Somaclonal Variations Introduction
- The genetic changes observed in the plants that are regenerated through the invitro cultures of somatic cells, are called as somatic variations.
- Term coined by Larkin and Scowcroft, 1981 (Soma, means vegetative and clone, means identical copy).
- Other terms used to describe such variations are gametoclones, calliclones, protoclones or mericlones.
- Depending upon the objective, these may be desirable or undesirable.
- Variation may be temporary or permanent.
- Major traits: diseases resistance, tolerance to abiotic stress, higher yield, better quality, ploidy level, pigmentation, etc.
Concepts covered:
- Somaclonal Variations introduction
- Source of Variations
- Molecular Mechanisms
- Methods to generate Somaclones
- Applications
Origin of Somaclonal Variations
- Pre Existing Variability
- In vitro induced Variability
Pre Existing Variability
- Plant tissues during differentiation for specialized functions, may accumulate mutations.
- Highly differentiated tissues may have more variations.
- Number & amount of mutations increases with the age of tissue.
- May undergo duplication resulting in polyploidization of the body cells.
Polysomaty
- Occurrence of cells with different ploidy levels in the same organ or tissue.
- Results from endo-reduplication of the genetic material.
- Evolutionary strategy to amplify the desirable genes and accelerate the plant growth.
- Endoreduplication results in increase in the size of organs.
- More common during cell differentiation and expansion.
- Environmental factors like light, temperature, nutrition etc can influence degree of endoreduplication.
In Vitro Induced Variations
- Explant are excised from parent and are cultured on artificial culture media in aseptic conditions.
- It undergo various processes of de-differentiation, redifferentiation and other morphogenic responses are induced.
- These events are stressful for the living tissue and may introduce genetic variations (eg: protoplast is without cell wall, resembles the infective process of some pathogens)
- Growth regulator stimulation cause somaclonal variations.
Factors that affect the In Vitro Induced Variations
- Age of the culture
- Frequency of variations increases with each multiplication cycle.
- Time period, for which culture is maintained under in vitro conditions.
- Composition of the culture medium
- Use of growth hormones (GH) enhances accumulation of variations.
- Potency of variation differs among different hormones.
- 2,4-D is highly mutagenic, favors polyploidy
- Growth habit or donor plant genotype
Somaclonal Variations Mechanism
- Chromosome number changes
- Gene Mutations
- DNA amplifications
- Hypomethylation of DNA
- Transposable Elements.
Chromosome number changes
- Ploidy changes are commonly observed in tissue culture raised plants.
- May arise from pre-existing variability or induced in in vitro cultures Structural changes in chromosomes like deletion or inversions etc.
Gene Mutations and DNA amplification
- Plant genomes can undergo multiple mutations during tissue cultures.
- Introduction of somaclonal variation may not be random process and part of a genome may be more susceptible to stress.
- Amplification of the specific DNA segments has reported and associated with the trait like amplification of glutamine synthase gene for herbicide resistance in alfalfa.
Hypomethylations of DNA
- In vitro cultures, directly influence the methylations patterns, usually causes hypomethylations.
- Growth regulators may induce specific type of methylation patterns like kinetin is associated with hypomethylations.
Transposable Element Activation
- Invitro culture stress can activate silent transposable elements.
Isolation of Somaclones
- In vivo Selection
- In vitro Selection
In vivo Selection
- Explants are cultured on suitable culture medium
- Cultured normally and plants are regenerated.
- Regenerated plants adapted to the field conditions
- Screening of regenerant for desired phenotypes.
- Selection of somaclonal variants
In vitro Selection
- Explants are cultured on suitable culture medium
- Callus proliferation and maintenance
- Calli are screened and selected for desirable trait.
- Resistant calli regenerated
- Regenerated somaclones are tested for desired trait
Invitro Selection Advantages
- Million of cells can be challenged with desired stress.
- Inputs w.r.t resources and efforts are also small.
- Trait is selected at initial stages hence it is less laborious and more productive.
Detection of Somaclonal Variants
- Cytological Methods
- Microscopic analysis of the karyotypes,
- Flow cytometry.
- Molecular Markers (Protein /DNA bases analysis)
- Protein-based markers like Isozymes. Altered electrophoretic mobility, altered protein levels, or loss/gain of protein
- DNA based markers like RFLP, RAPD, AFLPs, microsatellites, etc. Rapid DNA sequencing and lower cost have made sequencing-based markers more popular.
Advantages and disadvantages of somaclonal variation in plant tissue culture
Advantages of somaclonal variation
- Not good for micropropagation.
- Variation introduced are random, hence large number of progenies need to be screened.
- Most of the somaclonal variations may not be useful.
- Optimized regeneration protocols are required to create somaclones for any plant species.
- Variations are unpredictable and uncontrolled.
- May result in negative variations along with desired traits.
Disadvantages of somaclonal variation
- It can be used to generate new traits in the existing cultivar.
- Cultivars exhibiting disease resistance. Mildew resistance in Barley, resistance to fusarium in banana and tomato
- Tolerance to various abiotic stress factors like salt, drought, cold etc. Salt and heat tolerance in flax
- Tolerance to herbicides and resistance to insect damage.
- Other agronomically important traits like improving the quality, better yield, fruit quality etc.
- Variation in leaf and flower morphology and color variants.
