Role of epigenetic diversity in crop improvement
Authors: Gayacharan*, Nupur Mondal
ICAR-National Bureau of Plant Genetic Resources, New Delhi-110012
Shivaji College, University of Delhi, New Delhi-110027
*Email: gayabio83@gmail.com


What is epigenetics?

Epigenetics is the study of heritable or non-heritable changes in gene function without changing nucleotide sequences in the genome. Waddington (1942) defined epigenetics as “the study of heritable phenotypic variations that are not the result of variations in DNA sequence.” Russo et al (1996) further improved it and defined epigenetics as ‘all meiotically and mitotically heritable alterations in gene expression caused by mechanisms other than changes in DNA sequence.’

Well known examples of epigenetics

X chromosome inactivation : It is a highly evolutionary evolved process of sex determination in many life forms. In case of mammals where XY is male and XX is female, one extra X chromosome in females is transcriptionally inactivated through heterochromatinization for normal development process.

Inactivation of transposons and repetitive sequence : Transposable elements (TEs) and other types or repetitive sequences constitutes more than 50 % of the total genome of several organism including human. Being so frequent, active TEs can be sometimes lethal when targets critical genes, frequent chromosome breakage, illegitimate recombination and genome rearrangement. TEs can also affect adjacent genes by altering its splicing, polyadenylation patterns, or by functioning as enhancers or promoters. Therefore, to combat their negative effect each genome has evolved epigenetic mechanisms to suppress their activity. There are various epigenetic mechanism like post-transcriptional silencing of TEs by RNAi and chromatin modifications through DNA methylation and histone modifications targeting TEs. Similar mechanism is involved in silencing repetitive genes in the genome.

Transgene silencing : Transgene silencing is likely evolved as defense mechanism from foreign invaders like viruses or foreign DNA molecules. In case of genetically modified organisms, sometimes transgenes are not expressed and even they can suppress endogenous genes if they are sufficiently homologous. This is also a similar process to TEs inactivation.

Para-mutation : This epigenetic phenomena was first discovered in genes involved in anthocyanin synthesis pathway in maize by Alexander Brink (1950s). It is an interaction between alleles that results in a heritable expression change of one allele. The allele with reduced expression is then able to initiate silencing of other active alleles in subsequent generations. This is governed by DNA methylation mechanism.

Somaclonal variation : This is an epigenetic phenomena observed in vegetatively propagated or tissue cultured plants. This is defined by appearance of new phenotypes higher than the normal expected frequency which can be a stable or unstable phenotype (Kaeppler et al., 2000). The frequent phenotypic changes are particularly unstable type which is mainly due to high level of chromatin remodeling occurring during de-differentiation and differentiation of tissues in vitro tissue culture process.

Genomic imprinting : Generally we call it as an epigenetic phenomena that results genes to be expressed in a parent-of-origin-specific manner. Genomic imprinting have been reported in plants, animals and fungi. ‘Parental genomic imprinting is characterized by the expression of a selected panel of genes from one of the two parental alleles (Feil and Berger, 2007).’

Self-defense mechanism in Bacteria : Bacteria are constantly exposed to parasitic viruses called bacteriophages. Bacteria has evolved several defense mechanisms to survive the bacteriophage attacks, one of them is restriction site modification. This defense mechanism involves two types of enzymes that is restriction endonuclease (REase) and a methyltransferase. (MTase). REase cleaves dsDNA of intruding bacteriophages while MTase blocks the restriction site in host bacteria so it does not restrict its own genome.

DNA repair mechanism :

DNA polymerase add nucleotide with extraordinary degree of fidelity, but wrong base addition happens with varying frequency (1/104 to 1/105) among organisms. This mismatch nucleotide is repaired by strand discrimination mechanism, where template DNA (true to type) is identified by methylation marks on it in its adenine nucleotides. Methyl group is added in N6 position of all adenines within (5’) GATC sequences by Dam methylase. DNA mutation also take place in later stage of cell due to several exogenous and endogenous factors. Several epigenetic factors along with DNA repair machinery involved restore original DNA sequence.

Epigenetic mechanisms

DNA Methylation is a conserved heritable epigenetic modification resulting from the enzymatic addition of a methyl moiety to DNA. This is catalyzed by a family of conserved DNA MTases. Most common methylation sites are symmetric cytosine CpG and CpNpG in plants (Matzke et al., 2001).

