How Epigenetics Can Help Farmers Grow Healthier and More Resilient Crops

Contributing authors: Eleni Tani (Agricultural University of Athens, Greece), Cristina Vettori (Institute of Biosciences and BioResources, CNR, Italy), Federico Martinelli (University of Florence, Italy).

What is epigenetics, and how is it related to farming? 

In the last decades, humanity has seen remarkable increases in crop yields. Genetics has played a central role in generating more productive varieties, exhibiting increased resistance to diseases and pests, and better adapting to different environmental conditions. Through breeding, best-performing plants are selected and crossed with other plants that carry desirable traits. This leads to the generation of new varieties with improved characteristics. In addition, genetics has contributed to the generation of hybrid crops, the results of crossing different parental plants to produce an offspring that inherits the best traits of both parents. Hybrid crops outperform their parents as they can be better adapted to local conditions and exhibit improved resistance to pests and diseases. By this, food security for the growing global human population is ensured.

However, pressure from climate change, limited access to water for irrigation, poor soil quality, and limited availability of arable land keep the demand for even higher-yield crops to meet the growing global food demand. Current models predict a decrease in the yields of all major crops due to their vulnerability to high temperatures, altered rainfall patterns, and elevated carbon dioxide concentrations from greenhouse emissions. Therefore, there is an urgent need to explore alternative genetic tools that will maintain or even boost crop yield under more unfavorable conditions. Such a tool is epigenetics: the changes in the expression of genes that are not caused by changes in the DNA sequence itself but by heritable chemical modifications in the DNA or proteins called histones associated with the DNA.

Enzymes can methylate DNA by adding a methyl group (a small chemical unit) to specific spots on a DNA molecule. These spots can be relevant for the control of the expression of a gene. When they are hypermethylated, meaning too many methyl groups are added to the DNA molecule, the expression of the gene can be reduced or turned off. On the other hand, hypomethylation refers to when too few methyl groups are added to the DNA molecule in these same regions. This can lead to increased expression of a gene or even the activation of a gene that is normally silent, meaning that it is not expressed. Epigenetic modifications are influenced by environmental factors such as temperature, light, and nutrients and can turn a gene on or off without changing the sequence of proteins. Consequently, epigenetic modifications can significantly affect plant growth, development, and adaptation to changing environments.

One example of epigenetic regulation is vernalization, the process by which some plant species, like winter cereals, require exposure to prolonged periods of cold temperatures in order to transition from the vegetative to the reproductive phase. This mechanism ensures that their fragile floral tissues are not damaged by winter frost. During vernalization, the DNA methylation status of specific genes is altered, leading to changes in gene expression that promote flowering. One of these essential genes is the FLOWERING LOCUS C (FLC) gene, as shown by several studies in Arabidopsis thaliana. This small plant belongs to the mustard family (Brassicaceae) and is used as a model plant in genetic and epigenetic research. Changes in DNA methylation levels at the FLC promoter region can alter its expression and, as a result, the timing of flowering, which is a critical determinant of crop yield.

Another example is potato late blight disease caused by the oomycete pathogen Phytophthora infestans. DNA methylation at the promoter region of the R3a resistance gene in potato regulates its expression and confer resistance to this disease. In particular, hypermethylation of the R3a promoter reduces its expression, while hypomethylation increases its expression and enhances resistance to late blight. These findings suggest that epigenetic regulation of R3a can play a critical role in modulating potato resistance to this devastating disease.

The presence and future of epigenetics in crop improvement

Epigenetic changes can affect yield by altering the response of crops to different environmental conditions: they can have a positive impact by increasing their adaptation capacity and optimizing their response by helping them to “remember” past stress events. Understanding the epigenetic mechanisms involved in yield under different environmental conditions, how they are involved in pest and disease resistance, and how they can influence nutrient uptake can help farmers secure production, increase their income, and apply sustainable crop management by reducing the use of fertilizers and pesticides.

