A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan

SIMPLE SUMMARY: Buffaloes, as a form of livestock, have a huge economic impact, especially in the Asiatic market. In Pakistan, the production of buffaloes for either their milk or meat has increased beyond the overall level of cattle production. The domestication of Nili–Ravi buffaloes from the Nili and Ravi breeds and their selection for their milk production also indicate the economic potential of buffalo breeds in Pakistan. However, very limited genetic information is available for their characterization. Therefore, to identify the selection markers relevant to Pakistani buffalo breeds, available genome sequences of Pakistani buffalo breeds and buffalo breeds from 13 other countries were retrieved from our previously published study. These data were then analyzed through our developed pipeline for potential breed-specific markers. The novel aspect of this pipeline is that it compares single-nucleotide polymorphisms (SNPs) in the same position for possible allele differences among breeds. This approach is different from other currently available tools, which select SNPs based on whether their position is present or absent in one breed compared with others. This study also highlights how the Nili breed, which was previously thought to be lost due to Nili–Ravi domestication, has maintained its separate breed status and requires a breed conservation program. ABSTRACT: Domestic buffaloes (Bubalus bubalis), known as water buffaloes, play a key role as versatile multipurpose agricultural animals in the Asiatic region. Pakistan, with the second-largest buffalo population in the world, holds a rich domestication history of buffaloes. The overall trends in buffalo production demand the genomic characterization of Pakistani buffalo breeds. To this end, the resequencing data of Pakistani breeds, along with buffalo breeds from 13 other countries, were retrieved from our previous study. This dataset, which contained 34,671,886 single-nucleotide polymorphisms (SNPs), was analyzed through a pipeline that was developed to compare possible allele differences among breeds at each SNP position. In contrast, other available tools only check for positional SNP differences for breed-specific markers. In total, 1918, 1549, 404, and 341 breed-specific markers were identified to characterize the Nili, Nili–Ravi, Azakheli, and Kundi breeds of Pakistani buffalo, respectively. Sufficient evidence in the form of phenotypic data, principal component analysis, admixture analysis, and linkage analysis showed that the Nili breed has maintained its distinct breed status despite sharing a close evolutionary relationship with the Nili–Ravi breed of buffalo. In this era of genome science, the conservation of these breeds and the further validation of the given selection markers in larger populations is a pressing need.