Several possible mechanisms are responsible for the origin of somaclonal variation. Number of processes can operate simultaneously in one culture. The mechanisms are: 1. Karyotypic Change 2. Chromosomal Rearrangement 3. Nucleotide Pool Imbalance 4. Cryptic Transposable Elements 5. Gene Amplification 6. Somatic Gene Rearrangement 7. Somatic Crossing Over.
Mechanism # 1. Karyotypic Change:
Several plants alter their chromosome number in culture and culture derived plants. Gross karyotypic alterations have been observed in tissue cultured plant cells. Certain karyotypic changes such as aneuploidy or polyploidy is responsible for the generation of somaclones. It is possible that variations occur in plants having normal karyotype.
For example, studies on five protoclones of tobacco shows that normal karyotype proved the requirement of further cyto-logical investigation. It is well documented that chromosome number shift in sugarcane can occur in culture and also in regenerated plants. In addition, several cauliflower somaclones had normal karyotype (2n = 18) and most of the garlic, lolium × fustula somaclones variants clearly exhibit normal karyotype.
These results have shown that gross karyotype change possibly originated from culture, and are not necessary for the formation of somaclones variation. Therefore implication of gross karyotype change for somaclones variation was a myth in the culture. There was not much emphasis on connection between karyotype changes and somaclones variation in cultured plants.
Mechanism # 2. Chromosomal Rearrangement:
It has been elusive that several cryptic chromosomal rearrangements in tissue culture conditions may be responsible for somaclonal variation in cultured cells. Tissue culture derived barley plants show breakage, reunion and translocations in their chromosomes. Similarly, the meiotic chromosome behavior of rye grass culturing suggested the presence of reciprocal translocations, deletions and inversions.
The same line of chromosomal irregularities such as breaks, acentric and centric fragments, ring chromosomes and micronucleii was noticed in the mixaploid garlic plants. The extent of somaclonal variation in the above set of chromosomal rearrangement resulted in the considerable loss of certain genetic material which may result in somaclonal variations, appears visible in the phenotype.
While affecting the gene during chromosome breaks neighbouring genes also get affected. If reunion or transposition to a different site occurs then, distant gene functions may also be altered. This phenomenon is known as the position effect and is believed to occur in plants such as Oneothera. These cryptic changes associated with chromosomal rearrangement not only result in the loss of genes and their functions but also the expression of genes.
In the tissue culture induced chromosomal rearrangement, potentials of late replication of DNA have been recognized. In the callus cultures of Crepis capillaris, the SAT chromosome involved in 80% of the rearrangement with the break points corresponding to a region of late DNA synthesis was proved that any perturbation affecting the synchrony between chromosome replication during S-phase and cell division would invariably attract chromosomal aberrations.
The synthesis of seed storage proteins are controlled by multi gene families. Wheat seed proteins like gliadins are encoded by multi gene families. In many somaclonal families heritable variation of gliadin proteins are determined by electrophoretic banding profiles, loss of specific bands, appearance of new bands and changes in band intensity are some of the heritable changes associated with gliadin proteins.
Mechanism # 3. Nucleotide Pool Imbalance:
Availability of deoxyribonucleotide reserve within the cells exhibits significant influence on the fedility of prokaryotic and eukaryotic DNA metabolism, including precursor biosynthesis, replication and repair.
Imbalance in the nucleotide reserve may have serious implications on nuclear DNA as well as organellar DNA mutation. In addition, wide array of anomalies like chromosomal aberrations, aneuploidy, and sister chromatid exchange, increased sensitivity to mutagens and cold witnessed inside the cells result in high degree of genetic variation.
Plant tissue and cell culture provides ideal conditions for the induction of imbalanced nucleotide reserve pool particularly during serially transfer from depleted to fresh medium. That means media component gets completely depleted towards the end of subculture. As a consequence, metabolic process fluctuates with subculture intervals and may be responsible for somaclonal variation.
Mechanism # 4. Cryptic Transposable Elements:
Transposable elements are movable genetic elements widely present in prokaryote to eukaryotic system. Transposable elements can influence the expression of neighboring genetic elements due to its excision and reinsertion process. Excision of transposable elements may attract rearrangements of adjacent chromosomal sequence.
The concept of the controlling elements was developed by Maclintock in maize plants. Involvement of transposable elements in the generation of somaclonal variation was developed by Larkin and Scowcraft. Subsequent reports in maize consolidated his hypothesis. Activation of maize transposable elements following tissue culture has been documented for Ac transposable system.
Discovery of Ac element has been documented in embryo drived callus culture of maize. It is well conceivable that transposition events may result in somaclonal variation. The tissue culture environment is highly conducive for DNA sequence transposition. The discovery of activation of maize transposable in tissue culture reveals that there is a possible relationship between somaclonal and transposable elements.
The occurrence of unstable alleles has been one of the significant factors associated with transposable elements activity. Experiment with tissue culture induced single gene variation shows that most variants exhibit stable expression over several generations. However, instability of expressions has been recorded in the anthocyanin level of alfalfa flower.
Mechanism # 5. Gene Amplification:
In higher organisms, certain specific genes can undergo amplification during differentiation or in response to environmental pressure. Gene amplification was evidenced in several animal systems, for example, in mouse cell culture, the dihydrofolate reductase (DHFR) gene was found to have amplified more than 200 folds, while selecting resistant cell line to methotrexate which inhibits DHFR activity.
Plant system also has gene amplification process. Gene amplification in response to herbicide has been reported in alfalfa and petunia cell culture. In alfalfa cell suspension culture there was 4-11 fold amplification of glutamine synthase (GS) gene. Similarly, in herbicide tolerant petunia cells, enoyl pyruvyl shikimate-3-phosphate (EPSP) synthase gene was amplified to 20 folds.
There has been report on amplification of genes in response to herbicide selection in alfalfa and petunia cells in culture. Alfalfa suspension cells exhibiting resistance to phosphinothricine were characterized by 4-11 fold amplification of glutamine synthase gene and consequently 8-fold increase in corresponding mRNA level. Similarly, amplification of EPSP synthase gene was also noticed in cell tolerance to glyphosate herbicide.
Mechanism # 6. Somatic Gene Rearrangement:
Several examples of somatic gene arrangement have been recorded in animal system, in which mouse embryonic cells to plasma cells involves chromosomal gene arrangement. It is assumed that the germ line cells are unaffected.
It would also be possible that somatic gene arrangement will also occur in higher plants. If so then the regenerated plants from somatic cells by culture encourages somatic gene rearrangement seen in the new germ line.
Mechanism # 7. Somatic Crossing Over:
Generally, crossing over takes place in germ cells. But crossing over in vegetative cells is rare and this was witnessed in Drosophila. However, this has been reported in plants like Nicotiana tobaccum, Lycopersicum esculentum, Tradescantia hirsuites and Gossipium barbadens.
Several environmental factors are responsible for crossing over in vegetative cells. For example, X-ray irradiation enhanced crossing over frequency in soyabean. Tissue culture conditions are suitable for the generation of genetic variation.
Hence, somatic crossing over is one of the phenomena contributed in the production of somaclones. Somatic crossing over frequency is significant if the exchange were asymmetric or between non-homologous chromsomes.
In addition, asymmetric level of sister chromatid exchange in somatic cells led to deletion and duplication of genetic material. Asymmetric sister chromatid exchange in Vicia faba were thought to occur mainly in AT rich segments.