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<p>Gir cattle, an indigenous zebu breed, hold a unique position in the global dairy industry due to their exceptional tolerance to tropical climates, disease resilience, and ability to survive in resource-limited conditions. In the study, the genome-wide identification and annotation of SNPs and selective sweeps was done in Gir cattle using the ddRAD sequencing method. The study identified 1,939,949 SNPs, with the majority located in the intron region (48.68%), followed by the intergenic region (41.98%). The classification of SNPs by functional class revealed a maximum rate of 58.07% for silent mutations, 41.01% for missense mutations, and 0.92% for nonsense mutations. The genetic diversity analysis revealed the degree of heterozygosity as 0.2892 against the expected heterozygosity of 0.325. Further selection signatures were identified by four different methods, and nine genes were found common, which included Metazoa_SRP, U6, U1, 5S_rRNA, MACROD2, PHACTR1, SNORA70, HS3ST4, and DLG2. Out of total genes identified, 894 genes were shared by at least two approaches. Functional enrichment analysis revealed that glutamate receptor activity and olfactory receptor activity were among the most significant biological functions. Integration of Gene Ontology (GO) term analysis with pathway enrichment using ClueGO highlighted several key biological processes and pathways, including the glutamate receptor signaling pathway, organization of plasma membrane–bounded cell projections, neuron differentiation, walking behavior, and mechanoreceptor differentiation. The results of functional profiling of QTLs in Gir cattle revealed that 51% of the QTLs were of milk association, while 20% were of reproduction and 11% were of production association. So, the present study provides insights into the adaptive evolution of Gir cattle and offers clues regarding genomic regions associated with economically important traits in this breed.</p>

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Genome-Wide SNP and Selective Sweep Analyses Identify Key Genes Associated with Adaptation and Economic Traits in Indian Gir Cattle

  • 期刊论文

  • 发表日期：

    2026年1月14日

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  • Raja Thiruvothur Venkatesan,
  • Singh Umesh,
  • Kumar Sushil,
  • Singh Amit Kumar,
  • Alex Rani

摘要

Gir cattle, an indigenous zebu breed, hold a unique position in the global dairy industry due to their exceptional tolerance to tropical climates, disease resilience, and ability to survive in resource-limited conditions. In the study, the genome-wide identification and annotation of SNPs and selective sweeps was done in Gir cattle using the ddRAD sequencing method. The study identified 1,939,949 SNPs, with the majority located in the intron region (48.68%), followed by the intergenic region (41.98%). The classification of SNPs by functional class revealed a maximum rate of 58.07% for silent mutations, 41.01% for missense mutations, and 0.92% for nonsense mutations. The genetic diversity analysis revealed the degree of heterozygosity as 0.2892 against the expected heterozygosity of 0.325. Further selection signatures were identified by four different methods, and nine genes were found common, which included Metazoa_SRP, U6, U1, 5S_rRNA, MACROD2, PHACTR1, SNORA70, HS3ST4, and DLG2. Out of total genes identified, 894 genes were shared by at least two approaches. Functional enrichment analysis revealed that glutamate receptor activity and olfactory receptor activity were among the most significant biological functions. Integration of Gene Ontology (GO) term analysis with pathway enrichment using ClueGO highlighted several key biological processes and pathways, including the glutamate receptor signaling pathway, organization of plasma membrane–bounded cell projections, neuron differentiation, walking behavior, and mechanoreceptor differentiation. The results of functional profiling of QTLs in Gir cattle revealed that 51% of the QTLs were of milk association, while 20% were of reproduction and 11% were of production association. So, the present study provides insights into the adaptive evolution of Gir cattle and offers clues regarding genomic regions associated with economically important traits in this breed.