Somaclonal Variation: Sources, Achievements and Advantages
Authors: Kana Ram Kumawat, Ravi Kumar and Madhu Choudhary

Genetic variation found to occur between somaclones in plant tissue cultures was called somaclonal variation. This variation includes aneuploids, sterile plants and morphological variants, sometimes involving traits of economic importance in case of crop plants. The usefulness of variation was first demonstrated through the recovery of disease resistant plants in potato (resistance against late blight and early blight) and sugarcane (resistance against eye-spot disease, Fiji disease and downy mildew).

Sources of variation

The following are main sources of somaclonal variation:

Changes of mother plant origin: Chimeral rearrangement of tissue layers. These layers can be rearranged during rapid cellular proliferation. Therefore, regenerated plants may contain a different chimeral composition or may no longer be chimera at all. Cell variation also occurs if callus is initiated from explants containing differentiated and matured tissues that have specialized function.

Explant derived variation: The most stable cultures are obtained from meristematic tissue of a mature plant or tissues of a very young organ of meristematic nature. Polyploid cells can give more variability than diploids.

Ploidy changes: Three phenomena that occur during mitosis lead to most changes in ploidy like (i) Endomitosis (sister chromatids separate within the nuclear membrane, but there is neither spindle formation nor cytoplasmic division) (ii) Endoreduplication (chromosomes at interphase undergo extra duplications) (iii) Spindle fusion (giving binucleate or multinucleate cells).

Gross structural rearrangements: These appear to be a major cause of somaclonal variation. These involve large segments of chromosomes and so may affect several genes at a time like (i) Deletions (ii) Inversions (iii) Duplications and Translocations.

Transposable elements: These are segments of DNA that are mobile and can insert into coding regions of genes, typically resulting in a lack of expression of the gene. The culture environment may make the transposable elements more likely to excise and move.

Point mutations : This is the change of a single DNA base, if they take place within a coding region of a gene and result in the alteration of an amino acid, can lead to somaclonal variation. Point mutations are often spontaneous and are more difficult to detect. Note that they result in single gene changes.

Structural changes in the DNA sequence: Chromosomal rearrangements, point mutations, or transposition of transposable elements can occur during culture. These changes can occur spontaneously or can be induced with chemicals or radiation.

DNA methylation: Most of the mutational events occasioned by tissue culture are directly or indirectly related to alterations in the state of DNA methylation. A decrease in methylation correlates with increased gene activity.

Lack of nucleic acid precursors: Shortage of the precursor necessary for rapid nucleic acid biosynthesis, which occurs in many tissue cultures.

Growth regulators: One of the triggers of polyploidy in vitro is growth regulators; both kinetin and 2,4-D have been implicated.

Composition of culture medium: The level of KNO3 influences the albino plants from wheat cultures. Level of organic N2, chelating agents and other micro nutrients are other factors.

Culture conditions: Temperature, method of culture etc.

Effect of the genotype: Effects of the culture process itself (lengthy culture periods, growth and other aspects of the culture medium may also affect the ploidy of the cultured cells. Medium that places cells under nutrient limitation will favor the development of "abnormal" cells.


Over a dozen varieties have been developed through the exploitation of somaclonal variation.

  • ‘Ono’ variety of sugarcane is a Fiji disease resistant somaclone of the susceptible cultivar ‘Pindar’. It was identified by screening of plants regenerated from unselected calli. ‘Ono’ also shows yield advantage over ‘Pindar’ and has been cultivated to a limited extent in Fiji.
  • A sweet potato cultivar ‘Scarlet’ was selected from shoot tip culture derived clones. ‘Scarlet’ is comparable to the parent cultivar in yield and disease resistance, but shows darker and more stable skin colour, which is a desirable quality trait.
  • A geranium variety called ‘Velvet Rose’ is a somaclone of ‘Rober’s Lemon Rose’. The new variety has twice the chromosome number of the parent variety.
  • An alfalfa variety called ‘Sigma’ is a polycross of selected somaclones.
  • In India, a somaclonal variant of Citronella java, a medicinal plant, has been released as ‘Bio-13’ for commercial cultivation by CIMAP (Central Institute for Medicinal and Aromatic Plants), Lucknow. Bio-13 yields 37% more oil and 39% more citronellol than the control varieties.
  • A somaclonal variant of the B. juncea variety ‘Varuna’ has been released for commercial cultivation as ‘Pusa Jai Kisan’. The new variety has bolder seeds and some yield advantage over the parent variety Varuna.


The following are main advantages of somaclonal variation:

  • Somaclonal variations occur in rather high frequencies, which is a great advantage over conventional mutagenesis.
  • Some ‘new’ alleles or even ‘new’ mutations may be isolated which were not available in the germplasm or through mutagenesis, e.g., joint less pedicel mutant in tomato.
  • Use of somaclonal variation may reduce by two years the time required for the release of new variety as compared to mutation breeding. This is because somaclonal variations are usually free from undesirable features like sterility, while induced mutations are generally associated with such defects, which necessitate one or two backcrosses with the parent variety.
  • A very effective selection can be practised at the cell level for several traits, e.g., disease resistance etc. This approach effectively selects few desirable cells from among millions with relatively small effort, time, cost and space requirements.
This is the only approach for the isolation of biochemical mutants, especially auxotrophic mutants, in plants.

About Author / Additional Info:
Post-Graduated in subject of Plant Breeding and Genetics from SKNAU, Jobner