Genetic Charaterization of Indian Indigenous Cattle Breeds

Using the Illumina 770k bovine SNP assay, we genetically characterized 15 Indian indigenous cattle breeds and 1 non-descript indigenous population, which is the largest sample of Indian breeds yet studied. 15.6% of the animals were found to have more than 1% recent Bos taurus admixture and were removed or separately analysed. Inbreeding levels for the Indian indigenous breeds, based on FIS and diagonal elements of the GRM, were similar compared to European taurine breeds. We did not find evidence for historical admixture with Bos taurus during breed formation. Only 1.4% of the genetic variance in allele frequencies was between breeds, compared to about 42.4% for European taurine breeds. Consequently, Indian breeds can be treated as a single population for some purposes, such as SNP assay design.