Whole-Genome Re-Sequencing Reveals Genetic Diversity and Population History of Arunachali Mithun (Bos frontalis)

The Arunachali mithun (Bos frontalis) is a semi-domesticated bovine of profound cultural and economic significance to the indigenous Arunachali tribal communities of Northeastern India, yet it remains among the least genomically characterised large ruminants, leaving its conservation status without an empirical genetic foundation. We performed whole-genome re-sequencing (~10× coverage) of 11 individuals and analysed 4,943,593 high-quality biallelic single nucleotide polymorphisms (SNPs) after stringent quality control. Genome-wide mean observed heterozygosity (Ho = 0.2854), expected heterozygosity (He = 0.3347), and nucleotide diversity (π = 7.16 × 10−4) revealed moderate genetic diversity, substantially lower than that of related commercial bovine species. A consistent heterozygosity deficit (Ho − He = −0.0493) and the convergence of four independent inbreeding coefficients around 0.143–0.147 indicated moderate inbreeding of predominantly reflecting an ancient origin, corroborated by runs of homozygosity (ROH) analysis in which 93.2% of 24,937 detected segments fell in the short length class (100–250 kb). Linkage disequilibrium decayed from r2 ≈ 0.57 at <100 kb to a plateau of r2 ≈ 0.33 beyond 4–5 Mb, consistent with a small effective population size (Ne) declining from approximately 101,850 (~2228 generations ago) to approximately 160 (~5 generations ago), with ab Ne of approximately 3865 at ~100 generations ago and 423 at ~10 generations ago. These findings establish a whole-genome-based genetic diversity baseline for the Arunachali mithun and provide actionable genomic evidence for conservation and managed breeding interventions.