Comparative analysis of genome wide difference in Red Sindhi and Holstein cattle breeds using dense SNP marker

Genomic selection programs for the improvement of dairy and beef cattle breed has become a reality due to the availability of detailed genomic information. In this study, we compared the whole genome of Red Sindhi (Bos indicus) and Holstein (Bos taurus) cattle breeds using the Illumina Bovine HD SNP BeadChip for better understanding of genomic selection and utilization for improved breeding programme in Pakistan. One hundred and five samples consisting of 25 Red Sindhi and 70 Holstein were genotyped. Analysis of both breeds showed different spectra of single nucleotide polymorphisms (SNP) frequencies. Significant (p< 0.001) difference between these two cattle breeds in minor allele frequency (MAF) was observed. The average minor allele frequencies (MAF) were 0.18 ± 0.15 and 0.22±0.16 for Red Sindhi and Holstein, respectively. Total of 777, 962 SNPs were identified successfully. About 71% and 79% were polymorphic in Red Sindhi and Holstein, respectively. Polymorphic and fixed SNPs were not distributed uniformly across the chromosomes between these two breeds. Fixed SNPs numbers were higher on all chromosomes in Red Sindhi cattle, which show genetic uniqueness of Red Sindhi breed. The results of this study suggest that the rate of polymorphisms can be effectively used for breed identification, evolutionary studies and whole genome association studies.