The Possible Mechanisms Causing Somaclonal Variation

In this article, we will discuss about the possible mechanisms causing somaclonal variations.

What is Somaclonal Variation?

Plants derived from tissue culture has been variously referred to as somaclones or calliclones or protoclones and the variations displayed by such plants are simply called ‘somaclonal varia­tion’.

According to Larkin and Scowcroft (1986), ‘somaclonal variation is the genetic variability which is regenerated during tissue culture.’

Vari­ations for karyotype, isoenzyme characteristics and morphological variations in somaclones have been commonly observed. Such variations mani­fest themselves as heritable mutation and persist in the plant population even after transplanta­tion to the field.

Sometimes, phenotypic varia­tions may arise in the progeny of plants regener­ated from culture, but after the transplantation to the field, the plants exhibit the parental char­acteristic during their further growth and devel­opment. Such variations are not considered as somaclonal variations.

Mechanisms Causing Somaclonal Variation:

The somaclonal variation may be attributed to either:

(i) Pre-existing variation in the somatic cells of the explant (genetic) or

(ii) Variation gen­erated during tissue culture (epigenetic). Often both factors may contribute.

The original ploidy level of the plant or plant organ from which the explant is taken, may play an important role in somaclonal variation. Meristematic explants such as apical meristem, derived from either shoot apex or axillary bud,’ have a lesser degree of genetic variability as com­pared to plants regenerated from non-meristematic explants which generally produce genetic variability.

Cells of meristematic explant divide by normal mitosis and cells are maintained at a uniformly diploid level. However, the cells in non-meristematic explant are the derivatives of the meristematic part of the plant and during their subsequent differentiation, do not divide by normal mitosis, but undergo DNA duplication and endoreduplication.

The varying degrees of endoreduplication results in the cells. Endoredu­plication leads to the formation of chromosomes with four chromatids (diplochromosomes), chro­mosomes with eight chromatids (quadruplochromosomes) and polytene condition (polychromosomes).

When the cells of various genomic constitu­tion of the initial explants are induced to divide in culture, the cells may exhibit changes in chro­mosome number such as aneuploids and poly­ploids, but very often from these mixoploid cal­lus cultures. Organogenesis and/or embryogen­esis occur mostly from diploid cells. Therefore, pre-existing variations in the explant tissue does not always rule out the somaclonal variation in culture.

In sugarcane somaclonal variants, cor­relation between changes in chromosome num­ber and certain traits such as Fiji disease resis­tance and morphological modification could not be found. Again normal karyotype was found amongst most of the cauliflower somaclonal vari­ation.

The presence of several chromosomal aberrations such as reciprocal translocation, deletions, inversion, chromosome breakage, re­union, multi-centric, acentric fragments, heteromorphic pairing etc. were found among the so­maclones of barley, ryegrass, garlic and oat. Be­sides these relatively large changes in chromo­some constitution, there are examples of phenotypic variation which can be observed in plants regenerated from cultured cells or protoplasts where no apparent chromosomal abnormalities are seen.

This variation often occurs at a high frequency. The apparent non-chromosomal vari­ation in regenerated plants has a genetic basis. There is now sufficient direct as well as circum­stantial evidence to indicate that most of the variations seen in culture or in regenerates oc­cur during the culture phase. This does not pre­clude pre-existing variation in the original explant as providing some of the variations, but this seems to be a small component.

Not only the source of explant, explant age are the cause of variation among the regenerants in culture, cultural environment, duration of culture, chem­ical additives and growth stimulants or regula­tors are also associated with the genetic vari­ability of regenerated plants from tissue cultures derived from such explants. Even under most favourable conditions, mutations will occur at a low frequency in a growing culture.

This vari­ation may not only be attributed to the many varied nutrient media used and different cultural conditions adopted but also to mutagenic effects of metabolic products that accumulate in the medium. We are still largely ignorant of the fun­damental cause of chromosomal mutation. Par­ticularly, extended culture periods can result in cell lines and regenerated plants with chromoso­mal abnormalities.

A component of the culture medium that is capable of inducing chromosomal variation could also cause nuclear gene muta­tion. Apart from karyotype abnormalities, there is little hard evidence to support or favour any one of several possible mechanisms to account for somaclonal variation. Chromsomal abnor­malities are part of the spectrum of somaclonal variation and they, as well as other classes of somaclonal variants, may have a more funda­mental biological basis.

DNA sequence ampli­fication could be one of the mechanisms respon­sible for somaclonal variation. Such amplifica­tion could lead either to increased synthesis of a specific gene product or to perturbations in developmental timing of gene activity if the re­peat sequences function in new chromosomal lo­cations. Barbara McClintock postulated the ex­istence of genetic elements which transpose from one location in the genome to another in eukaryotes. Transposition occurs in both somatic and germ lines cells.

By virtue of their movement, transposable elements can inactivate structural genes, other gene regulation, possibly reactivate silenced genes and can generate duplications and deficiencies. Though not understood, genomic and developmental shock can induce the trans­position of mobile elements.

Concrete evidence has yet to be presented that transposition events are a cause of somaclonal variation in plants. A greater understanding of somaclonal variation will only come from the molecular analysis of mutants. The cloning and sequencing of vari­ant genes will provide information on changes in copy number, integrity of the structural gene and its regulator sequences.