   • Through the somatic embryo-genic plant tissue culture technique, researchers have identified soma-clonal variations as the cells attempt to adapt to their in vitro conditions.
   • Such differences arise due to genome rearrangement and not due to any changes in the sequence of DNA.
2. Chromosomal mutations with genotypic variations:
   • It also contributes phenotypic variants or chromosomal mutations in plants with beneficial characteristics.
   • These genotypic variations also lead to aneuploidy and polyploidy, which is used by plant biotechnologists to achieve high quality yields from plants such as cotton and onion.
   • In addition, for inbreeding, vegetative and seed propagation, such variants are useful. Especially gene methylation occurs in these variants.
3. Transgenic plants:
   • Epigenetics is beneficial for in vivo propagated plants.
   • In addition to generating and controlling transgenic plants with desirable characteristics, the implementation of epigenetic modifications can also produce and control natural processes such as flowering, fruiting, germination, dormancy, etc.
   • One such effective way of provoking temporary inactivation or activation of certain genes without the induction of any genetic mutation is chromosome methylation.
   • Over time scientists have been successful in producing transgenic crops that can withstand stress conditions through these alterations.
   • They produce sustainable crops on a large scale and by decreasing greenhouse effects, contribute to environmental conservation.

Noble plant phenotypes produced by Epigenetics:

Following noble phenotypes have been produced through epigenetics:

1. Enhancement in nutritional value:
   • Improvement in nutritional value; Scientists have been able to express certain genes during specific crop development using RNA interference technology.
   • Up until now, this technique has been used to reduce gossypol lines in cotton plants.
   • Furthermore, it has been used to reduce the content of caffeine in coffee plants, to increase the development of amylase in wheat crops and to improve the quality of tomatoes.
2. Dosage compensation:
   • Research into epigenetics allowed scientists to understand the role of the dosage of the parental plant genome in the development of endosperm or seeds.
3. Tolerance against stress conditions: 
   • Under environmental stress, modifications can down regulate certain genes. For example, salinity, intense cold, heat and drought etc.
   • For example, inactivation of genes through epigenetics provide certain resistance abilities to rice crops incourse of their reproductive and vegetative stages.
4. Virus resistance improvement: 
   • Using RNA interference, Researchers have developed  BBrMV ( Banana Bract Mosaic virus) and resistant banana varieties

What are the disadvantages and limitations of epigenetics mechanisms?

• The following are the drawbacks of epigenetic processes during in vitro callus tissue cultivation:
  • They can provide variants that are genetically unstable.
  • Extensive trials are required for the application of such variant crops
  • Unwanted characteristics can be expressed phenotypically
  • It can produce a dangerous genetic mutation.
  • In addition, transgenic crops produced using epigenetics may contain protein content that is modified.
  • Some are phenotypically unobvious and in some cases, may cause an allergic reaction and spread this allergic epidemic.
  • Phenotypic as well as genotypic changes arise from epigenetic variations.
  • Despite being heritable, when transmitted over many generations, there is still disagreement with the Mendalian epigenetic model. It is however clear that epigenetics regulate the growth of a plant rather than inherited characteristics.

What are the future aspects of epigenetics in plants?

• The further study of epigenetics and its understanding can be implemented for wide areas. Such as:
  • Plant generation in a new habitat.
  • Crop manipulation for generating biofuels
  • Reducing the development time of crops
  • Induction of plants, regardless of seasonal changes, to produce fruits or flowers throughout the year.
  • These can generate heterosis and cross-breeding that provides better quality for plants than their parent plants.
  • Magnify stress adaptation in them.
  • These may produce heterosis and cross breeding that give plants with quality better than that of their parent plants.
• It can appear to be an efficient way to eradicate hunger and food crop production with extra nutritional values in nations facing severe environmental stresses such as Ethopia, Ghana, etc.
• It therefore intends to bring cost-effective crops to combat global food demand with characteristics that can guarantee a healthy environment in less time.
• In the foreseeable future, epigenetics can even be used to modify weed genomes in such a way as to either obstruct their growth among desirable plantlets or incorporate characteristics to render them beneficial to humanity.