Data from: 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 differences between breeds. The results from the iHS method
revealed selection signatures in two genomic regions for Bonsmara, six for
Simmental, four for Nguni, and one for Angus cattle.  Ten regions
were found to be under selection, with BTA 12 being shared between Nguni
and Bonsmara. Comparisons across populations using  Rsb, and Fst
methods performed better and  revealed the most specific genomic
regions that varied in selection between breeds. Gene annotation analyses
linked candidate genes to several Quantitative Trait Loci (QTL). For
example, in Simmental cattle's FAM110B gene was linked to carcass
weight and body confirmation score. Bonsmara showed fewer candidate genes,
such as CDK8 and FLT1, whereas Angus had none on BTA 18. Nguni identified
potential genes such as CRB1, PLAG2GA, and VASH2, with CDK8 shared by
Bonsmara and Nguni on BTA 12. Further cross-population studies revealed
candidate genes associated with certain traits, genes including as PLCXD3,
FAM149B1, and GRIK2 for Bonsmara versus Nguni, and SLIT2 and TSPAN9 for
Simmental vs Angus. The study also emphasised gene related to meat
quality, reproduction, health, illnesses, fertility, and body conformation
score. Gene interaction study with the STRING database revealed a network
of 63 candidate genes, demonstrating the structure of genetic connections,
some biological processes. The study found that iHS performed well in
population analysis with Nguni cattle, having exhibited the highest number
of signatures across the genome, and significant signatures were also seen
in comparisons between Nguni and Bonsmara using the Fst and Rsb methods.
Furthermore, the study discovered that a bigger number of genes were
connected with various traits, including sperm count and insemination per
conception, sensitivity to bovine respiratory disease, and ease of
calving. This genomic analysis underlined the relevance of the genetic
relying which distinguishes distinct breeds. This understanding has the
potential to significantly enhance selective breeding and increase
desirable traits in cattle herds. This genomic analysis underlined the
significance of the genetic basis for breed-specific traits. This
understanding has the potential to drastically improve selective breeding
and increase desirable traits in cattle herds.