Tag-SNPs identification in Gaddi dogs in the light of divergent canine breeds

Abstract

Abstract The present research proposal was designed to explore the tag-SNPs in indigenous Gaddi dogs concerning other popular dog breeds maintained in India and to determine the genome-wide distributed SNPs, haplotype and linkage disequilibrium (LD). In this study, ddRAD-GBS custom sequencing was done using Illumina 150 bp paired-end sequencing of fifty dog samples. A total of 3,56,461 SNPs loci were screened, out of which 75811 high-quality SNPs were screened. Linkage disequilibrium (LD), Haplotype analysis, and tag-SNP identified using pipelines based on Linux using bash. sed and awk coding, R-environment. The cataloging of the tag-SNPs associated with underlying different pathways and the validation of selected genes based on Th1 (IL-2, TNF-alpha), Th2-biased pathways (IL-10), and diseases-associated (CDK2, TTC8) using q-real-time PCR. The results indicated about 2033 tag-SNPs were found to be statistically significant (P < 0.000001) and cataloged the associated genes. The relative expression of genes was expressed in both groups. The IL-10 gene shows significant difference between the two groups (P < 0.05). The findings provide important information for future allele/gene identification using genome-wide association studies (GWAS) for dog-breeding programs. This is the maiden report on tag-SNPs and the population structure of the Indian dog breeds (Gaddi & Mudhol Hound) at the molecular level.