Genomic Signals of Adaptation and Evolution Uncovered through Whole-Genome SNPs and InDels in Pandharpuri Buffaloes

Abstract Buffaloes are central to tropical livestock systems, valued for their resilience and high-quality milk. Pandharpuri buffaloes, distinguished by sword-shaped horns, adaptability to intermittent milking, and localized distribution, represent a valuable Indian genetic resource for studying adaptation and lactation biology. This study aimed to identify genome-wide single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in Pandharpuri buffaloes and to functionally annotate them for biological significance. Whole-genome resequencing data were processed and aligned to the Murrah reference genome, and variants were subsequently classified according to predicted functional impact. Functional annotation was performed using SnpEff, and Gene Ontology (GO) analysis was applied to assess enrichment of biological processes. A total of 27009882 SNPs and 3368500 InDels were detected. Most were classified as modifiers, followed by low-, moderate-, and high-impact categories. Coding variants were dominated by silent and missense mutations, with a missense-to-silent ratio of 0.63. GO analysis revealed enrichment of lactation and mammary gland development pathways across all variants, while high-impact and missense variants were associated with immune, metabolic, and stress-response pathways. These findings highlight the genetic and evolutionary basis of productivity, adaptation, and resilience in Pandharpuri buffaloes and provide a foundational genomic resource to support future studies, including genome-wide association analyses and genomic selection for economically important traits.