Vol. 10, Special Issue 1, Part B (2026)

Understanding genomic regions under selection is crucial for improving productivity and resilience in indigenous livestock. In this study, whole-genome resequencing (LC-WGS) was performed on Malpura and Patanwadi sheep to identify nucleotide diversity patterns and selection signatures associated with immune and production traits. After stringent quality control, 8.37 million and 8.19 million SNPs were retained for Malpura and Patanwadi, respectively. Genome-wide nucleotide diversity (π) was estimated using sliding-window analysis, and the top 5% genomic regions were subjected to functional enrichment. Both breeds exhibited strong enrichment of immunity-related pathways, including Type I interferon receptor binding, natural killer cell activation, and antiviral dsRNA recognition. Malpura displayed higher enrichment intensity for antiviral and immune cell-mediated pathways, while Patanwadi showed elevated representation of haptoglobin-haemoglobin complex and acute-phase inflammatory responses. Production-related selection signatures highlighted distinct metabolic specialization: Malpura showed enrichment for fructokinase activity, keratin filament binding, and reproductive pathways, whereas Patanwadi exhibited enrichment for oxygen transport and haemoglobin-binding functions consistent with wool production efficiency. Several key genes, including β-defensins (DEFB1, DEFB5), interferon-stimulated genes (MX1, ISG15, IRF3, IRF7), and lipid-metabolism genes (FASN, ACAA1, ACAA2), were identified within the selected regions. These findings demonstrate strong directional selection for pathogen resistance and production performance in semi-arid Indian sheep breeds and provide genomic resources for future genetic improvement and conservation strategies.