Whole-genome resequencing and functional annotation of genetic variants in the Gaddi dog from the Western Himalayas

Introduction The Gaddi dog, sometimes called the Himalayan sheepdog, is a livestock guardian breed from the Himalayas. This breed has been associated with migratory pastoral systems for centuries and is known for its endurance and adaptation to harsh environmental conditions. However, the breed is currently facing genetic dilution due to the lack of dedicated breeding programs. Methods In this study, whole-genome resequencing of the Indian Himalayan shepherd dog (Gaddi dog) was performed using Illumina paired-end sequencing technology. Whole-genome resequencing was conducted at a mean sequencing depth of approximately 40× per individual. Sequence reads were aligned to the reference genome, and variant detection and functional annotation were performed using the Genome Analysis Toolkit (GATK) pipeline. Results Whole-genome resequencing of two dogs generated 10,914,188 SNPs. Functional analysis highlighted genetic pathways related to metabolism, muscle contraction, and platelet activation, which are important for survival in extreme environments. Functional annotation of high-impact variants identified genes such as TTN, SALL4, and SLC30A6, which are associated with muscle contraction, signal transduction, and metabolic processes. Discussion The findings provide preliminary genomic insights into genetic variants potentially associated with endurance and environmental resilience in the Gaddi dog. These results may support conservation efforts, breed improvement programs, and future research on environmental adaptation and performance in working dog breeds.