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<p>Scanning genomes for selection signals could illuminate the impact of domestication, natural, and artificial selection on the phenotypic traits of cattle breeds. The present study investigated the diverse genomic selection signatures using whole genome sequencing data from 15 pooled samples of five indigenous cattle breeds of Tamil Nadu: Alambadi, Bargur, Kangayam, Pulikulam, and Umblachery. Two approaches, namely composite likelihood ratio (CLR) and fixation index (<i>F</i><sub>ST</sub>), were employed to detect selection signatures from the 1,390,449 filtered single-nucleotide polymorphisms. The analysis identified 7250 and 806 genomic regions containing selective sweeps in 1238 and 101 candidate genes using CLR and <i>F</i><sub>ST</sub> methods, respectively. These regions were predominantly associated with production traits (<i>PAIPI, NNT</i> and <i>OCIAD1</i>), coat colour (<i>MC1R, KIT, KDR</i> and <i>PDGFRA</i>), disease resistance (<i>TCF25, CDH15</i> and <i>SPIRE2</i>), and adaptation to tropical climates (<i>SLC22A31</i> and <i>SPG7</i>). Particularly, six regions were shared across all the five cattle breeds, of which, five were intergenic regions and one had a candidate gene, <i>GALNTL6</i>, associated with susceptibility to bovine tuberculosis. A total of 12 candidate genes were common between CLR and <i>F</i><sub>ST</sub> methods, relating to production, disease resistance, and behavioural traits. NETWORK analysis revealed six candidate genes allied with calving ease (<i>JAK1</i> and <i>DOCK1</i>), milk fat yield (<i>ITGA1</i>), bovine respiratory disease susceptibility (<i>ITGA3</i> and <i>ITGAL</i>), and meat and carcass traits (<i>EPS15L1</i>). This study presents the first genomewide map of selective sweeps in Tamil Nadu cattle breeds, providing insights into selection signatures and candidate genes that could enhance genome-assisted breeding for improved production and health.</p>

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Genomewide signatures revealing new evidence for selection of important traits in indigenous cattle breeds of Tamil Nadu, India

  • 期刊论文

  • 发表日期：

    2026年3月17日

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  • S. Vani,
  • D. Balasubramanyam,
  • S. M. K. Karthickeyan,
  • K. G. Tirumurugan,
  • A. Gopinathan,
  • P. Hepsibha,
  • B. Jaya Madhuri

摘要

Scanning genomes for selection signals could illuminate the impact of domestication, natural, and artificial selection on the phenotypic traits of cattle breeds. The present study investigated the diverse genomic selection signatures using whole genome sequencing data from 15 pooled samples of five indigenous cattle breeds of Tamil Nadu: Alambadi, Bargur, Kangayam, Pulikulam, and Umblachery. Two approaches, namely composite likelihood ratio (CLR) and fixation index (FST), were employed to detect selection signatures from the 1,390,449 filtered single-nucleotide polymorphisms. The analysis identified 7250 and 806 genomic regions containing selective sweeps in 1238 and 101 candidate genes using CLR and FST methods, respectively. These regions were predominantly associated with production traits (PAIPI, NNT and OCIAD1), coat colour (MC1R, KIT, KDR and PDGFRA), disease resistance (TCF25, CDH15 and SPIRE2), and adaptation to tropical climates (SLC22A31 and SPG7). Particularly, six regions were shared across all the five cattle breeds, of which, five were intergenic regions and one had a candidate gene, GALNTL6, associated with susceptibility to bovine tuberculosis. A total of 12 candidate genes were common between CLR and FST methods, relating to production, disease resistance, and behavioural traits. NETWORK analysis revealed six candidate genes allied with calving ease (JAK1 and DOCK1), milk fat yield (ITGA1), bovine respiratory disease susceptibility (ITGA3 and ITGAL), and meat and carcass traits (EPS15L1). This study presents the first genomewide map of selective sweeps in Tamil Nadu cattle breeds, providing insights into selection signatures and candidate genes that could enhance genome-assisted breeding for improved production and health.