Genomic insights into milk production, growth, and adaptation traits in Jamunapari goats through whole-genome re-sequencing

Abstract

The Jamunapari goat, a prominent indigenous breed of the Indian subcontinent, is highly valued for its superior milk yield, growth performance, and adaptability, playing a crucial role in sustaining rural livelihoods. This study investigated the genomic underpinnings of these economically important traits through whole-genome re-sequencing of 15 unrelated Jamunapari goats from Mathura, Uttar Pradesh. Blood-derived DNA samples were sequenced, aligned to the ARS1 goat reference genome, and analyzed, resulting in the identification of 22,175,381 single nucleotide polymorphisms (SNPs). Selection signatures were detected using intra-population approaches, including nucleotide diversity (π), Composite Likelihood Ratio (CLR), and Runs of Homozygosity (ROH), leading to the identification of 892 candidate genes. Key genes such as VPS13C, COPS3, ABI2, STIM1, GPX1, EP300, CDK4, and RHOA were associated with lactation, growth, and thermotolerance. Functional enrichment analysis using DAVID and KEGG pathways revealed the involvement of critical biological pathways, including Thyroid Hormone, Hippo, and Rap1 signaling, linked to metabolism, tissue development, and environmental resilience. Protein-protein interaction network analysis conducted via STRING and Cytoscape identified 15 hub genes, notably POLR2A, EP300, and CDK4, suggesting their central roles in regulatory networks of adaptation. These findings provide valuable insights into the evolutionary selection and breeding history of the Jamunapari goat, offering a genomic foundation for targeted breeding programs aimed at enhancing productivity and resilience under challenging agro-climatic conditions.