Tracing India's Canine Heritage through SNP-Based Haplotype Identification

Dog breeds/germplasm in India is mostly unexplored and the population structure of owned dogs has not been studied at all. The current study was designed to determine the haplotypes and explore the population structure among divergent breeds of dogs using genome-wide distributed SNPs, followed by validation of selected haplotypes through PCR-sequencing. The research employed custom ddRAD-GBS sequencing carried out using Illumina 150bp paired-end sequencing of 50 dog samples generated 2,18,433 high-quality SNPs meeting the screening criteria. The data was further analyzed for population structure assessment and haplotype identification using bash, and R-environment. Subsequently, three haplotypes (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). The results revealed notable connections between dog breeds from Punjab and Haryana, while the affiliation with Karnataka was found to be less pronounced. The sequencing results indicated that CELSR1 and GBGT1 genes contained SNPs, with the AFAP1 gene lacking SNPs. The results also provided insights into the molecular-level population structure, SNPs, and haplotypes of diverse dog breeds reared in India. This SNP variation could be used for molecular characterization of indigenous dogs.