Random DNA samples  of Eleven Indian native cattle breeds (Bos indicus) of Sahiwal (SW), Tharparker (TP), Gir (GR), Ongole (OG), Hariana (HR), Kankrej (KN), Kangayam (KG), Hallikar (HK), Vechur (VC), Ladakhi (LC) and Siri (SR)  were genotyped using 777K Illumina Bovine HD BeadChip.
A total of 178 samples from eleven indigenous cattle breeds, representing diverse agro-climatic regions and utility purpose, were genotyped using the 777K BovineHD BeadChip (Illumina). After stringent sample- and marker-level quality control (missing genotype rate > 10%, HWE P = 0.001, and MAF < 0.05), 158 high-quality individuals and 504,003 autosomal SNPs were retained. These data were used to investigate genome-wide diversity, Selection signature, heterozygosity-rich regions (HRRs), and breed clustering across the eleven breeds.