Introduction
Somaclonal variation, what is it and why would a tissue culture lab care to know about, and monitor it? In this blog post, we’ll go over what it is, how it occurs, pros and cons of somaclonal variation, how to test for it and more!
| Key Topics Discussed |
| – What somaclonal variation is |
| – How it occurs |
| – Advantages and disadvantages |
| – How to identify it |
| – How to avoid or stimulate it |
Definition of Somaclonal Variation in Plant Tissue Culture
Somaclonal variation is a natural occurrence when plants grown in culture exhibit unexpected changes. These variations can be both good or bad depending on the goal for the explant in culture. Are you looking for repeatable gene expression, or are you looking for new phenotypes from one parent plant?
How Does Somaclonal Variation Occur in Tissue Culture?
[1]“The triggers of mutations in tissue culture had been attributed to numerous stress factors, including wounding, exposure to sterilants during sterilization, tissue being incomplete, imbalances of media components such as high concentration of plant growth regulators, sugar from the nutrient medium as a replacement of photosynthesis in the leaves, lighting conditions, and the disturbed relationship between high humidity and transpiration”
Advantages and Disadvantages
| Aspect | Advantages | Disadvantages |
| Genetic Diversity | Introduces new genetic variations, leading to diversity in traits and characteristics. | Unpredictable changes may result in undesirable traits. |
| Improved Crops | Potential for developing crops with improved resistance to diseases or environmental stress. | Unintended changes might lead to reduced crop quality. |
| Research Opportunities | Provides a platform for studying genetic and biochemical processes in plants. | Difficulty in controlling and predicting specific changes. |
| Biodiversity Conservation | Contributes to the conservation of plant biodiversity. | Risk of losing original genetic traits in the process. |
| Disease Resistance | Potential for developing plants with increased resistance to specific diseases. | Some variations may lead to increased susceptibility to other diseases. |
| Stress Tolerance | Possibility of creating plants that are more tolerant to environmental stress conditions. | Unintended negative effects on plant stress responses. |
How to Identify Somaclonal Variation
There are a few ways to determine if somaclonal variation has occurred. Rather than waiting to grow the regenerated plant from culture and observe any visual or chemical differences, that only covers the easily identifiable changes that occurred (if any). This is where using Random Amplified Polymorphic Dna (RAPD) and gel electrophoresis comes in. But how does this work?
Using Gel Electrophoresis
There are a few steps involved to be able to visualize DNA to understand if somaclonal variation took place. It starts with PCR amplification, and ends with comparing the gel to the original “fingerprint” that was taken from the plant the explant was sourced from.
Step 1: PCR Amplification
Scientists use Polymerase Chain Reaction (PCR) to selectively amplify specific regions of the plant’s DNA, including those with somaclonal variation.
Step 2: DNA Fragment Separation
The amplified DNA fragments, potentially reflecting somaclonal variation, are subjected to gel electrophoresis.
Step 3: Gel Electrophoresis Separation
DNA fragments are loaded onto a gel, and an electric field is applied, causing fragments to move through the gel based on size.
Step 4: Visualization
After electrophoresis, the gel is stained, and DNA bands are visualized under UV light. Each band represents a DNA fragment, aiding in the identification of somaclonal variation.
Step 5: Comparative Analysis
By comparing banding patterns between plants with and without somaclonal variation, researchers can identify differences that indicate the presence of genetic changes.
It’s important to note that while gel electrophoresis is a powerful tool for detecting changes in DNA patterns, further analysis, like DNA sequencing may be needed to precisely characterize the nature of the variations that occurred (if any).
Is It Reversible?
In most cases, somaclonal variation is irreversible. Once genetic changes occur during the process of plant tissue culture, they typically become a permanent part of the plant’s genetic makeup. This is due to somaclonal variation effecting and modifying the plant’s DNA, and DNA changes are generally stable and heritable. Reversing the variation would involve additional genetic manipulation or breeding techniques in attempts to induce, or better said, reintroduce the traits that were lost or hindered during somaclonal variation. This is assuming that the original explant donor is no longer available to source material from. The most effective way to “reset” the DNA is to start with plant material that has not undergone genetic variation.
