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Somaclonal variation is not restricted to, but is particularly common in, plants regenerated from callus. The variations can be genotypic or phenotypic, which in the latter case can be either genetic or epigenetic in origin. Typical genetic alterations are: changes in chromosome numbers (polyploidy and aneuploidy), chromosome structure (translocations, deletions, insertions and duplications) and DNA sequence (base mutations). A typical epigenetics-related event would be gene methylation.
If no visual, morphogenic changes are apparent, other plant screening procedures must be applied. There are both benefits and disadvantages to somaclonal variation. The phenomenon of high variability in individuals from plant cell cultures or adventitious shoots has been named somaclonal variation.
The major likely benefit of somaclonal variation in plant is improvement. Somaclonal variation leads to the creation of additional genetic variability. Characteristics for which somaclonal mutants can be enriched during in vitro culture includes resistance to disease pathotoxins, herbicides and tolerance to environmental or chemical stress, as well as for increased production of secondary metabolites. Micropropagation can be carried out throughout the year independent of the seasons and plants.
A serious disadvantage of somaclonal variation occurs in operations which require clonal uniformity, as in the horticulture and forestry industries where tissue culture is employed for rapid propagation of elite genotypes.
Reducing somaclonal variation
Different steps can be used to reduce somaclonal variation. It is well known that increasing numbers of subculture increases the likelihood of somaclonal variation, so the number of subcultures in micropropagation protocols should be kept to a minimum. Regular reinitiation of clones from new explants might reduce variability over time. Another way of reducing somaclonal variation is to avoid 2,4-D in the culture medium, as this hormone is known to introduce variation. Vitrification hyperhydracity may be a problem in some species.[clarification needed] In case of forest trees, mature elite trees can be identified and rapidly cloned by this technique.
High production cost has limited the application of this technique to more valuable ornamental crops and some fruit trees.
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