Background: DNA transposons helitrons are mobile genetic elements responsible for major
movements of the genetic material within and across different genomes. This ability makes helitrons
suitable candidate elements for the development of new approaches of multilocus genotyping of
livestock animals, along with the well-known microsatellite loci.
Objective: We aimed to estimate the informativeness of helitron and microsatellite markers in assessing
the consolidation and the "gene pool" standards of two commercial dairy cattle breeds (Ayrshire
breed and holsteinized Black-and-White cattle) and one local breed of Kalmyk cattle, and to reveal
any interbreed difference in the organization of genomic regions flanked by helitrons in the studied
Method: We used the combination of two highly-polymorphic genomic elements – helitrons and
trinucleotide microsatellites (AGC)6G and (GAG)6C, respectively – for genome scanning of the sampled
groups of cattle. Also, we pyrosequenced the genomic regions flanked by the inverted repeats of
3'-end of Heligloria family of helitron fragments.
Results: Generally, the both combinations of markers generated polymorphic spectra, based on which
certain interbreed differentiation could be observed. The analysis of the identified interspersed repeats
suggests that in factory and local cattle the genomic regions flanked by helitron fragments are shaped
differently and contain different superfamilies of transposable elements, especially retrotransposons.
Conclusion: Despite the well-known fact of retrotransposon-dependent microsatellite expansion, our
data suggest that, in the cattle genome, the DNA transposons and microsatellites can also be found in
close neighbourhood, and that helitrons and retrotransposons may form domains of increased variability
– targets for factors of artificial selection.