How to Predict Successful Plant Transformation Through the Epigenetic Code of DNA?

The transformation process is able to affect the DNA methylation patterns
in the plant genomes.
【Image: Provided by Dr. Pao-Yang Chen’s Lab; Illustration: @Nien Illustration

In the world of technology, we can not only track the movement of stars, but also delve into the intricate and fascinating cells of plants. Maybe you were familiar with the term “genetically modified” or “GMO,” which represents a captivating scientific technique to cultivate plants artificially in order to enhance their beauty, flavors strength, and resilience to environmental challenges. You might wonder how scientists ensure that newly introduced genes are successfully integrated into a plant genome during the process of genetic modification. It is within this realm of exploration that the plant scientists have pioneered novel approaches, using the observation of plant DNA to aid in predicting the vibrant world after genetic modification. This innovation not only profoundly impacts agriculture but also ignites fresh inspiration in the field of genetic science.

🌾DNA, the code that carries the genetic information of plants, encodes the secrets of their growth and development.

To unravel the mysteries of GMOs, it is crucial to recognize the vital role of DNA. DNA, much like fingerprints, contains information related to the growth and development of plants, as well as the response to changing environments. If the DNA fingerprints are a cookbook, the process of introducing genes into plant DNA would be like adding new ingredients to this recipe, resulting in a wholly fresh flavor for the dish. Plant scientists often insert specific genes into plant DNA in order to create new traits, such as pest resistance, enhanced disease immunity, or increased yield. To accomplish this, it is crucial and challenging to verify whether these introduced genes can effectively operate within plants. This process resembles skillfully incorporating new ingredients into a traditional recipe, requiring careful examination and fine-tuning. Throughout this process, it is noteworthy that “DNA methylation” plays a key role.

🌾DNA methylation is a process by which methyl groups are added to the DNA. It may influence gene expression in plants, thereby affecting their traits.

Methylation on DNA is like a highlight in a cookbook. DNA methylation helps plants to rapidly modulate gene activities without changing any DNA. It is a dynamic and reversible process facilitating swift adaptation to environmental changes and diverse growth stages.

As DNA methylation typically suppresses gene activity, genes that are unmethylated tend to exhibit a higher transcriptional potential. By modulating gene activities through adding or removing methyl groups on DNA, plants are able to precisely control the activation or silencing of specific genes in response to specific stressful conditions, such as extreme temperatures, drought, or pathogen infection. This delicate regulatory mechanism is very important for plants to swiftly adapt to diverse environments and climates, ensuring sustained growth and reproduction.

🌾Plant DNA Methylation Research Detected Side Effects of Genetic Modification

Plant scientists have discovered that the distribution of methylation in transgenic plants may differ from those in non-transgenic plants. When introducing foreign genes into plants, the highly artificial experimental process has been shown to impact the distribution of methylation on DNA. Dr. Pao-Yang Chen and Dr. Jo-Wei Allison Hsieh from the Institute of Plant and Microbial Biology at Academia Sinica carefully designed and examined the impact of each key treatment from this complicated process of “genetic modification” on plants, further pinpointing the primary sources that influence methylation distribution. Dr. Hsieh found that the changes in methylation distribution during this process were not as random as previously thought. Instead, the DNA inserted by foreign DNA exhibited specific methylation patterns that affect numerous downstream genes and traits. These unexpected outcomes can be referred to as the “side effects” of genetic modification. Discovering these side effects are the critical first step for improving genetic modification technically, enhancing our understanding of genetically modified plants even further.

Different combinations of the transformation treatments affect distinct downstream genes.

🌾Changes of DNA methylation in transgenic plants could be early predictors of successful genetic modification in crop improvement.

Assessing the success of genetic modification often requires lengthy waiting until plants finally display new traits. Nowadays, scientists could possibly predict successful genetic modification at the early callus stages – DNA methylation could be one of the key strategies if the differences in the distribution of DNA methylation on specific regions in transgenic plants could be consistently detected in the callus stage and mature plants. These regions could potentially be developed into so called differentially methylated region (DMR) biomarkers for predicting the success of genetic modification.

DMR biomarkers are likely to offer several advantages, particularly in the fields of agriculture and food production. It has the potential to significantly accelerate crop improvement. Traditional breeding processes are time-consuming, and this new approach can provide indicators of successful genetic modification when the plant is still in the early callus stage. This not only saves time but also reduces costs, making both the development and application of genetically modified crops more accessible. Furthermore, this approach can also be extended to crops with lower transgenic efficiency, such as indica rice or other high-value crops like barley, maize, and oats.

DMR biomarkers provide deeper insights into plant genomes and physiological processes, thereby accelerating crop improvement. By observing changes in DNA methylation, plant scientists can know how plants respond to stress and environmental changes. This provides new insights for improving plant cultivation and management strategies, and contributes to a deeper understanding of adaptation mechanisms in nature.

Further Exploration and Research
Dr. Pao-Yang Chen and Dr. Jo-Wei Allison Hsieh have recently conducted a comprehensive examination on rice transformation by revealing the impact of these critical transformation treatments on genome-wide DNA methylation and the transcriptome. Their results highlight the specificity of impacts triggered by individual transformation treatments during rice transformation with the potential association between DNA methylation and gene expression, that is, the side effects of genetic modification. These changes in gene expression and DNA methylation were found to explain a significant portion of somaclonal variations, that are way beyond the tissue culture effect, and be attractive resources for crop improvement.

Jo-Wei Allison Hsieh, Pearl Chang, Lin-Yun Kuang, Yue-Ie Hsing, Pao-Yang Chen* (2023)
Rice transformation treatments leave specific epigenome changes beyond tissue culture. Plant Physiology.

🌾Embracing a new era in crop enhancement

In this era of emerging and breakthrough technologies, scientists continually seek superior methods to enhance agricultural production and food supply. By recognizing the role of DNA methylation in transgenic crops, we now have a more accurate prediction for success of genetic modification to save time and resources, elevating the effectiveness of crop improvement. This line of research examining the safety and sustainability of genetically modified crops is likely to have positive influences on our environment and health.