In this thesis more than 777000 single nucleotide polymorphisms (SNPs) from several indicine and taurine cattle breeds were used to evaluate differences in the genome of these two bovine subspecies, including assessment of the levels of linkage disequilibrium (LD), detection of signatures of selection (SS), and evaluation of the levels of taurine introgression in two important Brazilian indicine breeds. Analyses of LD decay at different distances and application of a lower marker density and a set with a specific minor allele frequency (MAF) distribution, showed higher LD and an advantage in the use of higher densities especially at close inter-marker distances. Lower levels of LD in indicine breeds were confirmed, particularly at less than 100kb inter-marker distances, and no effect of MAF on the estimation of r LD levels was observed. Application of two methods for discovery of SS confirmed the usefulness of using higher density genotypes and the potential of comparing the genome of subspecies and different purpose breeds. Several genes were suggested as candidate SS and strategies adopted to retrieve functional information provide further insight into the possible source of selection and involvement in productive and adaptive processes. Use of a composite of multiple tests for selection increases the evidence of strong selective pressure, while the comparison of regional LD allowed detection of regions harboring Copy Number Variations (CNV) possibly acting as targets of selection. Finally, evaluation of the levels of admixture in Nelore and Gir revealed minor levels of taurine introgression, confirming historical and molecular records of crossbreeding with taurine populations. Lower than 1% mean taurine ancestry, supports intense backcrossing with pure indicine animals in the expansion of the breeds, while evidence of both African and European taurine introgression make creole breeds a possible source of the introgression.