In this, an approach was based on identifying association of animal production traits’ variability to polymorphism in different genome elements, from microsatellite loci to millions of single nucleotide polymorphisms (SNPs), in genome-wide sequencing. <...> Despite numerous accumulated data, the development of relatively simple, fast and affordable to interpretation methods of polyloci genotyping (genome scan) for assessing breed «gene pool standard» or genomic selection is still actual. <...> The mobile genetic elements, being high polymorphic genomic sites, can serve as anchors in a multi-locus genotyping. <...> The species-specific retrotransposons such as L1_BT LINE which present in the bovine genome with high frequency and the endogenous retrovirus ENV1_BT are of particular interest. <...> In this regard, the aim of this work was the comparative analysis of polymorphism in genomic DNA fragments flanked by inverted repeats of nucleotide sequences homologous to fragments of these retrotransposons in genomes of specialized dairy Ayrshire and Black and White Holstein breeds and the Kalmyk beef breed. <...> A recombination between L1_BT LINE and ENV1_BT we reported earlier turned out to be conservative in studied breeds. <...> Since the genetic relationships identified from distribution patterns and length polymorphisms of DNA flanked by ENV1_BT inverted repeats differed significantly between specialized dairy breeds and local meat breed but were low variable within the breeds, this allowed to conclude about its relatively low transposition activity. <...> The PIC values (polymorphic information content) for spectra produced in PCR with the endogenous retrovirus ERV1_BT fragment as a primer ranged from 0.075 to 0.089 for studied breeds. <...> Distribution of inverted repeats homologous to L1_BT was different in character and varied among breeds and within breeds, the PIC values were substantially higher and ranged from 0.062 to 0.260. <...> Thus, the use of multi-locus genotyping of transposable elements is effective for the purposes of animal genetics and breeding but their application depends on transposition activity. <...> Our data showed that the ENV1_BT inverted repeats seem to be convenient marker in genetic differentiation among breeds and revealing «gene pool standard», whereas more transposable L1_BT elements are more relevant in indicating individual variability within a breed. <...> In recent years, a possible inclusion of genomic selection in traditional cattle breeding programs attracts the increasing attention [1-4]. <...> To identify the genomic targets of artificial selection <...>