Genome-wide scans reveal selection signatures and cross-population variation in South African and European beef cattle breeds

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.  These selection signatures provide insights into how evolutionary forces have shaped a population over time.In this study, a total of 96 samples were collected in several farms from four different cattle breeds, namely South African indigenous Nguni (n = 28) and Bonsmara (n = 21), Scottish Angus (n = 22), and Swedish Simmental (n = 25). Genotyped samples were subjected to quality control, and a total of 105,675 SNPs from 78 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  using cross-population extended haplotype homozygosity ( XP-EHH), relative extended haplotype homozygosity (Rsb), and fixation index (Fst) methods, to assess the genetic differ..., , , # Cattle Genotyped Data

[https://doi.org/10.5061/dryad.qjq2bvqq3](https://doi.org/10.5061/dryad.qjq2bvqq3)

**Populations and Samples**

Ninety-six semen samples from Nguni: n = 28, Bonsmara: n = 21, Angus: n = 22, and Simmental: n = 25 were randomly collected from four provinces Mpumalanga (25.4294°S, 29.3306°E), Northwest (25.6318°S-27.7829°E), Gauteng (26.2708°S, 28.1123°E), and Limpopo (23.0353°S 29.6583°E) of South Africa. Following sampling, traits like: sperm motility, Progressive motility, of the fresh bull semen were individually recorded, and the samples were then cryopreserved at the Agricultural Research Council (Animal Production Germplasm Conservation & Reproductive Biotechnologies) in Irene, South Africa.

 **DNA extraction, genotyping, and quality control.**

Genomic DNA was extracted from semen samples according to the manufacturer's protocol using a NucleoMag® pathogen extraction kit. Quantification was performed using Qubit® 2.0, and quantified DNA was genotyped ...