Study of genetic variation at molecular level has evolved very rapidly since the late 20th century. Molecular data provides reliable genetic variation due to the detection at DNA level and different techniques are available for identifying genetic variation between individuals, breeds, and species (Avise, 2004). Protein polymorphisms were the first genetic markers for the studies of livestock species in the 1970s and replaced by the restriction enzymes analysis in 1980s. Genetic markers are useful in both basic (phylogenetic analysis and gene selection) and applied (marker assisted selection and paternity testing) research. In recent years, polymerase chain reaction based genotyping methods has provided the rapid and easy assay for genetic data analysis. Single nucleotide polymorphism (SNPs) are the most common form of polymorphism and believed to contain valuable information, widely used as genetic markers in population genetics and molecular ecology studies. Btau_4. 2 and UMD 3.1 are two different bovine genome assemblies, which are available (Bovine genome sequencing and analysis consortium, 2009; Bovine HapMap consortium, 2009; Zimin et al., 2009 and Hailu et al., 2011) and led to the development of Illumina Bovine HD SNP (more than 777,000 SNPS) BeadChip genotyping array (Van Tassel et al., 2008;