Somaclonal Variation: Its Genetic basis and Significance in Crop Improvement
Author: Prasanta Kumar Majhi
M. Sc. (Agri.), Junior Research Scholar, Department of Genetics and Plant Breeding, College of Agriculture, UAS, Dharwad, Karnataka, India.


  • Somaclonal variation is the variation in the tissues or plants derived from the in vitro somatic cell culture i.e. callus and suspension culture.
  • The term ‘somaclonal variation’ introduced by Larkin and Scowcroft in 1981 to describe all those variations which occurs in plants regenerated from any form of cell cultures or it refers to the heritable changes which accumulated in the callus from somatic explants and expression in the progeny of in vitro regenerates obtained from callus.
  • The somaclonal variation may be due to genetic or it may also result from culture induced epigenetic changes.
  • The epigenetic changes are expressed as cell; culture stage but usually disappear when plants are regenerated or reproduce sexually.
  • It is a wide spread phenomena reported in monocots (wheat, rice and maize), dicots (tomato, tobacco, brassica) and asexually propagated crop plants.

Based on the tissue from which the variation may arises, the somaclonal variation may be classified as:

  • Gametoclonal variation: Variation observed among the plants regenerated from gametic cultures.
  • Androclonal variation: Variation observed due to anther or pollen culture.
  • Gynoclonal variation: Variation observed due to ovule or ovary culture.
  • Protoclonal variation: Variation observed among plants due to protoplast culture.
  • Calliclonal variation: Variation observed among the plants due to callus culture.

  • Callus cultures are established from suitable explants and multiplied through periodic sub-culturing.
  • Similarly, cell suspension culture can be established by transferring actively growing callus to constantly agitated liquid medium and can be maintained or multiplied through periodic sub-culturing.

Various approaches are followed to isolate the somaclonal variants and these are:

  • Screening:
  • Large numbers of plants or cells are screened to isolate the variant individuals.
  • This approach is only feasible technique for the isolation for the mutants for yield and yield related traits, generally the R­ 1 progeny are scored for the identification of the variant plants and R2 progeny lines are evaluated for conformation.
  • Cell selection:
  • In cell selection approach, a suitable selection pressure is applied which permits the preferential survival/growth of variant cells only.
  • For example, selection of cells resistance to herbicides, various toxins and salt concentrations.
  • When the selection pressure allows only the mutant cells to survive and divide i.e. called positive selection. On the other hand, in the cause of negative selection, the wild type cells divide normally and therefore are killed by counter selection agent e.g., 5BUdR or arsenate.

  • The somaclonal variation may be genetic or epigenetic causes but out of these two, genetic variations are heritable where the epigenetic variation caused by cultural conditions is not heritable and hence no significance in sexually reproducing crops.
  • The genetic variation may be due to the following causes :
  • Chromosomal changes:
  • Polyploidy, aneuploidy (monosomic and trisomic) observed in oats, ryegrass, wheat, triticale and potato.
  • Deletion, inversion, translocation and duplication frequently observed in barley, wheat, potato and maize.
  • Recombination and chromosomal breakage occurs in preferential regions or ‘hot spots’ therefore causes higher rate of variation.
  • Mitotic crossing over:
  • Mitotic crossing over may account for some of the genetic variation that leads to the recovery of homozygous recessive single gene mutations in some regenerated plants.
  • Apparent point mutation:
  • The recessive single gene mutation are suspected if variants does not express itself in the R0 plants but the self-fertilized R1 progeny segregates in an expected 3:1 Mendelian ratio for a morphological trait.
  • Observerved in Maize, tobacco, rice and wheat etc.
  • Cytoplasmic genetic changes:
  • Mitochondrial DNA (mt-DNA) and chloroplast DNA are responsible for this variation.
  • In maize sensitivity to host specific toxin of Drechslera maydis race T, the causal agent of southern corn blight is associated with genotypes containing Texas cytoplasm (cms-T).
  • Restriction pattern changes in chloroplast DNA (cp-DNA) of tomato and mitochondrial DNA of potato have been observed.
  • Deamplification and amplification:
  • Deficiencies in ribosomal DNA (r-DNA deamplification) although not associated with changes in plant morphology but have been observed but iin molecular level in flax, triticale and potato.
  • On the other hand, gene amplification i.e. duplication have been observed in tobacco and tomato.
  • Transposable element activation:
  • Chromosomal breakage and fusion are the major cause of transposable element activation.
  • Observed in tobacco, alfalfa and maize.
  • Transposable elements are known to cause phenotypic changes in plants and their activation during in vitro culture causes somaclonal variation.
  • Virus elimination:
  • Virus infection in several instances causes changes in plant’s reaction to some other diseases.
  • For example, prior infection with barley yellow dwarf virus causes susceptibility to powdery mildew in oats.
  • Methylation and Demethylation of DNA:
  • Tissue specific DNA methylation and demethylation causes the somatic variation.
  • Gene activity like, transcription, replication and structural chromatin organization are somewhat related to DNA methylation.
  • Altered expression of multigene family:
  • Cultural conditions may regulate the expression of the multigene family in a way that a member gene which previously expressed some ergonomically important genes, including those for glidins, zeins, glutelins and alpha-amylase are coded on multi-gene family.
  • Heritable somaclonal variation observed for glidin- a storage protein and beta-amylase in wheat.

