Evaluation of two bovine SNP genotyping arrays for breed clustering and stratification analysis in well-known and breeds.

The present study aimed to evaluate the efficiency of two Bovine SNP genotyping arrays (i.e., 50 K and HD) for breed clustering and stratification related studies in and breeds. The whole-genome SNP data at two densities were assembled into three datasets (A, B and C). Dataset A ( = 213) included 50 K genotypic data for five (Holstein-Friesian, Guernsey, Brown Swiss, Angus and Jersey) and two (Gir and Nellore) breeds. Dataset B ( = 241) included the same breeds with HD density data. Dataset C ( = 299) included 50 K SNP genotypic data for six (Holstein-Friesian, Jersey, Guernsey, Brown Swiss, Angus and Hereford) and six (Hariana, Kankrej, Brahman, Nellore, Sahiwal and Gir) breeds. The analysis was done using ADMIXTURE program (bioinformatics-based) and cross-validation errors and Principal Component Analysis (statistical analysis). The proportion of polymorphic markers and minor allele frequencies were assessed for each breed. The proportion of markers polymorphic was consistently higher in breeds when compared with breeds from group. Minor allele frequency estimates and ADMIXTURE results showed differential patterns for both the lineages. However, no significant increase in the accuracy of genomic clustering was found on moving from 50 K to HD density data.