Genomic insights into six dog breeds owned in India: a ddRAD sequencing approach

The current study reports the maiden investigation aimed at molecular characterization of population structure and the discovery of tag-SNPs in the indigenous Gaddi and Mudhol Hound breeds, along with four other foreign breeds owned in India, using genome-wide SNP markers. Forty-six (46) dogs were genotyped using genotyping-by-sequencing double-digest restriction site-associated DNA (GBS-ddRAD), which identified 75,811 high-quality SNPs. Genetic analyses of the SNP data indicated significant variability within and between the experimental breeds, with indigenous breeds having a higher proportion of unique genetic variants. Linkage disequilibrium can indicate how genes are grouped on chromosomes and can help researchers understand genetic diversity and evolutionary relationships. A total of 2,033 tag-SNPs were identified across the six divergent dog breeds (p < 10− 6), representing the most informative markers within the dataset. These tag-SNPs were distributed across chromosomes 1–19, indicating regions of concentrated genetic variation, with the maximum (i.e., 242) number of tag-SNPs on chromosome 5 (Clu5: NC_051809.1). These findings echo the maiden report on tag-SNPs of Indian indigenous dog breeds (Gaddi dog and Mudhol Hound) and also provide comprehensive genomic insights. This knowledge base will further help researchers identify breed-specific molecular signatures and develop conservation strategies. It will also support future genome-wide association studies (GWAS) for trait and disease mapping in Indian dog breeds.