Genome-wide characterization of genetic diversity and breed discrimination markers in Tharparkar cattle

Tharparkar, an indigenous milch breed from India, is known for producing high-quality milk and being able to thrive in dry and desert settings. This breed is very important for the livelihoods of rural communities. This work aimed to assess genetic diversity using double digest Restriction site-Associated DNA (ddRAD) sequencing and to identify breed-specific single nucleotide polymorphisms (SNPs) for the creation of an ultra-low-density SNP panel derived from five significant indigenous breeds of India. We genotyped 48 animals from the Livestock Research Station (LRS) in Beechwal under RAJUVAS, Bikaner (Rajasthan). After careful filtering, we got 121,554 high-quality biallelic SNPs. The population exhibited an average minor allele frequency of 0.249 ± 0.117, with the mean expected and observed heterozygosity values of 0.347 ± 0.103 and 0.291 ± 0.078, respectively. The genomic inbreeding coefficients calculated by several methodologies (F_HOM, F_UNI, F_GRM and F_ROH) varied from 0.106 to 0.125, signifying a low to moderate degree of inbreeding. The prevalence of short runs of homozygosity (0-2 Mb) indicates minimal recent inbreeding, with inbreeding mostly resulting from ancient common ancestry, perhaps due to genetic drift or founder effects. The effective population size in recent generations was approximated at 82.6. To find informative SNPs that are distinctive to each breed, we used pre-selection statistics using the TRES (Toolbox for Ranking and Evaluation of SNPs) tool. Then, we used the MAF-LD approach on a reference dataset of 260 individuals from five different Indian cow breeds. This method found 309 SNPs in 260 individuals from the reference set and 77 unique SNPs that were only found in Tharparkar. These SNPs could differentiate Tharparkar apart from other breeds in both the reference and validation datasets. These results give us important information about the genetic diversity of Tharparkar cattle, show how useful ddRAD sequencing is for detecting breed-specific SNPs and stress the necessity for targeted conservation initiatives to ensure the breed's sustainability.