Changes in the cytoplasmic genome have also been observed in somaclones. Gengenbach et al. (1977) observed that maize genotypes having male sterile cytoplasm were also sensitive to the toxin secreted by the microorganism Drechslera maydis race T. In an attempt to combine resistance to toxin with the Texas male sterile cytoplasm trait in maize plant, they succeeded in selecting resistant plants associated with concomitant reversion to male fertility.

Another aspect of single gene mutation responsible for somaclonal variation relates to transposable elements. Varia­tions have been reported as a result of insertion of plasmid like DNA in the mitochondrial genome of cell cultures of maize, tobacco, wheat, and alfalfa.

Further recombination or chromosome breakage at a preferential region or "hot spots" of a particular chromosome affect the genome in a disproportionately high frequency, resulting in altered phenotypic expressions.Recent studies have shown that changes in the organelle DNA, isoenzyme and protein profiles correlate with the occurrence of somaclonal variation in plants.

Some restriction enzymes can readily be distinguished between internal and external cytosine methylation patterns at the restriction site, which appears altered in somaclonal variants. Carlson (1983) considered somaclonal variation to be due to dominance of nonlethal mutations that lead to heterozygosis with a wild type allele.