Although research on plant epigenetics has significantly advanced in recent years, its application for breeding and crop improvement is still in its infancy. This is because the complexity of epigenetic regulation and inheritance makes it challenging to develop practical and effective strategies for crop improvement. Researchers currently address four main challenges:

1. Stability: Epigenetic modifications may not be stable over generations and can be influenced by environmental factors. Therefore, ensuring that the desired trait will be passed down to future generations is challenging.
2. Heritability: Epigenetic changes can be passed down to the next generation, but the rate of inheritance is generally lower than that of genetic changes. This makes it harder to breed crops with desirable traits based on epigenetic changes.
3. Complexity: Epigenetic modifications are complex and can be influenced by many factors. Understanding the interactions between these factors and how they affect gene expression and phenotype can be challenging.
4. Induction of changes: The induction of epigenetic changes currently relies on the genetic manipulation (e.g., mutation) of genes involved in the regulation of these modifications. The legislative framework prohibits such approaches in many countries, like in Europe.

While environmental stimuli or chemical treatments can also induce epigenetic changes, further research is required to evaluate the effectiveness, stability, and safety of these methods for crop breeding. Nevertheless, there are companies investing in epigenetic breeding (or epi-breeding) showcasing the significance of this approach for crop improvement. Sound Agriculture has introduced a novel breeding process to cultivate the Summer Swell tomato, a new tomato variety with enhanced flavor and longer shelf life, both on the vine and after purchase. Sound Agriculture promises to develop plant traits ten times quicker than conventional breeding techniques through the innovative method called On-Demand Breeding, which employs epigenetics. Epicrop Technologies Inc. uses epigenetics to improve sorghum yields.

Overall, while epigenetics offer a promising avenue for crop improvement, significant challenges still need to be overcome before it can be widely adopted as a breeding tool. Nevertheless, it is expected that the rapid advances in epigenetic research and technology will hold great promise for improving crop yields and enhancing food security in the future.

Epigenetics from the farmer’s perspective

Plant epigenetics can have significant implications for farmers, as it allows for the modification of gene expression without altering the DNA sequence. This can lead to the development of crops with desirable traits such as increased yield, improved disease resistance, and better adaptation to environmental stress. Epigenetic modifications can also be passed down through generations, creating stable, heritable changes in crop characteristics. Additionally, epigenetic tools can be used to identify and monitor changes in crop epigenomes in response to environmental stressors, providing valuable information for farmers on optimizing crop growth and yield in changing conditions. The regulation of yield, a quantitative trait, involves multiple loci and is influenced by environmental factors. The control of agronomic traits (characteristics), including yield, has been significantly impacted by epigenetic mechanisms such as DNA methylation, histone modification, and chromatin remodeling. Overall, plant epigenetics present a promising avenue for enhancing agricultural productivity and sustainability from the farmer’s perspective.

EPI-CATCH: Exploring the Power of Epigenetics to Create Elite Crops for a Changing Climate 

EPI-CATCH (EPIgenetic mechanisms of Crop Adaptation To Climate cHange) is a COST Action initiative that was launched in 2019. EPI-CATCH brings together scientists and researchers from various fields with the goal of understanding how epigenetic mechanisms help plants to adapt to changing environmental conditions. EPI-CATCH aims to:

1. Facilitate collaboration and exchange of knowledge and techniques related to epigenetics among researchers, breeders, and other stakeholders.
2. Develop new methodologies and models to understand better the role of epigenetic mechanisms in plant adaptation to environmental stresses driven by climate change.
3. Identify and develop epi-molecular markers associated with highly desired agronomic and qualitative traits in crops to enable targeted, gene-specific modifications to the epigenome.
4. Investigate the factors affecting the stability and heritability of epigenetic variations in crops to avoid inducing epialleles that are unlikely to be stable during the breeding process.
5. Develop a better understanding of the mechanisms inducing and stabilizing epigenetic variation and stress memory in crops using interdisciplinary techniques, strategies, and methods.
6. Standardize methodology in plant epigenetics/epigenomics and integrate these data with other “omic” approaches for a more comprehensive understanding of crop genotype-environment interactions, epigenetic variations, and stress memory.

EPI-CATCH is an innovative and collaborative initiative that aims to advance our understanding of epigenetics in crop improvement, with the ultimate goal of enhancing food security and sustainability in the face of climate change. For information, visit www.epicatch.eu.