Crop Epigenetics

Global climate change and environmental degradation are increasing the unpredictability and severity of abiotic stresses, and are major limiting factors to crop production and food security worldwide. In recent years, biotechnologies such as genetically modified organisms (GMOs) have emerged to combat these challenges. However, such practices are not without controversy, and recent discoveries and advancements in crop epigenetics are disrupting agronomy, demonstrating the potential to enhance crop performance without the need for genetic modification.

Background

Plants are indispensable to life on earth. Since the beginning of civilization, humans have domesticated both plant and animal species for agricultural purposes. Selecting populations with desirable traits based on gene variants, known as alleles, and breeding high yielding genotypes has allowed crop production to increase and become better adapted to environmental changes.

Unlike animals, however, plants are stationary and therefore more vulnerable to environmental stresses such as high temperature, drought, pathogens, parasites, and poor soil conditions. Plants respond to such stressors with a range of mechanisms we know now are triggered by gene expression. Epigenetics is the study of how and when genes are expressed under the influence of mostly external factors. Crop epigenetics examines the mechanisms that crop species have evolved to adapt to biotic and abiotic stress. Once these epigenetic changes are established, it is possible for them to be inherited from one generation to the next. Inheritance occurs through epigenetic alleles (or alleles having the same DNA sequence but different DNA methylation patterns), which in turn leads to higher polymorphism and eventually to newer phenotypes.

In 1999, a groundbreaking discovery of epimutations in tomatoes (Solanum lycopersicum) linked epigenetic mechanisms with an important agronomical trait, colorless nonripening. This paved the way for further research to investigate the underlying epigenetic mechanisms for important heritable crop traits in tomatoes, such as ripening and stress response.

More recently, new technologies and breeding methods have improved agricultural production worldwide by enhancing agronomic traits, for example increased stress tolerance and yield, and enhanced nutritional quality.

Emerging Research in Epigenetics

The role of methylation

Research has shown that DNA methylation, acetylation-deacetylation, and small RNAs are involved in most aspects of the plant lifecycle, and are involved in the regulation of gene expression, without any change in DNA. The best-studied epigenetic mechanism is DNA methylation, which according to researchers, can typically act to repress gene transcription or "silence" a gene to generate new ‘epigenetic’ variants that could include epi-alleles that confer desirable changes to crop phenotype.

Specific abiotic stresses being investigated include drought, low relative humidity, low temperatures, salt, and heavy metals. Changes to methylation patterns are also being observed in response to biotic stresses such as plant-herbivore and plant-pathogen interactions.

DNA Damage Response Systems

More recently, scientists have been working on the development of DNA damage response systems to ensure optimal growth and survival of plants despite the condition to which they are exposed, such as poor environmental conditions including the aforementioned abiotic stresses.

By using methods such as co-immunoprecipitation and mass spectrometry, such as Hyperspectral Sensor Imaging (HSI) through Fiber-optic Biosensors, researchers discovered an epigenetic regulation mechanism involved in DNA damage repair in plants, which lies in a histone demethylase enzyme called lysine-specific demethylase 1-like 1 (LDL1) combined with a conserved protein called RAD54.

The approach silences specific genes to remove the cell’s “epigenetic memory,” thus creating an intermediate parcel of pluripotent callus cells. Then, different genes are stimulated in the cells supporting the callus transmutation into an infant tissue made up of totally different cell types. The stimulation provokes a regenerative process that leads to shooting induction, which ultimately leads to the formation of stems and leaves. Moreover, an essential finding on this epigenetic mechanism is that these new stems and leaves do not require seeds to grow. These approaches help shed light on the possibility of increasing the productivity of staple grains and vegetable crops in a more environmentally friendly way.

Plants can also increase their resilience to biotic or abiotic threats via "priming," a process by which the responsiveness of their immune system intensifies after recognition of specific signals from their environment. This provides potentially long-lasting protection and is based on eliciting a faster and/or stronger reaction upon subsequent challenge by the same or related stressor.

Emerging Technological Solutions

Methylation markers have immense value in identifying which direct and indirect interventions can induce changes to the genomes of the crop, and to what end, can be used as a diagnostic tool for stress. In a technique known as DNA Fingerprinting, a robust set of methylation markers or methylation profiles can be identified and used to diagnose when crops are being exposed to biotic or abiotic stresses.

Genome-wide methylation profiling or mapping of epigenetic marks led to the development of epigenomics, an emerging field that is expanding our ability to explain observed phenotypic variation through the identification of multiple cellular products such as RNAs, protein–DNA interactions, chromatin modifications, and chromatin accessibility.

Other critical tools include the use of mathematical models and algorithms for the enhancement and identification of heritable epigenetic phenotypes which may also contribute to more successful breeding programmes for crops.

Epigenetics can be contrasted with methods of gene editing and modification. CRISPR, for example, is used in very targeted manners, for example, by developing new model systems or by stimulating the effect of treatments using genetic editing, there is still a lot to be discovered in terms of side-effects and reversibility. Scientists have been looking into the consequences of this gene-editing technique, especially given the fact that it may be impossible to reverse or turn off these edits. Unlike gene-editing however, epigenetic changes do not change the DNA sequence and are reversible.

A Future with Crop Epigenetics

Advances in our understanding of the links between gene expression and plant traits, particularly traits that are valuable for agronomy, mean that a more tailored approach can be taken to enhance crop performance that is both sustainable and natural.

Methylation markers will be developed for many crop species able to track developmental progression and also the exposure and response of the plants to the stresses they are experiencing. This offers a range of opportunities for the improvement in varietal selection, crop management, pest and viral resistance, and to control and regulate the quality of agricultural products.

Epigenetics could also be used to monitor biotechnological systems and provide early warnings regarding the potential risk to ecosystems. Epigenetic mechanisms may generate explanations for unresolved observations in the domain of ecotoxicology, thus creating a device to monitor agriculture and thereby improve food security.

It is even possible that epigenetic fingerprinting of airborne pollen samples for signatures of stress could eventually augment existing monitoring of the landscape for the effects of climate change or to track new epidemiological events, and so facilitate more timely and targeted interventions.