Genomic Survey of Selection Footprints in Three Buffalo Breeds from Eastern Europe

The buffalo is an important agricultural species due to its many productive characteristics, which encourage its use worldwide. Uncovering the processes of selective sweeps is critical for a comprehensive understanding of genomic mechanisms that influence phenotypic differentiation in buffalo. This study aims to refine signatures of selection in Bulgarian (BUL), Hungarian (HUN), and Romanian (ROM) buffalo breeds using runs of homozygosity (ROHs), the integrated haplotype score (iHS), the standardized log-ratio of the integrated site-specific extended haplotype homozygosity (EHH) between pairs of breeds test (Rsb), and cross-population EHH (XP-EHH) approaches. The SNP dataset of 160 genotypes from BUL, HUN, and ROM buffalo breeds was genotyped using the Axiom® Buffalo Genotyping Array 90K from Affymetrix. By combining the ROH, iHS, Rsb, and XP-EHH methods, we identified many important genomic regions and candidate genes associated with milk production (SLC24A2, TMEM132C, and ALCAM), reproduction (CSMD1, NTS, PLIN2, GPC5, and FSHR), growth (MYOM2, CLN8, and RRAGA), immune response (METTL25, MLLT3, NAALADL2, and GAB2), and adaptation (ADAMTSL1) in BUL, HUN, and ROM buffalo breeds. Our findings highlighted selection signals and genes related to important economic traits in the BUL, HUN, and ROM buffalo breeds, providing promising candidate genes for further research and inclusion in conservation and selection plans for these breeds.