Population Genomics of the Bovine Sialic Acid Network Reveals Functional and Evolutionary Diversity Across European and South African Cattle Breeds

**Background:** Sialic acids, mainly N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc), are terminal monosaccharides of glycans involved in numerous physiological processes, such as immune and neuronal function. Their biosynthesis, transport, transfer and turnover depend on a network of genes, but genetic studies in cattle have mostly addressed individual genes or genetic associations with milk oligosaccharide concentrations, leaving variation across this network largely uncharacterized. In bovine milk, sialylated glycans that depend on this network vary among animals and change rapidly during early lactation. We therefore characterized variation in 13 selected genes of the bovine sialic acid network using whole-genome sequence data from European and South African cattle. **Results:** We analyzed 346 animals from 12 European and 4 South African breeds. Of 9,724 variants in the 13 target genes, 8,675 were intronic and 62 were predicted to alter the amino acid sequence. Integration of SIFT predictions, Rate4Site conservation and protein context, with population representation as supporting evidence, identified 15 prioritized candidates, including 7 high-priority candidates in NEU3, ST8SIA2, ST8SIA4, CMAH and ST3GAL4. The most differentiated candidates were not among the 15 prioritized variants. NEU3 Y136H showed the largest regional contrast in allele frequency (0.83 in South African and 0.34 in European cattle), whereas several prioritized candidates were represented by a single allele in the South African cohort. Genome-wide principal component analysis of 950,219 linkage-disequilibrium-pruned SNPs separated South African from European cattle along the first component, which explained about 25% of the variance. None of the 220 analyzed common pathway SNPs exceeded the corresponding genome-wide differentiation thresholds at breed, country or regional level. Within the ascertained pathway SNPs, diversity was higher in South African breeds, and Tajima's D was shifted toward positive values in European breeds and centered near zero in South African breeds. **Conclusions:** This study provides a network-wide map of predicted protein-altering variation in the bovine sialic acid pathway and identifies 15 candidates for functional investigation, most of them rare. Because the most differentiated variants were not those with the strongest functional support, population contrasts, evolutionary conservation and protein context provide complementary evidence for selecting candidates. The analyzed common pathway SNPs did not show exceptional differentiation relative to the genome-wide background. The candidates provide specific targets for genotyping, enzyme-level testing and genotype-informed milk phenotyping.