Genome-Wide Identification, Annotation of SNPs, and Selective Sweeps in Indian Horse and Pony Breeds

The genomic diversity among Indian horse and pony breeds was investigated to under-stand how their unique traits, shaped by different environments, might help improve their health and performance. A cost-effective genetic analysis method of the genome-based ddRAD approach was used to identify admixture. The investigators identified 322732 variants, of which 298782 were SNPs and 23950 were Indels across horses and ponies. In the thoroughbred horses, 149134 genetic variants were observed, of which 161002 were SNPs. 1631 positive selection signatures were found common among all horse breeds. 700 selection signatures were enumerated to 306 genes. SLC4A10, CADM1, AUST2, and LOC733058 genes contained more than 10 selection signatures. Many of these selection signatures were linked to important functions, such as brain development (via genes GRM8 and GRIK3), muscle strength (VDR), and tendon durability (TNC)—all of which contribute to horses’ athletic abilities. Genes such as ANK2, BCL2, and RYR2 possess pos-itive selection signatures and play central roles in managing calcium movement and heart function. These genes may help horses maintain lower heart rates during intense activity, enhancing their stamina and performance. This study offered insights to enhance horse welfare and performance globally, benefiting communities reliant on these animals.