Phylogeographic and genetic diversity analysis through genome-wide SNPs in indigenous and exotic canine breeds owned in India

The present study aimed to assess genetic diversity within six distinct dog breeds (Labrador Retriever, German Shepherd, Pug, Mudhol Hound, Tibetan Mastiff, and Gaddi) sampled from four different Indian states: Punjab, Himachal Pradesh, Haryana, and Karnataka. The research employed double digest restriction-site associated-DNA-genotyping by sequencing (ddRAD-GBS) analysis followed by next-generation sequencing (NGS), specifically using Illumina 150 bp paired-end sequencing to analyze the genetic makeup of fifty canine samples. A total of 3,56,461 SNP loci were identified across the samples, with 75811 high-quality SNPs selected. R programming and Linux-bash coding were employed to conduct population genetic and phylogenetic analyses including genetic distance, construction of phylogenetic trees, principal component analysis, and population structure assessments to distinguish the dog populations based on their historical origins. The results revealed there was a close genetic similarity between samples collected from Punjab and Himachal Pradesh, followed by Karnataka, and Haryana. It is inferred that the divergent dog breeds harbor distinct genetic uniqueness based on specific geographical regions. The findings offer valuable insights for future research involving allele/gene identification through genome-wide association studies (GWAS) and marker-assisted selection (MAS), enhancing genetic improvement in breeding programs. The study expands understanding of the genetic structure of popular indigenous and exotic canine germplasm. This research represents the first study on molecular-level characterization of the native Gaddi dog and Mudhol Hound breed.