author(s)
Sheikh Firdous Ahmad, Manjit Panigrahi, Rouf Rashid Dar, Ajaz Ali, Waseem Akram Malla and Bharat Bhushan

abstract
Population structure and diversity analysis form an important part of genetic structure studies in livestock populations. Genomic breed clustering is an important approach to study population genetic structure based on genotypic data. In the present study, 50K SNP genotypic data pertaining to the total of 83 animals belonging to six indicine cattle breeds were used to assess genomic breed clustering amongst them. The six breeds included Hariana (10), Kankrej (10), Tharparkar (12), Red Sindhi (10), Sahiwal (17) and Gir (24). These were arranged in different datasets and a separate dataset was prepared with combined data of all six breeds (dataset A). After processing the data for inclusion thresholds and quality filters, only polymorphic markers with definite chromosomal coordinates were left. Further analysis in terms of polymorphism proportion, average MAF values and chromosome-wise marker coverage parameters was done. Chromosome-wise marker coverage depicted the efficient distribution of SNP variant markers across the whole genome. All the breeds of dataset A were exclusively clustered in ADMIXTURE programme into separate clusters except Red Sindhi population. With PCA based approach, diverse nature of individual populations and stratified breed-group clustering along two axes was evident with three breeds stratified separately and the rest three positioned in a single cluster. Sufficient levels of variation of single dimensional nature were explained by first two principal components in each dataset. The Indian indigenous cattle breeds were thus found to maintain efficient population genetic structure amongst them.