Indian Journal of Animal Research
SCOPUSWeb of Science
  • Year: 2026
  • Volume: 59
  • Issue: 8

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

  • Author:
  • Dapinder Singh1, Shashi Kant Mahajan2, Neeraj Kashyap3, Chandra Sekhar Mukhopadhyay1*
  • Total Page Count: 10
  • Page Number: 1267 to 1276

1Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141 012, Punjab, India.

2Department of Veterinary Surgery and Radiology, College of Veterinary Sciences, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141 012, Punjab, India.

3Department of Animal Genetics and Breeding, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141 012, Punjab, India.

*Corresponding Author: Chandra Sekhar Mukhopadhyay, Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141 004, Punjab, India. Email: csmukhopadhyay@gadvasu.in

Abstract

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.

The research utilized custom double-digest restriction site-associated DNA sequencing genotyping-by-sequencing (ddRAD-GBS) with Illumina 150 bp 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).

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.

Keywords

Dogs, Haplotype, Population structure, R-coding, SNPs