India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and F _ST methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and F _ST analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included SLC37A1, PDE9A, PPBP, CXCL6, RASSF6, AFM, AFP, ALB, ANKRD17, CNTNAP2, GPC5, MYLK3, and GPT2. These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds.

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