Molecular Markers for the Detection and Analysis of Somaclonal Variation

A diverse number of molecular techniques are nowadays available to approach the analysis of the genetic stability of plant material regenerated from tissue culture. Different molecular markers based on PCR provide useful tools to check the genetic and epigenetic variations associated to in vitro culture. Arbitrary amplifications, such as those obtained through RAPD, ISSR and AFLP markers, allow the assessment of the appearance of somaclonal variation, even in species with an unknown genome. Besides, specific markers as SSR may be employed in species for which genome information is available. Likewise, epigenetic changes are detected through molecular markers such as MSAP and metAFLP, based on AFLP technique. Recent studies are incorporating new sequencing technologies to explore changes in the genome of the regenerated plants capable of detecting genetic and epigenetic changes, allowing to evaluate simultaneously changes in gene expression associated to these variations. Regardless of the detection technique employed, the appropriate selection of samples and controls is important to obtain a reliable analysis of the genetic and epigenetic changes associated to a tissue culture process.