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<p>This study presents a whole-genome re-sequencing (WGR) analysis of two genetically and functionally distinct indigenous Indian cattle breeds, Sahiwal and Kangayam, to explore genetic diversity, population structure, and selection signatures. High-quality sequencing data (~ 8 × depth) generated over 21 million SNPs per breed, with 7.48% in Kangayam and 7.91% in Sahiwal being putatively novel, highlighting breed-specific genetic uniqueness. Nucleotide diversity (π) was slightly higher in Sahiwal (0.0032) than Kangayam (0.0030), while inbreeding coefficients (F<sub>IS</sub>) indicated greater diversity in Kangayam. LD decay&#xa0;observed in WGR data (r<sup>2</sup> ≥ 0.2 extending up to ~ 98 kb in Kangayam and ~ 57 kb in Sahiwal), indicated large effective population sizes and supported the potential for genomic selection. However, LD decay appeared slower when using high-density (HD) SNP chips, with r<sup>2</sup> ≥ 0.2 extending up to ~ 155 kb in Kangayam and ~ 75 kb in Sahiwal, compared to whole-genome resequencing (WGR) data. This discrepancy is attributed to differences in marker density, allele frequency distribution, and ascertainment bias. Although WGR captures rare variants and offers finer resolution of linkage disequilibrium (LD) patterns, SNP chips generally target common variants that may lead to an overestimation of LD levels. Population structure analyses showed homogeneous clustering in Kangayam and moderate variability in Sahiwal. Selection signature detection revealed breed-specific genomic regions. Kangayam exhibited enrichment of immunity (<i>BOLA-DQB</i>), stress tolerance (<i>DNAJC14, DNAJC18</i>), and aggressive behavior (<i>GAD2</i>) related genes, while Sahiwal showed enriched genes related to milk production (<i>FTO</i>, <i>SCD</i>), thermo-tolerance (<i>HSPA4, DNAJB6</i>), and reproduction (<i>GOLGA4, OSTC</i>). Notably, <i>ETNPPL</i> and <i>OSTC</i> were under selection in both breeds, suggesting convergent adaptive traits. KEGG pathway analysis revealed functional enrichments aligning with breed purposes like draught utility in Kangayam and dairy traits in Sahiwal.&#xa0;Together, these findings advance our understanding of genomic diversity and adaptation in native&#xa0;Indian cattle breeds, provide candidate regions for future investigation, and support sustainable livestock genetic resource management in line with SDG 15 (Life on Land).</p>

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Contrasting genomic architectures and linkage disequilibrium landscapes with insights into adaptive potential of Sahiwal and Kangayam cattle from whole-genome resequencing

  • 期刊论文

  • 发表日期：

    2026年6月22日

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  • Subrata Koloi,
  • Kusum Mehla,
  • Indrajit Ganguly,
  • Sanjeev Singh,
  • Satpal Dixit

摘要

This study presents a whole-genome re-sequencing (WGR) analysis of two genetically and functionally distinct indigenous Indian cattle breeds, Sahiwal and Kangayam, to explore genetic diversity, population structure, and selection signatures. High-quality sequencing data (~ 8 × depth) generated over 21 million SNPs per breed, with 7.48% in Kangayam and 7.91% in Sahiwal being putatively novel, highlighting breed-specific genetic uniqueness. Nucleotide diversity (π) was slightly higher in Sahiwal (0.0032) than Kangayam (0.0030), while inbreeding coefficients (FIS) indicated greater diversity in Kangayam. LD decay observed in WGR data (r2 ≥ 0.2 extending up to ~ 98 kb in Kangayam and ~ 57 kb in Sahiwal), indicated large effective population sizes and supported the potential for genomic selection. However, LD decay appeared slower when using high-density (HD) SNP chips, with r2 ≥ 0.2 extending up to ~ 155 kb in Kangayam and ~ 75 kb in Sahiwal, compared to whole-genome resequencing (WGR) data. This discrepancy is attributed to differences in marker density, allele frequency distribution, and ascertainment bias. Although WGR captures rare variants and offers finer resolution of linkage disequilibrium (LD) patterns, SNP chips generally target common variants that may lead to an overestimation of LD levels. Population structure analyses showed homogeneous clustering in Kangayam and moderate variability in Sahiwal. Selection signature detection revealed breed-specific genomic regions. Kangayam exhibited enrichment of immunity (BOLA-DQB), stress tolerance (DNAJC14, DNAJC18), and aggressive behavior (GAD2) related genes, while Sahiwal showed enriched genes related to milk production (FTO, SCD), thermo-tolerance (HSPA4, DNAJB6), and reproduction (GOLGA4, OSTC). Notably, ETNPPL and OSTC were under selection in both breeds, suggesting convergent adaptive traits. KEGG pathway analysis revealed functional enrichments aligning with breed purposes like draught utility in Kangayam and dairy traits in Sahiwal. Together, these findings advance our understanding of genomic diversity and adaptation in native Indian cattle breeds, provide candidate regions for future investigation, and support sustainable livestock genetic resource management in line with SDG 15 (Life on Land).