SNPs with intermediate minor allele frequencies facilitate accurate breed assignment of Indian Tharparkar cattle.

Abstract Tharparkar cattle breed is widely known for its superior milch quality and hardiness attributes. This study aimed to develop an ultra-low density breed-specific single nucleotide polymorphism (SNP) genotype panel to accurately quantify Tharparkar populations in biological samples. In this study, we selected and genotyped 72 Tharparkar animals randomly from Cattle & Buffalo Farm of IVRI, India. This Bovine SNP50 BeadChip genotypic datum was merged with the online data from six indigenous cattle breeds and five taurine breeds. Here, we used a combination of pre-selection statistics and the MAF-LD method developed in our laboratory to analyze the genotypic data obtained from 317 individuals of 12 distinct breeds to identify breed-informative SNPs for the selection of Tharparkar cattle. This methodology identified 63 unique Tharparkar-specific SNPs near intermediate gene frequencies. We report several informative SNPs in genes/QTL regions affecting phenotypes or production traits that might differentiate the Tharparkar breed.