Mitogenome Insights Into the Domestication and Phylogeography of Zebu Cattle: A Focus on Pakistani Breeds and Asian Lineages

Zebu cattle (Bos indicus) represent a critical livestock resource in the arid and semi-arid regions, known for their disease resistance, heat tolerance and physiological hardiness. Despite their agricultural importance, the precise matrilineal evolutionary history, genetic diversity and demographic trajectory remain incompletely resolved within the broader context of South Asian cattle domestication. This study explores the phylogeographic patterns and maternal lineage diversity of zebu cattle through complete mitochondrial genomes (mtDNA), the D-loop, and hypervariable regions from 50 individuals of 10 indigenous Pakistani breeds. These breeds were classified into three regions: North Pakistan, Central Pakistan/Punjab (Indus Valley region) and South Pakistan (the site of Mohenjo-Daro). Our data include 183 newly generated sequences and are supplemented with comparative datasets from 19 countries. Analysis reveals South Pakistan, especially the Mehrgarh area, as a key potential domestication epicentre, exhibiting highest nucleotide diversity (π = 0.01480) across Asian zebu populations, accompanied by ancient maternal lineages estimated to date back approximately 2.17 million years. Highest haplotype diversity was observed in Punjab (0.901 ± 0.014) followed by Southern Pakistan (0.893 ± 0.026). Phylogenetic and demographic analyses (mismatch distribution, Fu's Fs) further support an early dispersal scenario (I1 haplogroup) originating in Mehrgarh and radiating through the Indus Valley into broader Asian lineages. These findings enhance our understanding of the domestication origins of Bos indicus, its implications for breed conservation and sustainable livestock management.