Advantages | Disadvantages |
---|---|
Cheaper than other methods of genetic manipulation | Can lead to genetically unstable and undesirable variants |
No need for containment | May not be suitable for operations requiring clonal uniformity |
Tissue culture systems available for more plant species than other methods | Selected variants are random and genetically unstable |
Can generate genetic variability for plant/crop improvement | Requires extensive and time-consuming screening for desirable variants |
Can enrich for traits such as herbicide resistance, stress tolerance, and increased secondary metabolites | May not be suitable for breeding new species |
Can be used to obtain genetic variants that are difficult to breed or have narrow genetic bases | May not be suitable for operations requiring true-to-type plant material |
Applications of Somaclonal Variations
The five applications are:
- Production of agronomically useful plants
- Resistance to diseases
- Resistance to abiotic stresses
- Resistance to herbicides
- Improved seed quality.
Production of agronomically useful plants
As a result of somaclonal variations, several novel variants of existing crops have been developed, e.g., pure thorn-less blackberries. In Table, somaclonal variations in a selected list of crops with useful and improved morphological characters are given. The crops include rice, wheat, maize, sugarcane, potato, carrot etc.
Resistance to abiotic stresses
Somaclonal variation has resulted in several interesting biochemical mutants, which are being used in plant metabolic pathway studies, i.e. amino acid and secondary metabolic pathways. Investigations have shown that the level of free amino acids, especially proline, increases during cold hardening.2 In vitro selection has also been used to obtain plants with increased acid soil, salt, aluminium and herbicide resistance.
Lazar et al. (1988) developed somaclonal variants for freezing tolerance in Norstar winter wheat
It has been possible to develop biochemical mutants with abiotic stress resistance.
- Freezing tolerance e.g. wheat.
- Salt tolerance e.g., rice, maize, tobacco.
- Aluminium tolerance e.g., carrot, sorghum, tomato.
Resistance to diseases
Resistance was first reported in sugarcane for eye spot disease (Helminthosporium sacchari), downy mildew (Sclerospora sacchari) and Fiji virus disease by regenerating plants from the callus of susceptible clones and screening the somaclones.
Somaclonal variations have largely contributed towards the development of disease resistance in many crops e.g. rice, wheat, maize, sugarcane, tobacco, apple, tomato.
Resistance to herbicide
Certain somaclonal variants with herbicide resistance have been developed. Selected examples are given
- Tobacco resistant to glyphosate. (an analogue of the natural amino acid glycine)
- Carrot resistant to glyphosate.
Improved seed quality
A new variety of Lathyrus sativa seeds (grass pea, legume) with a low content of neurotoxin has been developed through somaclonal variations.
FAQs
Somaclonal Variation is a phenomenon observed in plants regenerated from somatic cells in tissue culture. Somatic cells, which are differentiated cells of a plant, undergo a regeneration process in vitro, leading to the development of whole plants. However, during this regeneration, genetic changes, known as Somaclonal Variations, can occur, resulting in plants with altered traits compared to the parent plant
Somaclonal Variations arise from several sources, including spontaneous mutations in the DNA sequence, chromosomal rearrangements, and epigenetic modifications such as changes in DNA methylation. The stress conditions imposed by the in vitro culture environment contribute to the genetic instability, leading to variations in the regenerated plants.
The molecular mechanisms of Somaclonal Variations involve various processes. Point mutations can occur in specific genes, altering their function. Changes in DNA methylation patterns can affect gene expression, and the activation of transposons (mobile genetic elements) can lead to genomic rearrangements. The stress-induced by the tissue culture conditions triggers these molecular changes, contributing to the observed genetic variations.
Somaclones are generated through different methods in plant tissue culture. Callus induction involves the formation of undifferentiated cell masses from explants, which can then develop into whole plants. Protoplast culture involves isolating individual plant cells, removing their cell walls, and regenerating plants from these protoplasts. Organogenesis is the process of inducing the formation of new organs or tissues from cultured cells or explants. Each of these methods provides opportunities for genetic variations to arise during the regeneration process.
Somaclonal Variations have practical applications in plant breeding and crop improvement. By selecting and propagating plants with desirable traits resulting from somaclonal variations, breeders can develop improved crop varieties. This can include traits such as disease resistance, stress tolerance, improved yield, and altered flowering patterns. Somaclonal Variation serves as a valuable tool for introducing genetic diversity into breeding programs, complementing traditional breeding methods.
Somaclonal variation in plant tissue culture has both advantages and disadvantages. One major advantage is that it leads to the creation of additional genetic variability, which can be useful for developing traits such as herbicide resistance, tolerance to environmental stress, and increased production of secondary metabolites. It is also cheaper than other methods of genetic manipulation and does not require containment.
However, somaclonal variation can also lead to genetically unstable and undesirable variants, which may not be suitable for operations requiring clonal uniformity, such as in the horticulture and forestry industries. Additionally, selected variants are random and require extensive and extended field trials. The molecular mechanisms underlying somaclonal variation involve cytological, biochemical, and genetic/epigenetic changes. These somaclones are generated through plant tissue culture techniques, which involve the isolation and culture of plant cells or tissues in a nutrient medium under sterile conditions.
References
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752953/
- https://www.plantcelltechnology.com/blogsomaclonal-variation-in-tissue-culture-definition-and-causes/
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9821087/
- https://en.wikipedia.org/wiki/Somaclonal_variation
- https://www.youtube.com/watch?v=3ldYQRmuqtE
- Duong Tan, Nhut & Nguyen, Hai & Minh-Thu, Pham-Thi & Thi, Nguyen Ngoc & Hien, Truong & Trần, Trọng-Tuấn & Nam, Nguyen & Huy, Nguyen & Hoang, Chien & Jain, Shri. (2013). Protocol for Inducing Flower Color Somaclonal Variation in Torenia (Torenia fournieri Lind.). Methods in molecular biology (Clifton, N.J.). 11013. 455-62. 10.1007/978-1-62703-074-8_34. ↩︎
- Introduction to Plant Biotechnology H.S. Chawla ISBN 978-1-57808-636-8 ↩︎