Histone modifications include methylation, acetylation and phosphorylation. Histone protein are post-translationally modified at several sites mainly at lysine, serine and arginine residues. Specific combination of histone modification in chromatin is termed as Histone codes’ which dictate specific transcriptional response and cellular functions (Turner, 2002).

RNA based epigenetic mechanism controls gene actions and genome organization through RNA degradation, DNA methylation, histone modifications. RNA based mechanism governs the co-suppression (transgene silencing) of both the transgene and homologous plant gene, directs the methylation of DNA and histone protein causes heterochromatinization and also suppresses the transposons activity.

Factors attributing epigenetic diversity

Genetic diversity is universally known as the base material for natural and artificial selections which results in adaptation and speciation. Another dimension of diversity is epigenetic diversity which is like all time ghost on genetic material plays immense role in evolutionary processes. Unlike basic mechanisms of genetic variation i.e. DNA mutation and recombination, epigenetic variation attributing factors are DNA methylation, histone modifications, RNA interference, etc. Epigenetic mechanisms are governed by cascades of highly regulatory processes in response to various external forces to control targeted gene expression. Further this epigenetic diversity is selected upon and influenced by myriad of external forces like biotic stresses, abiotic stresses, climatic changes and anthropogenic activities. This epigenetic diversity is proving as important as genetic diversity for crop improvement (Springer and Schmitz, 2017).

Utilization in crop improvement

There is tremendous amount of research work done in epigenetics and now it is gaining momentum in its application. Because of high density availability of epigenetic markers and their direct involvement in gene expression, the science is being increasingly used for crop improvement. Several methods of epigenetic profiling like methylation based arrays, methyl binding PCR, MSAP, ChIP-Seq, ChIP-chip, methylated DNA immunoprecipitation sequencing (MeDIP-seq), methylated DNA capture by affinity purification (MethylCap-seq), reduced representation bisulfite sequencing (RRBS), methylation based whole genome sequencing technologies (e.g. Infinum® Assay, Roche 454 GS FLX, HiSeq and Life Technologies SOLiD), etc. are being utilized in identifying useful epigenetic variations and utilizing them in crop improvement programs. Differential epigenetic regions in genome are being used for identifying responsive genes and correlating them with the targeted traits. Similarly epiRILs (epigenetic recombinant inbred line) are being formed by crossing between genetically identical, but epigenetically different individual plants and these lines are as important as RILs (Cortijo et al, 2014). RNAi and Virus-Induced Gene Silencing (VIGS) is successfully being utilized for nutritional improvement (Sinha and Patil, 2017), providing plant immunity against viruses (Voinnet, 2001), etc. Several differential methylation based methods are used for identifying responsive genes to drought, yield, etc. (Bachem et al 1996; Gayacharan and Joel, 2013). There has been several studies on identifying epigenetic markers and their role in trait development (King et al, 2010).

References:

1. Bachem CWB, van der Hoefen RS, de Bruijn SM, Vreugdenhil D, Zabeau M, Visser RGF (1996) Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J 9: 745-753
2. Cortijo, Sandra, René Wardenaar, Maria Colomé-Tatché, Arthur Gilly, Mathilde Etcheverry, Karine Labadie, Erwann Caillieux et al. "Mapping the epigenetic basis of complex traits." Science 343, no. 6175 (2014): 1145-1148.
3. Feil, R., & Berger, F. (2007). Convergent evolution of genomic imprinting in plants and mammals. TRENDS in Genetics, 23(4), 192-199.
4. Gayacharan and Joel, A. J. (2013). Epigenetic responses to drought stress in rice (Oryza sativa L.). Physiology and Molecular Biology of Plants, 19(3), 379-387.
5. King, G. J., Amoah, S., & Kurup, S. (2010). Exploring and exploiting epigenetic variation in crops This article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”. Genome, 53(11), 856-868.
6. Sinha, S. K., & Patil, B. L. (2017). Applications of RNA-Interference and Virus-Induced Gene Silencing (VIGS) for Nutritional Genomics in Crop Plants. Phytonutritional Improvement of Crops, 185.
7. Springer, N. M., & Schmitz, R. J. (2017). Exploiting induced and natural epigenetic variation for crop improvement. Nature reviews genetics, 18(9): 563.



About Author / Additional Info:
Scientist (Agri-biotechnology)