User:Epigeny/sandbox

Terminology and historical aspects
Somaclonal variation  is one of the terms used to describe the variability of regenerated plants issued from calluses obtained by in vitro tissue culture. After initiation of plant regeneration through in vitro tissue cultures summarized by Gautheret since the 1950's , the first observations of unexpected variability were essentially reported since the end of 1969's and the beginning of 1970's. It was showed modifications at many biological levels as external or phenotypic traits, but also biochemical functioning and sometimes in chromosome numbers or organisation.

Not only regenerated plants from calluses or cells of somatic tissues of homozygous material showed this variability, but also plants issued from somatic embryos obtained on anther diploid tissues, and gametophytic plants from pollen or unfertilized ovaries. So in vitro regenerants from most tissues are concerned with this variability, and the term "vitrovariation" is also used sometimes.

The genetic heredities of the new characteristics of the vitroplants originated from tissues of homozygous plants have thus been analyzed. In some cases, they showed to be transmitted through either successive selfings or after reciprocal crosses. Futhermore, beyond mutations phenomenon, chromosome numbers or structural chromosomic modifications concerning some of these changing, for others, all the heredities studies through data associated with statistical analyses of either qualitative (morphological, biochemical) or quantitative characters (developmental), led consistently to epigenetic behaviours.

Biological bases of somaclonal variations
High mutation levels were often observed in plants issued from long duration in vitro calluses cultures, and in some species modifications concerning karyotypic abnormalities (aneuploidy, polyploidy) were dectected by chromosome countings in the cells of the strains or in the roots tips of the regenerated plants. Chromosomal rearrangements, as translocations, deletions, insertions or duplications, can also be one of the cause of variation, and all these are summarized in many review publications. But one must not forget that more surprising modifications can appear supported by epigenetic bases. One of the epigenetics-related event might be gene methylation, but small interfering RNA (related to microRNA) should well also be concerned.

Duration of in vitro culture and variability
It has long ago been demonstrated that duration of in vitro callus stage shows to be related to an increase of mutation frequencies and variabilities of the regenerated plants (Skirvin, Janick, Deshayes, Buiatti, and many others), while epigenetics modifications seem to appear right from the start of the in vitro cycles, and their frequencies show to be stabilized by the third or even second transfer (-)

Experiments to clarify the location of the genetic bases of the modifications
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.

Advantages
The major likely benefit of somaclonal variation is plant/crop 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, high salt concentration, mineral toxicity and tolerance to environmental or chemical stress, as well as for increased production of secondary metabolites.

suitable for breeding of new species

Disadvantages
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.
 * Sometimes leads to undesirable results
 * Selected variants are random and genetically unstable
 * Require extensive and extended field trials
 * Not suitable for complex agronomic traits like yield, quality etc.
 * May develop variants with pleiotropic effects which are not true.

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, commonly referred to as hyperhydricity in the tissue culture world, may be a problem in some species. Hyperhydricity is a physiological malformation that results in excessive hydration, low lignification, impaired stomatal function and reduced mechanical strength of tissue culture-generated plants. 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.