UDK 636.1/.2:599.723:575.174.015.3 ISSR-PCR AND MOBILE GENETIC ELEMENTS IN GENOMES OF FARM MAMMALIAN SPECIES 2 All-Russia Research and Development Institute for Livestock Husbandry, RAAS, Dubrovitsy settlement 142132, Moscow province, Russia 1 Russian State Agrarian University – Moscow Timiryazev Agricultural Academy, Moscow 127550, Russia e-mail: vglazko@yahoo.com V.I. Glazko1, E.A. Gladyr’2, A.V. Feofilov1, N.V. Bardukov1, T.T. Glazko1 Received January 11, 2013 S u m m a r y Highly polymorphic ISSR-PCR markers, the DNA fragments flanked by invert microsatellite repeats, are widely applied with the aim of the genomic scan (polyloci genotyping). <...> The sequencing of such DNA fragments from domestic horse and cattle genomes testified the close connection between the inverted microsatellite repeats and products of recombination between endogenous retroviruses. <...> Mutual genomic positioning of microsatellites and endogenous retroviruses as a source of polymorphisms of ISSR-PCR markers was discussed. <...> Current transition from genetics to genomics, from the study of individual genetic elements to the comparative analysis of entire genomes in nanometric scale opens up new possibilities for investigating genetic structures and their dynamics in different groups of living organisms. <...> Genomic scanning is becoming of particular importance as a basis for the analysis of gene pools of agricultural species, since only using the sufficient amount of genomic molecular markers is the way to preserve, manage, and improve biodiversity of such species. <...> Scanning may be performed at the level of a few tens or hundreds of markers, as well as complete sequencing of a whole genome (1). <...> Today, there are many methods of genome scanning, one of which is in polylocus genotyping for DNA fragments of different lengths flanked by inverted repeats of microsatellite loci (inter-simple sequence repeats - ISSR-PCR markers) (2). <...> Inverted repeats are of particular interest, because the capability of DNA to formation of a secondary structure (bulges, loops) is the basis of genomic instability in points of their location (3). <...> One of the features of ISSR-PCR markers, as well as other repeats such as SINE, is their uneven distribution over the genome (3, 4). <...> Moreover, as it was found earlier, certain ISSR-PCR markers in the genome of domestic horse show <...>