Conservation & local programs

Revealing the Footprints of Balancing Selection in the Sheep Genome

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Abstract

Detecting footprints of selection is an essential component of evolutionary and population genomics. Although positive and purifying selection have been widely examined, our understanding of balancing selection in livestock species remains limited. Understanding this mechanism is essential because if a trait is maintained by balancing selection, its performance is most probably directly linked to the level of genetic diversity. In a period when most livestock populations experience a gradual loss of diversity, mainly due to intensive selection, genes under balancing selection may be especially vulnerable. This raises the question of whether genetic variation in genomic regions affected by balancing selection should receive higher attention compared to other parts of the genome. In this study, we investigated the footprints of balancing selection in the sheep genome by analyzing genomic data of multiple sheep breeds genotyped by the HD SNP BeadChip. After quality control, the dataset comprised 527,823 autosomal SNPs from 319 individuals representing 13 breeds. To identify genomic regions potentially shaped by balancing selection, six different statistical approaches were applied, including the Non-central deviation statistic, Tajima's D, β statistic, B-statistic, heterozygosity-rich regions, and runs of homozygosity deserts. Each approach was computed separately for each breed, and the top 1% of values per approach were selected. SNPs exceeding the threshold in at least two methods were classified as signatures of balancing selection. On average, 4,343 SNPs per breed were identified as signals of balancing selection. Comparison of genomic coordinates revealed that 11,052 SNPs were shared as signals in two or more breeds, and a total of 45 SNPs distributed across five regions on four chromosomes were detected in all 13 breeds. Gene annotation identified 3,670 genes located within selection signals across the whole metapopulation. Functional enrichment analysis revealed 210 significantly enriched KEGG pathways and GO terms. The most enriched categories included hormone and neuroendocrine signaling (estrogen, GnRH, oxytocin, and growth hormone), immune-related signaling (chemokine, T- and B-cell receptor, and FcγR-mediated phagocytosis), as well as processes involved in cell adhesion, cytoskeletal organization, and energy metabolism. These functional groups indicate that balancing selection in sheep predominantly affects genes related to reproduction and endocrine regulation, immune response, energy metabolism, and cellular integrity. These results provide new insights into genomic regions influenced by balancing selection and highlight multiple shared regions across breeds. Understanding this component of genetic diversity may help preserve functional variation essential for the long-term adaptability of sheep populations. Moreover, identifying balancing selection acting on traits such as reproduction and immune response provides insight into the biological mechanisms underlying these traits and may support their future improvement. This research was supported by the VEGA 1/0316/25 and APVV-20-0161 projects and and COST Action - CA22112: European Network on Livestock Phenomics (EU-LI-PHE).

Keywords: 2026

How to Cite:

Halvoník, A., Moravčíková, N., Pálešová, K., Vostrá-Vydrová, H., Vostrý, L. & Kasarda, R., (2026) “Revealing the Footprints of Balancing Selection in the Sheep Genome”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285600. doi: https://doi.org/10.31274/wcgalp.23747

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