Riverine buffalo domestication likely occurred around 6300 years ago in Northwestern India. Murrah and Surti are important buffalo breeds that originated in this region and the gene flow from these buffaloes to Mehsana buffalo has long been proposed. However, the extent to which Murrah and Surti ancestry diffused across Mehsana has not been investigated thoroughly. Therefore, we investigated the global and local ancestry of Indian Mehsana buffalo using double digest restriction-site associated DNA sequencing data. Principal component analysis, global ancestry analysis, admixture dating, and three population tests revealed with statistical significance that Mehsana is a unique population. Hence, the hypothesis that Mehsana is a crossbreed between Murrah and Surti is not supported by these findings. However, we noticed that some individuals of Mehsana, 6 out 15, were admixed having 41% Murrah-specific ancestry and 11% Surti-specific ancestry. Local ancestry and post-admixture selection signatures (PASS) in admixed Mehsana individuals revealed PASS in the Mehsana genome, that is, on Bubalus bubalis autosomes (BBA), 1–23 linked from Surti and on BBA, 24 linked from Murrah. Interestingly, upon functional enrichment of these signatures, several adaptation-related genes and pathways were ascertained to Surti, while Murrah-derived regions featured genes involved in fatty acid synthesis (Acyl-CoA Synthetase Short-Chain Family Member 2 (ACSS2)) and milk production. Based on local ancestry analysis, we infer that the introgression of the Murrah genome into Mehsana happened in recent times and that of the Surti genome happened in ancient generations. The finding that Mehsana is an independent population highlights the importance of recognizing distinct genetic lineages in domesticated species. This has global implications for reevaluating the origins and uniqueness of other livestock breeds often assumed to be hybrids. Practically, these findings open up new avenues for selective breeding to preserve traits such as disease resistance, adaptability, and production efficiency. Further studies in larger samples are called for.
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