Genomic Signatures of Selection Reveal Breed-Specific and Shared Adaptive Regions in South African Beef Cattle

In genetics and evolutionary biology, selection signatures refer to distinct genomic patterns that reflect the action of natural and artificial selection on populations over time. Detecting such signatures provides critical insights into adaptive evolution and breed differentiation, especially in livestock populations subjected to diverse production environments and breeding objectives. In this study, a total of 96 samples were collected from four different cattle breeds, namely, South African indigenous Nguni (n = 28), Bonsmara (n = 21), Angus (n = 22), and Simmental (n = 25). The samples were genotyped using the Illumina Bovine SNP 150K BeadChip and subjected to quality control. Selection signatures were identified using the integrated haplotype score (iHS) method and the fixation index (Fst) method to assess the genetic differences between breeds. The complementary application of within-population and cross-population approaches enabled the detection of both recent and divergent selective pressures. A total of twelve regions were found to be under selection, with Bos taurus autosome (BTA) 12 being common between Nguni and Bonsmara. Gene annotation analyses identified several genes, including FAM110B, CDK8, and FLT1 in Bonsmara cattle, whereas Nguni cattle indicated potential genes such as CRB1, PLA2G4A, and VASH2, with CDK8 common between Bonsmara and Nguni on BTA 12. Cross-population analyses further identified PLCXD3, FAM149B1, and GRIK2 as candidate genes differentiating Bonsmara from Nguni cattle, and TSPAN9 distinguishing Simmental from Angus cattle. These results indicated breed-specific adaptive divergence. The study revealed genomic regions that are under selection in South African Nguni, Bonsmara, and Simmental cattle, with less information for Angus cattle breeds. Several candidate genes were found to be associated with reproductive traits (such as sperm count and inseminations per conception), disease resistance (such as bovine respiratory disease), and calving ease. This study identifies breed-specific and shared genomic regions under selection across diverse cattle breeds, providing novel insights into the genetic basis of adaptation and production-related traits. These findings explain the potential application of selection signature analyses in genomic-assisted breeding programmes aimed at improving productivity, resilience, and sustainability of cattle populations.