Somaclonal variation in plants: causes and detection methods

Abstract

Plant tissue culture has become one of the fundamental tools of plant science research. It is extensively employed in the production, conservation and improvement of plant resources. The presence of somaclonal variation in populations derived from tissue culture is affecting the use of tissue culture negatively and has remained a major problem. Conversely, it is a source of new desirable clones/variants with better agronomic traits. In this review, we summarize the possible causes, detection methods and desirability of variants. Somaclonal variation is one of the most researched and reviewed topics. Hence, we restricted ourselves to outlining various examples which may be used as important references for researchers who intend to identify and/or characterize somaclonal variants while using tissue culture for research and production. Emphasis is placed on the negative effects of somaclonal variation. However, this review also includes examples of some useful variants generated as a result of somaclonal variation.

Somaclonal Variation During Picea abies and P. omorika Somatic Embryogenesis and Cryopreservation

“…The changes noted at CSE may result from a long-term proliferation/maintenance of ETs on the Picloram-containing medium (or from the stress caused by the conditions applied during maturation of somatic embryos, i.e., high osmoticum and the presence of ABA. The induction of somaclonal variation during SE is frequently ascribed to different physicochemical factors to which unprotected genetic material is exposed and reduced selection in the culture environment that enables the maintenance of mutated genomes (Bairu et al, 2011;Dey et al, 2015). Our results are consistent with the opinion that the cultivation period and conditions in which somatic embryos mature are likely the factors inducing somaclonal variations (Evans and Sharp, 1988;NawrotChorabik, 2009;Dey et al, 2015).…”

“…The risk of somaclonal changes to the genome of the propagated material is especially increased during SE, when the plant material is maintained in the form of callus (embryogenic tissue), which is particularly sensitive to such changes (Kunakh, 1999). Some results have shown that various changes at the morphological, biochemical, genetic and epigenetic levels appear not only during in vitro propagation (Bairu et al, 2011;Etienne and Bertrand, 2003;Peredo et al, 2006, Bradai et al, 2016, but also after cryopreservation, probably because of the routine use of factors with mutagenic effects, for example DMSO (Aronen et al, 1999). Genotypic instability during SE or storage in LN may have a significant influence on the quality of the material, i.e., clonal individuals obtained via tissue culture.…”

“…Microsatellites are 1-6 nucleotide-long DNA sequences occurring extremely commonly in the genomes of Eucaryota in the form of perfect or near-perfect tandem iterations (Ellegren, 2004;Lopes et al, 2009). The number of these repeats may easily change due to various factors including those directly related to the mutagenic factors associated with in vitro techniques (Bairu et al, 2011). SSR markers demonstrate an advantage over other types of molecular markers mainly due to their characteristics, i.e., a high degree of polymorphism because of an intrinsically high mutation rate, codominant inheritance and a wide distribution over the genome.…”

“…SSR markers demonstrate an advantage over other types of molecular markers mainly due to their characteristics, i.e., a high degree of polymorphism because of an intrinsically high mutation rate, codominant inheritance and a wide distribution over the genome. Additionally, the high reliability of this technique in comparison with other markers derived via random amplification of genome regions, such as RAPD, renders SSR a suitable tool for monitoring putative mutation events during SE (Bairu et al, 2011).…”

Micropropagation of the Narrow Endemic Hladnikia pastinacifolia (Apiaceae)

“…Several institutions, like the Kew and Missouri Botanical Gardens (Sarasan et al 2006), and the Botanic Garden of the University of Coimbra for endemic Apiaceae, are now using this strategy to propagate and maintain endangered and endemic species (Tavares et al 2009(Tavares et al -2010(Tavares et al , 2010b). The problems with such propagation include the potential for somaclonal variation, as a consequence of either genetic or epigenetic changes in the tissue culturepropagated material (Bairu et al 2011). To obtain plant material that is as genetically stable and uniform as possible, with a low probability of genetic or epigenetic variation, micropropagation must be carried out through shoot tip or axillary bud proliferation (Pierik 1991).…”