Somaclonal variation in plant tissue culture

Phenotypic abnormalities in plant tissue culture experiment, due to somaclonal variation?

Plant tissue culture is an important technology for the production of disease-free, and uniform planting material. But did you know that sometimes tissue cultured seedlings exhibit unexpected variations? Let us discuss these variations today.

You need to improve or design unique protocols for each species, as well as their varieties, in order to regenerate plants using tissue culture. Growing plants under specific laboratory conditions triggers stress in plant cells. In some cases, this stress contributes to the development of plants with unexpected phenotypic abnormalities.

What are phenotypic abnormalities?

The word phenotype in plants represent the appearance of the plants which resulted due to the genetics as well as the environment where this plant has been growing. You can refer the observable traits in plants such as height, biomass, leaf shape, color, and so on as ‘phenotype’. You can call the variations in any of such traits due to tissue culture practices as ‘phenotypic abnormalities’.

In most of the cases, you can restore variations induced due to tissue culture back to normal state by experimenting with different culture conditions.

Good news is that some of these variations are temporary as well as non-heritable and thus, plants can recover their original traits. However, long lasting changes can be induced as well.

What is somaclonal variation?

You can refer to the long-lasting changes induced by plant tissue culture as ‘somaclonal variations’. Somaclonal variants are not genetically identical to the original donor plant. This indicates that the genetic information in cells or the way the genes work has undergone changes. This situation occurs due to several cellular and genetic mechanisms under in vitro conditions.

The spontaneous variations are not exclusive to just plant tissue culture. Growers knew about such heritable variations even before genetics and plant breeding came into light. Several potato varieties, as well as dwarf bananas that are present today, are a result of spontaneous mutations. However, such mutations are frequently discovered in the in vitro generated “off-types” as compared to mutations occurring in nature.

Is somaclonal variation reversible?

Somaclonal variation cases can be classified as genetic or epigenetic variations. The epigenetic modifications are changes in the original phenotype without any actual change in the core genetics of the plant.  It is associated with the changes in plant proteins functions as well as behavior in nature. This type of developmental variations can be temporary, non-heritable and reversible. Some examples of epigenetic variation are male fertility, dwarfism, and partial fertility.

Genetic variations are permanent, as well as heritable and are easily transmitted to further generations. On the other hand, you can maintain epigenetic variations only by vegetative propagation such as, cutting, grafting, tissue culture, etc.

Why does somaclonal variation occur?

When you perform plant tissue culture your focus is on optimizing culturing conditions in order to achieve the optimal rate of multiplication. However, the optimized propagation conditions may not be the most favorable when it comes to maintaining the genetic integrity of plants.

Let us discuss a few factors that can increase the probability of getting off-types in plant tissue culture:

Plant species/varieties: Researchers have found somaclonal variations in several crop species such as: apple, potato, tomato, sugarcane, rice, etc. Within the same species, some genotypes are more likely to produce somaclonal variants even with the same culturing conditions.

Mode of regeneration: The regeneration method plays an important role in somaclonal variation. In your experiments, the probability of off-types will be higher when you take advantage of indirect regeneration — through callus. Explants experience stress when you try to regenerate a shoot or embryo indirectly.

The reprogramming of cells to form an organ requires ex­tensive proliferation by unorganized callus. Can you imagine the cell struggling through it?

There is always a probability of somaclonal variation, even with optimized protocols via indirect regeneration.

Genotype and ploidy level: The ploidy level refers to the complete set of chromosomes in cells. For example, diploid plants have two sets of chromosomes (2x) just like us humans. Polyploidy appears when plants have more than two sets of chromosomes, for example in tetraploid plants (4x) which have four sets.

The Rubus species can have chromosome sets from 2x to 12x genotypes! Blueberry, potato, and sugarcane are perfect examples of polyploid plants. The interesting fact is that plant tissue culture can lead to changes in the ploidy level of the plantlets. A different ploidy level will give plants a different appearance as well as change internal functions. Unfortunately, ploidy levels are not reversible.

Composition of the growing medium: According to scientists, some genotypes are more susceptible to abnormalities than others in presence of high plant hormone concentrations. Growth regulators, such as: 2,4- dichlorophenoxyacetic acid (2,4-D) and 6-benzylaminopurine (BA), have been involved in the induction of somaclonal variation.

Duration of the callus phase: In some cases, the severity of somaclonal variations increases with the age of the callus culture. The abnormal cells keep on cloning themselves and multiplying as time goes by. This has been reported in Arabica and Robusta coffee propagation by somatic embryogenesis where prolonged duration of callus phase resulted in variations.

Proliferation rate: Tissue culture method thrives on its capability of producing a large number of plants in short periods of time. But how much is actually enough?

In order to have higher proliferation rates, you often need to add high amounts of growth hormones in culture media. This high concentration is one of the major causes of somaclonal variations.

Total time in culture: In plant tissue culture it is better for you to minimize the amount of time that a culture is maintained in vitro. Long-term cultures can be an excellent source of variants.

In order to preserve genetic diversity in different crops, plants are maintained in vitro for long lasting periods. This may increase the probabilities of inducing somaclonal variations. As a result, these cultures are maintained in slow growth conditions in order to delay the growth and therefore, reduce chances of variations. 

Advantages of somaclonal variation

All plant breeding programs have one thing in common: generation of genetic variability. Plant tissue culture is an excellent tool for developing new variations at genetic level. The induction of somaclonal variations may result in the generation of novel mutants. For instance, somaclonal variation has been key for the improvement of sugarcane. In such cases, in vitro produced off-types are better than waiting for more than 10 years for a new variety from conventional breeding.

Limitations of somaclonal variation

Plant tissue culture is also popular for producing true-to-type plants which are identical to mother plants. However, somaclonal variations pose a threat especially to large scale tissue culture productions. Most of the traits obtained through somaclonal variation are random, and unstable.

Generating genetic variability is great from the breeding perspective. However, evaluating random mutations in the field requires a lot of capital investment, and efforts. It is also hard to predict the outcome of these variations at earlier stages.

We hope you got a glimpse of different aspects related to somaclonal variation. For more informational posts on different aspects of plant tissue culture, keep checking this space!

By Nataly Sánchez Del Río | 10-January-2022


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