Genome structure and genetic diversity

Genetic landscape of bovine genome attracts a lot of attention in recent years. This is due to the complexity of genomic selection task solution, i.e. the use of multilocus genotypes in order to simplify and hasten breeding. Accumulated data show that there is high evolutionary speed of different genetic elements and also they have structure functional polymorphism intensity (L. Chen et al., 2017). It was shown that interspersed repeats account for about 50 % of nucleotide sequence of the bovine genome (R.L. Tellam et al., 2009). Also it was found that some of the interspersed repeats cluster into conservative domains along the bovine genome due to joint localization (D.L. Adelson et al., 2009). The characteristics of domain distribution are still not fully studied despite the fact that it is very important to identify conservative and variable domains throughout the bovine genome to solve traditional tasks of their genetic resources management and controlling. In this work domain distribution of mobile genetic elements and their products of recombination in nucleotide sequences of 13,436,028 nucleotides of bovine chromosome 1 were analyzed by means of Repeat Masker mobile genetic elements database and Integrated Genome Browser software. It was revealed that the most prevalent types throughout analyzed region are SINE/tRNA-Core-RTE, LINE/RTE-BovB, LINE/L1 and LTR/ERV. Their joint localization in bovine genome has complicated structure. The most common pairwise clusters are SINE and LINE, SINE/tRNA-Core-RTE and LTR EVR, (LTR/ERVK)/(LINE/RTEBovB), (LTR/ERVK)/(LINE/L1). Two last pairs are the bases for such triple clusters as (LINE/RTEBovB)/(BTLTR1)/(LINE/RTE-BovB) and (LINE/L1)/(BTLTR1J)/(LINE/L1). It should be mentioned that there is no such clustering with other retrotransposons. It was revealed that there is some certain bias of these triple clusters high density to the distal end of studied region of chromosome 1. By the means of Integrated Genome Browser software the localization of obtained triple products of recombination between LINE and LTR ERV to structural genes was analyzed. It was found that only 34 clusters are localized in 12 structural genes (other are located in intergenic space). Besides, 10 and 12 copies are located in two genes that are closely connected with the function of central nervous system in mammals, grik1 and app. The fact that 9 copies of triple gene construct (LINE/RTE-BovB)/(BTLTR1)/(LINE/RTE-BovB) are found in each of two genes and (LINE/L1)/(BTLTR1J)/(LINE/L1) had only 1 copy in grik1 and 3 copies in app, suggests that these genes are ancestral targets for such insertions and their conservations. It also should be mentioned that (LINE/L1)/(BTLTR1J)/(LINE/L1) construct was found only in these two genes but not in other 10 genes where (LINE/RTE-BovB)/(BTLTR1)/(LINE/RTE-BovB) is also located. Specific features of distribution of products of recombination between LINE and LTR ERV throughout the studied chromosome 1 area and their localization in structural genes suggest the possible presence of structure functional elements there. Revealing of such elements is the subject of our further study.