Conservation & local programs

Genomic selection signatures and population differentiation in South African beef cattle breeds

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Abstract

In genetics and evolutionary biology, selection signatures refer to unique patterns in the genome that are related with the selection process. These selection signals reveal how evolutionary forces have altered a population throughout time. The current study aims to identify selection signatures and candidate genes for unique traits in four South African beef cattle breeds using FST statistical analysis. DNA was extracted from semen samples of Nguni (n = 28), Bonsmara (n = 21), Angus (n = 22), and Simmental (n = 25) and genotyped using the Illumina BovineSNP 150K BeadChip and transformed into Plink data into map/ped format using Genome Studio 2.0 software. Quality control removed SNPs with a genotyping rate of ≥ 95% and minor allele frequency of ≥ 0.05 were excluded from the dataset. Selection signatures between cattle breeds was detected for fixation index (FST) in R Studio environment using packages: data. table, qqman, biomaRt, clusterProfiler and org.Bt.eg.db, and statistically significant loci were identified using a Bonferroni-adjusted significance threshold (P < 0.05/N) to control for multiple testing. Genome-wide FST analysis revealed widespread genomic differentiation among South African and exotic beef cattle breeds, with significant SNPs distributed across multiple autosomes. The lowest genetic divergence was observed between Bonsmara vs Nguni (mean FST = 0.02), whereas moderate differentiation was detected for Angus vs Simmental (mean FST = 0.09), and higher levels of differentiation were detected in both the Bonsmara vs Angus (FST mean = 0.10) and Nguni vs Simmental (FST mean = 0.11) comparison. Also, candidate genes were identified, particularly in the Nguni vs Bonsmara comparison, including GRIK2 and PLXNC1, associated with fertility and disease susceptibility, for Bonsmara vs Angus comparison revealed GALNTL6 associated with disease susceptibility, and lastly for Nguni vs Simmental revealed the gene ADAMTS12 for body weight. In conclusion, the FST analysis revealed clear genomic differentiation among Bonsmara, Nguni, Angus, and Simmental cattle, reflecting differences in adaptation, selection history, and production objectives. These findings demonstrate that both artificial selection and environmental adaptation have shaped genomic diversity and breed differentiation in beef cattle.

Keywords: 2026

How to Cite:

Nephawe, K., Mtileni, B. & Modiba, M., (2026) “Genomic selection signatures and population differentiation in South African beef cattle breeds”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286396. doi: https://doi.org/10.31274/wcgalp.23981

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