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Epigenomics in Crop Breeding for Better Agriculture Tomorrow

By Shuvarghya Chakraborty

B.Sc. Agriculture (Hons.) Student (3rd Year)
Palli Siksha Bhavana (Institute of Agriculture), Visva Bharati
Email: suvarghya1999@gmail.com


Since the rediscovery of genetic principle of Mendel in 1900, the importance of genetics in plant breeding has been realized in full phase. But a question that gives unrest to the whole scientific community that to what extent only the genetics principles in crop breeding will feed the world population, particularly when the issue of climate change is knocking our doorsteps.in this regard it is important to think beyond THE GENETICS  particularly when we think of climate resilient agriculture.

What is Epigenomics?

The literal meaning of the word ‘Epigenetics’ is something which is beyond the genetic principles discovered so far. A famous British developmental biologist Prof. C. H. Waddington coined the term epigenetics in the year 1942. He used to describe the class of internal and external interactions between the environment and the genes leading to the development of the phenotype. But in precise terminology epigenetics refers to the alteration in the gene expression pattern without the change in the nucleotide level.

Generalized flowchart of Epigenomics (Source: ibit.ly/cmhj)

Manifestation of Epigenetics

Epigenetics mainly results from the covalent modification taking place at DNA level or histone protein level. There are some signature modification taking place at DNA or histone level that alters the chromatin accessibility to RNA Polymerase and thus affecting the gene expression level.

Some common modification of DNA and histone protein are:

  1. DNA Methylation level changes e.g. Hypomethylation and hypermethylation at the CPG Island of DNA.
  2. Histone protein Acetylation, Deacetylation and Methylation.
  3. Histone protein ADP Ribosylation.

Method to assess whole genome epigenomic modification

There are some novel methods to assess genome wide epigenome modification. Some important methods are as following

  • Chop PCR method
  • Whole Genome Chip Sequencing Assay
  • Determing epigenetics changes through Isoschizomers
  • Whole Genome Bisulfite Sequencing

But among them the most widely used and convenient method is Bisulfite Sequencing where Bisulfite is applied at two sample from two different condition to assess whole genome methylation profiles. Those CPG islands in the genome are methylated, Bisulfite (a Deaminating Agent) can’t deaminate those cytosine residues. But in CPG island where methylation has not taken place, Bisulfite deaminate that cytosine into uracil residue. After performing a polymerase chain reaction (PCR), when sequence the two genomic sample by NGS and align those reads with the reference genome available, whole genome methylation status can be compared between two sample and thus giving a deep insight into epigenetics modification.

(Source of the slide: ibit.ly/nhL2)

Epigenetics in Plant Life

There are many evidences about epigenetic modification that take place in normal developmental process of plants as well as in many biotic and abiotic stress tolerance mechanism. In developmental point of view vernalization of plants is a well-studied epigenetic phenomenon.

In vernalization, a gene called flc1 or vrn3 is epigenetically silenced following cold stimulus perception by shoot apex of the plants. The gene is a negative regulator of flowering response. So, after cold treatment this gene is epigenetically silenced and the receptive plants come into flowering earlier.

In stress tolerance mechanism, especially in biotic stress tolerance mechanism the effect of epigenetics is more pronounced. When a virus infects a plant, the plants deploy some non-coding RNA (miRNA, siRNA, shRNA) to silent the viral genome by epigenetic modification (mainly methylation) so that the virus cannot replicate in plant cell.

Also, in some abiotic stress conditions (e.g. drought stress, salinity stress, heat stress etc.) there are some epigenetic modification taking place in plant genome. For example, in drought stress the genes required for stomata opening becomes hypermethylated so that the plants can conserve water and do not get wilted. Also, in that condition the genes required for water uptake from soil is unregulated by epigenetic modification (by hyperacetylation or hypomethylation) so that the plants can absorb more water from soil and maintain the space (soil plant atmosphere continuum) even in drought or water stress condition.

How epigenetics help scientists to combat Agricultural Problems

Since green revolution we have achieved, the yield potential of the plants almost come to a plateau. Furthermore, there is a huge burden of biotic and abiotic stress on the plants that cause a huge quantum of yield drag. So, it’s time to think something smart and effective that will solve our problems to some extent. In this regard scientists look for epigenetics as a novel tool for genetic manipulation of crop plants.

There is a huge potential for targeted epigenome editing of crop plants to make them more fit for today’s climate change scenario. For epigenome editing we have to only prepare a modified CRISPER cas9 construct. Here we use the dcas9 (dead cas9 enzyme) that can only target the editing complex towards the target genomic location but do not have the capacity to cleave the DNA. Also we have to add some non-coding RNA gene segment to our editing construct that will selectively make epigenetic modification to the target genomic region. With the help of the above-mentioned paradigm, it is possible to modify as many as traits epigenetically. By this mechanism it is possible to up-regulate or down-regulate some genomic region selectively without change its nucleotide sequence.

Road Map of Epigenetics (Source: ibit.ly/PAga)

Recent progress and future goals

Already there has been some progress in field of epigenomics in crop plants to sustain world population. For example, Indian Agricultural Research Institute (IARI), New Delhi , Division Of Biochemistry has made a major research contribution in this regard. In this division under the supervision of Prof. Suresh Kumar, the epigenetic basis of Phosphorus Uptake has been elucidated and efforts has been taken to epigenitically modify the pup1 QTL in rice which is responsible of phosphorus uptake in rice.

There are many researches upcoming in this filed worldwide. But a long way has to be paved before to use this technology as a routine tool for genetic manipulation of crop plants. So definitely, much importance on research and development (R&D) is required to put in this regard. Further the trans-generational stability of such mitotic memory has to be assessed before using it as a potential plant breeding tool. But undoubtedly, this will open a new door to go one step closer to the ever-complex mystery of life.

Version Edited by Team Krishipathshala

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