How to Avoid (or stimulate) Somaclonal Variation
Explant Source
Genetic stability, age, and cell type, can influence the likelihood of somaclonal variation. Unstable genetics can allow for somaclonal variation to take place more easily than a genetic with strong, established traits that are predominantly observed in the offspring.
In regards to age, younger cells have less susceptibility to somaclonal variation due to greater genetic stability compared to older tissue. Older tissue may have accumulated more genetic changes over time, potentially leading to an increased chance of somaclonal variation.
Cell type is another factor to consider when avoiding somaclonal variation. Callus cells, masses of undifferentiated cells, have a higher chance of developing mutations as they are non-reproductive cells that are further away from the cell’s germ line. Reproductive cells, like shoot tips or meristems are closer to the cell’s germ line. Using cells that are closer to the cell’s germ line will lower the chances of somaclonal variation to occur.
Medium Components
Culture media provide the necessary nutrients, hormones, and conditions for the growth and development of plant tissues in vitro. The composition of the media can impact the genetic stability of the regenerated plants and influence the occurrence of somaclonal variation. Here’s how media components can influence the possibility of somaclonal variation.
Nutrient Composition:
The type and concentration of nutrients in the culture media can affect the growth and metabolism of plant cells. Imbalances or deficiencies in nutrients may induce stress and contribute to genetic changes, increasing the likelihood of somaclonal variation.
Hormones:
Plant growth regulators are essential components of culture media. Hormone concentrations and ratios influence the growth and differentiation of plant tissues.
Hormonal imbalances or variations in the concentration of growth regulators can impact genetic stability. Specific hormone treatments may lead to somaclonal variation, especially if the plant cells are exposed to stressful conditions.
Carbon Source
The type of carbon source in the media, like sucrose, provides energy for plant cells. Changes in the carbon source or concentration can affect the metabolic pathways and stress responses in the cells, resulting in somaclonal variation.
pH and Salts
The pH and salt levels of the culture media influence the overall environment for plant growth. Variations in pH or salt concentrations can affect cellular stress responses and gene expression.
Extreme pH or salt conditions may contribute to somaclonal variation by inducing stress on the plant cells.
Duration and Number of Culture Cycles
Accumulation of Mutations Over Time
Prolonged exposure of plant cells to the artificial conditions of tissue culture increases the chances of spontaneous mutations accumulating over time.
The longer the duration of culture, the higher the likelihood that genetic changes, including somaclonal variation, may occur.
Repeated Subculturing
Subculturing involves transferring a portion of the cultured cells to fresh media to continue their growth. Each subculturing event is considered a culture cycle.
Repeated subculturing introduces additional opportunities for mutations to arise during cell division and regeneration, increasing the chances of somaclonal variation.
Genomic Instability
Some plant species or genotypes may inherently exhibit genomic instability, making them more prone to somaclonal variation during prolonged culture periods or multiple culture cycles.
Genomic instability can be influenced by factors such as the genetic background of the plant, the tissue source, and the stress conditions encountered during culture.
Accumulation of Stress Responses
As culture cycles progress, plant cells may experience stress responses due to factors such as nutrient depletion, suboptimal hormonal balances, or physical manipulation during subculturing.
The accumulation of stress responses over multiple culture cycles can contribute to genetic changes, including somaclonal variation.
Conclusion
Understanding the triggers for somaclonal variation, such as stress factors during tissue culture, provides valuable insights into the delicate balance required for successful plant regeneration. The advantages of somaclonal variation, including enhanced genetic diversity and the potential for improved crops, also come with the risks of unpredictability and unintended outcomes.
The irreversibility of somaclonal variation adds a layer of complexity, emphasizing the need for meticulous planning and consideration in tissue culture practices. Being aware of these advantages and drawbacks will aid you in your research and experiments for your tissue culture plants!
Learning Opportunities
Want to learn how to tissue culture your favorite plant at home or in a commercial operation? We can teach you! We have multiple routes for becoming educated in plant tissue culture:
Online plant tissue culture training: https://temporaryshootsnrootslabs.site/online-training/
Inperson plant tissue culture training: https://temporaryshootsnrootslabs.site/in-person-instruction/
Plant tissue culture Facility consultation: https://temporaryshootsnrootslabs.site/facility-consultations/
Culture Connect, our plant tissue culture hotline: https://temporaryshootsnrootslabs.site/culture-lab-connect/
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