Genome-wide characterization of copy number variations in Nagami Mithun (Bos frontalis) using whole-genome resequencing.

Copy number variations (CNVs) represent an important source of structural genomic variation contributing to genomic diversity in livestock species. The Nagami Mithun (Bos frontalis), a semi-domesticated bovid indigenous to the forested hill regions of Northeast India, remains poorly characterized at the level of genome structural variation. In this study, whole-genome resequencing data from 12 Nagami Mithun individuals were analyzed to establish the first genome-wide copy number variation (CNV) map for this indigenous population. After quality filtering and alignment to the Bos taurus ARS-UCD2.0 reference genome, CNVs were detected using the read-depth-based tool CNVnator v0.4.1 with stringent filtering criteria (e-value < 0.05, q0 < 0.5, length > 1 kb). A total of 7273 CNVs were identified, including 5005 deletions (68.8%) and 2,268 duplications (31.2%), which were subsequently integrated into 1135 CNV regions (CNVRs). Population-level integration of individual CNVs resulted in 1135 CNVRs spanning approximately 173.4 Mb of the autosomal genome. Functional annotations identified 2281 genes overlapping CNVRs. Gene Ontology enrichment analysis identified overrepresentation of genes annotated to chemosensory perception, immune-related processes, and amino-acid transport functions, while KEGG pathway analysis identified enrichment of pathways annotated as natural killer cell-mediated cytotoxicity and antigen processing and presentation. CNV-QTL overlap analysis identified hypothesis-generating candidate genomic regions harboring genes (e.g., AFF2, EDA, COL4A5, TRPC5) that are associated with production, reproduction, and conformation traits in bovines, representing putative positional overlaps requiring future validation in Mithun populations. This study provides a foundational structural variation resource for future comparative, conservation, and functional genomic studies in Mithun. These findings provide a valuable genomic resource for future marker-assisted selection, comparative genomics, and conservation breeding programs aimed at preserving Nagami Mithun populations.