Genome-wide Scans Reveal Selection Signatures and Cross- Population Variation in South African and European Beef Cattle Breeds

Background In genetics and evolutionary biology, the concept of selection signatures is used to describe specific patterns in the genome that are associated with the process of natural selection. This natural selection can leave distinct genetic footprints of signatures, such as changes in allele frequencies, the presence of specific mutations, or patterns of genetic variation. Selection signatures provide information about the evolutionary forces that have shaped a population over time. Methods In this study, a total of 96 samples from four different cattle breeds, namely Nguni (n = 28), Bonsmara (n = 21), Angus (n = 22), and Simmental (n = 25) were subjected to quality control, following quality control, a total of 105,675 SNPs from 73 individuals remained for further analysis. Genomic signatures of positive selection within each breed were identified using the Integrated Haplotype Score (iHS) method, and cross-population comparison analysis was conducted using XP-EHH, Rsb, and Fst methods to assess the genetic differences between breeds. Results For the iHS analyses of individual breeds, two genomic regions identified signatures of selection for Bonsmara, six for Simmental, four for Nguni, and one for Angus. Ten regions were identified as being under selection, with BTA 12 shared between Nguni and Bonsmara. Cross-population comparisons using XP-EHH, Rsb, and FST methods revealed specific genomic regions differentially selected between breeds. Gene annotation analyses revealed candidate genes associated with several Quantitative Trait Loci (QTL). For instance, in Simmental cattle, the gene FAM110B was associated with carcass weight and body confirmation score. Bonsmara cattle had fewer candidate genes, including CDK8 and FLT1, while Angus revealed no candidate genes on BTA 18. Nguni cattle revealed the following candidate genes CRB1, PLAG2GA, and VASH2, with CDK8 shared between Bonsmara and Nguni on BTA 12. Cross population comparisons further revealed candidate genes associated with specific traits. For Bonsmara vs Nguni, genes including PLCXD3, FAM149B1, and GRIK2 were identified, whereas, for Simmental vs Angus, SLIT2 and TSPAN9 genes were identified. Furthermore, the study highlighted gene functions, revealing associations with meat quality traits, reproduction, health, diseases, fertility, and body conformation score. Gene interaction analysis using the STRING database identified a network of 63 candidate genes, revealing the structure of genetic interactions. Some genes had multiple functions, indicating multiple roles in various biological processes. Conclusion This extensive genomic study can assist in highlighting the importance of the genetic background of breed-specific traits, and in this way contributes to selective breeding and trait improvement in cattle populations.