A rather simple method of detecting DNA polymorphism in dogs in the form of amplification of random fragments of the genome using RAPD analysis with primers with arbitrary nucleotide sequences, which does not require prior knowledge of the sequences of nitrogenous bases of the detected DNA fragments, is considered. However, information about the complete genomes of the investigating species of organisms and, dogs in particular, allows with a preliminary in silico RAPD analysis to predict the expected results for each primer and their multiplex composition, which makes it possible at this stage to reject unsuitable primers before conducting "wet" experiments. In the case of known genomes of a number of related organisms for example in this case dogs, the multiplex RAPD analysis conducted in silico with six decameric primers, the sequences of which exclude the formation of homo- and heterodimers in PCR showed both genomic similarities and differences between different breeds, as well as with their wild relative gray wolf. Multiplex in silico RAPD analysis is a virtual PCR and if amplicons common to all studied organisms are removed from such amplification, leaving only significant ones, then this tool in the form of the ABCDNA_GS program created by us can be used to establish phylogenetic kinship, especially of those organisms whose genomes are highly collinear, which is just typical of the genomes of different dog breeds.
Simple method for analyzing the pattern of DNA polymorphism and its application to SNP data of human
