Tracing India’s Canine Heritage Through SNP-based Haplotype Identification

Background: The majority of dog breeds and germplasm in India remain largely unexplored, with no previous studies conducted on the population structure of owned dogs. This study aimed to fill this gap by identifying haplotypes and exploring population structure among different breeds of dogs using genome-wide distributed SNPs. Methods: The research utilized custom double-digest restriction site-associated DNA sequencing genotyping-by-sequencing (ddRAD-GBS) with Illumina 150bp paired-end sequencing of 50 dog samples, resulting in 2,18,433 high-quality SNPs meeting the screening criteria. Results were obtained on 46 dog samples which were analyzed for population structure and haplotype identification using bash and R-environment. Three haplotypes (located on AFAP1, CELSR1 and GBGT1 genes) were selected based on SNP density and haplotype length for validation via PCR, followed by paired-end Sanger sequencing in seven different dog breeds (n = 21). Result: The results revealed significant connections between dog breeds from Punjab and Haryana, with less pronounced affiliation with Karnataka. Sequencing results showed that CELSR1 and GBGT1 genes contained SNPs, while the AFAP1 gene did not. These findings provided insights into the molecular-level population structure, SNPs and haplotypes of diverse dog breeds in India. The SNP variation identified could be utilized for the molecular characterization of indigenous dogs.