Potato is an important global food source. The tetraploid potato is a genetically complex and heterozygous crop, which makes it difficult to introgress desirable traits from wild relatives. Therefore, in order to increase the genetic variability of the breeding material, mutagenesis is effectively used, for instance, by chemical agents.

This chapter summarizes the results obtained at the Maritsa Vegetable Crops Research Institute in Plovdiv, Bulgaria, with regard to the evaluation of the genetic diversity of local potato varieties and 16 advanced mutant lines (M1V8) and the corresponding parental components which were divided into four groups according the origin on the initial genotypes, using the retrotransposon-based molecular technique of inter-SINE amplified polymorphism (ISAP).

ISAP reactions with the two SINE families (SolS-IIIa and SolS-IV) proved to be the most efficient for the molecular identification. Of all the three reactions (SolS-IIIa-F/R, SolS-IV-F/R, SolS-IIIa-F/SolS-IV-R) performed on the 16 mutant lines, including parents and control lines, three mutant lines (M-I-8, M-IV-17, M-VII-27), two control lines (K-IV-3, K-VII-4), and all parent lines (PC428, PC490, PC707, PC538, PC757) were characterized by unique profiles.

The present study can be used as a basis for future research in potato breeding. The selection of mutant lines with high-productivity morphological and molecular data and their combination are of great importance for breeding new valuable mutant varieties.