Development of a sequence characterized amplified region (SCAR) marker for the identification of the potato cultivars Astrid and Mnandi

Astrid and Mnandi are two closely related potato cultivars of commercial importance in Southern Africa. Random amplified polymorphic DNA (RAPD) markers were screened and a sequence characterized amplified region (SCAR) marker was developed to distinguish between these two cultivars since it is very difficult to distinguish between them on morphological grounds alone. 96 RAPD primer combinations were screened in order to identify cultivar specific polymorphisms. A total of 706 loci were observed with an average of 7.3 loci per primer. Two polymorphisms unique to cv Mnandi, were identified with the decamer primers UBC-509 and UBC-582 and corresponded to the presence of fragments of 300 bp and 900 bp respectively. These fragments were cloned and the nucleotide sequences determined. The sequence of the fragment from UBC-509₃₀₀ was used to design a set of twenty mer SCAR primers. This set of SCAR primers amplified a 260 bp fragment unique to cv Mnandi, which could be used to distinguish the genotype from cv Astrid.