  • Degree of departure from organized growth:
  • Long term maintained callus culture and cell suspension culture are generally viewed as being genetically unstable and the plants regenerated from these cultures usually exhibit higher somaclonal variation.
  • Genetic constitution of the donor plant:
  • Somaclonal variation largely genotype dependent.
  • Polyploids generally exhibit higher chromosomal changes as compared to haploids and diploids.
  • Culture environment:
  • The degree of differentiation and the extent of proliferation largely depend on kinds and concentrations of growth regulators.
  • 2,4-D found to be produce more variation.
  • Ethylene (gaseous hormone) causes morphological variation in in vitro culture.
  • Tissue source:
  • D’ Amato (1985) grouped plants into two types viz., polysomatic and non-polysomatic plants.
  • In polysomatic plants, somatic cell may contain polyploidy and aneuploidy constituents. In non-polysomic plants the somatic cells exhibit the same polyploidy status as that of the zygotes.

  • Higher frequency of induction of variation.
  • Some unique desirable mutants are developed, joint less pedicel in tomato.
  • Reduces the time requirement to develop a new variety.
  • Used to identify new genotypes with all desirable characters.
  • It occurs for traits both nuclear and cytoplasmic traits.
  • Save time by reducing lengthy procedure of hybridization and selection.
  • Through wide hybridization it provides gene integration.
  • It can screen large number of plants at a time so save time, labours, space and other requirements.
  • This is the only approach for isolation of biochemical mutants in plants.
  • Helps in breaking the undesirable linkage.
  • Creates increased rate of recombination.

  • Reduced or no regeneration capacity of resistant clones.
  • This technique is applicable to only those species whose cell culture could regenerate complete plantlets.
  • Somaclones show undesirable genetic changes such as reduced fertility, growth even overall performance.
  • The phenotype expressed in selected cells may not be expressed by plant regenerated from them.
  • Only a small and variable proportion of plants is stable and transferred the character to the progeny.
  • Most of the variations are not useful.
  • Many somaclonal variants arise as a result of pleiotropic effects and may not be true variants.
  • There is very poor relationship between green house and field performance of somaclonal variants.


  • Somaclonal variation appears to be an important alternative for creation of genetic variability in crops where tissue culture plant regeneration system has been established.
  • Somaclonal variation has been described for a variety of both qualitative and quantitative traits.
  • Isolation of variants for disease resistance e.g., Helminthosporium leaf blight resistance in maize, bacterial wilt resistance in tomato.
  • A ‘Fiji’ disease resistance sugarcane line isolated from the variety ‘Pindar’ is released as a new variety called ‘Ono’.
  • Variation may arise for useful morphological characters. An improved scented Geranium variety named Velvate Rose has been developed from Rober’s lemon rose.
  • Isolation of genotypes resistance to abiotic stress e.g., high salt tolerance in tobacco.
  • Low temperature tolerance in chilli and tobacco ( N. sylvestris)
  • Isolation of mutants for efficient nutrient utilization. Tomato lines grow in phosphate deficient conditions due to high secretion of enzymes. Acid phosphatase has been isolated through in vitro selection.


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About Author / Additional Info:
I am currently continuing my M. Sc. (Agri.) on Genetics and Plant Breeding, College of Agriculture, UAS, Dharwad, Karnataka.