Genome-wide characterization of IBD-enriched regions, ROH, and selection signatures reveal genomic hotspot and adaptive evolution in beef cattle breeds

Abstract Identity-by-descent (IBD) segments are shared genomic regions inherited from a common ancestor. However, the genome-wide patterns of IBD-enriched regions (IBD-ERs), their overlap with runs of homozygosity (ROH) islands, and subsequent association with selection signatures in beef cattle populations remains poorly understood. In the present study, we analyzed whole-genome resequencing data from Mongolian cattle (MG), Red Angus cattle (RA), and crossbred individuals (HY) derived from MG×RA crosses to characterize population structure, IBD patterns, autozygous segments, and signatures of selection. Population genetic analysis revealed clear genetic stratification among the studied populations. Mongolian cattle exhibited higher genetic diversity, whereas Red Angus cattle demonstrated substantial genomic inbreeding and recent genetic resemblance. In total, 488 IBD-ERs were identified, 309 of which were breed-specific. Notably, a 6-Mb IBD-ER on chromosome 21 in Red Angus overlaps with ROH islands and contains an approximately 200 Kb core subregion supported by multiple positive selection signatures. Several genes annotated in this region (including PSMA6, PRORP, and MIPOL1) are closely associated with hoof health and disease resistance in cattle. Our results revealed strong correlations among IBD-ER, ROH islands, and selection signatures, underscoring the role of these genomic features in shaping genetic architecture of breeds and adaptive evolution. These findings advance our understanding of haplotype conservation and selection in beef cattle and provide valuable insights for designing future breeding programs for beef cattle.