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),andRomanian(ROM)buffalobreedsusingrunsofhomozygosity (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,andROMbuffalobreedswasgenotypedusingtheAxiom® BuffaloGenotyping 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, AcademicEditor: GuangxinE Received: 30April2026 Revised: 12May2026 Accepted: 14May2026 Published: 16 May2026 Copyright: ©2026bytheauthors. Licensee MDPI,Basel,Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY)license. MLLT3, NAALADL2, andGAB2), 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.