Selection of breed-specific SNPs in three Indian sheep breeds using ovine 50 K array

Abstract Recently DNA-based genetic purity determination tools have gained popularity, especially, in small ruminants like sheep. The objective of the present study was to select breed-specific SNPs for the three commercially important sheep breeds of India, i.e., Changthangi, Deccani, and Garole. Sheep genotype data (Ovine 50 K SNP array) from 344 individuals of eight sheep breeds (Garole, Deccani, Changthangi, Tibetan, Australian Merino, Dorset Horn, Rambouillet, and Irish Suffolk) were used as a reference population. Here, we used pre-selection statistics and the minor allele frequency–linkage disequilibrium (MAF-LD) method to analyze the reference population dataset. SNPs selection and breed assignment was executed with a panel of 768 markers for eight breeds near intermediate gene frequencies. We identified 95, 89, and 92 breed-specific SNPs for Changthangi, Deccani, and Garole, respectively. These informative SNPs were found to be associated with essential candidate genes associated with production and disease resistance. This methodology may be implemented in practice to identify individuals as being purebred or not.