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<p>This study is aimed to assess genomic diversity in Indian horses and ponies using a ddRAD-based approach. As these breeds are distributed across varied regions, this low-cost method was applied to detect admixture. We identified 322,732 genetic variants, including ~ 299,000 SNPs and ~ 24,000 INDELs. In Thoroughbred horses, 149,134 variants were observed, of which 161,002 were SNPs. Across all breeds, 1,631 positive selection signatures were detected, with 700 signatures mapped to 306 genes. Notably, SLC4A10, CADM1, AUST2, and LOC733058 contained more than 10 signatures. Most of these selection signatures contained genes that were found to have vital biological roles. Several genes play vital roles in neurological development (GRM8, GRIK3) and muscle/tendon strength (VDR, TNC), influencing athletic performance. Genes such as <i>ANK2, BCL2, and RYR2</i>&#xa0;possess positive selection signatures and act as hub genes that involve the transportation of calcium ions and cardiac regulation, which might be a reason for lowering heart rate in horses to cope with their high performance. These findings provide valuable genomic insights that can aid conservation, selective breeding, and the long-term management of indigenous equine resources in India. This aligns with United Nations Member States SDG. 15 (Life on Land).</p>

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Genome-wide SNP mapping and selective sweep analysis in Indian equine breeds

  • 期刊论文

  • 发表日期：

    2026年3月25日

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  • Anuradha Bhardwaj,
  • Jayakumar Sivalingam,
  • Yash Pal,
  • Varij Nayan,
  • Mamta Chauhan,
  • Sonali Soni,
  • Saroj Panghal,
  • Shiv Kumar Giri,
  • Mohan Malayaperumal,
  • Sarika Jaiswal,
  • Mir Asif Iquebal,
  • Vijay Kumar,
  • Dinesh Kumar,
  • Bhupendra Nath Tripathi

摘要

This study is aimed to assess genomic diversity in Indian horses and ponies using a ddRAD-based approach. As these breeds are distributed across varied regions, this low-cost method was applied to detect admixture. We identified 322,732 genetic variants, including ~ 299,000 SNPs and ~ 24,000 INDELs. In Thoroughbred horses, 149,134 variants were observed, of which 161,002 were SNPs. Across all breeds, 1,631 positive selection signatures were detected, with 700 signatures mapped to 306 genes. Notably, SLC4A10, CADM1, AUST2, and LOC733058 contained more than 10 signatures. Most of these selection signatures contained genes that were found to have vital biological roles. Several genes play vital roles in neurological development (GRM8, GRIK3) and muscle/tendon strength (VDR, TNC), influencing athletic performance. Genes such as ANK2, BCL2, and RYR2 possess positive selection signatures and act as hub genes that involve the transportation of calcium ions and cardiac regulation, which might be a reason for lowering heart rate in horses to cope with their high performance. These findings provide valuable genomic insights that can aid conservation, selective breeding, and the long-term management of indigenous equine resources in India. This aligns with United Nations Member States SDG. 15 (Life on Land).