Relationships between liver and rumen fluke infections, milk somatic cells and polymorphisms in the Toll-like receptor 5 gene and vitamin D metabolism-related genes in Holstein dairy cows

This study investigated polymorphisms in the genes CYP3A4, CYP2R1, and TLR5, and their associations with liver fluke (Fasciola hepatica) and rumen fluke (Calicophoron / Paramphistomum spp.) infections as well as with milk somatic cell count (SCC) as an indicator for mastitis in Holstein Friesian dairy cows. DNA sequencing of the genes' exons, 5'-, 3'-untranslated regions (UTR), introns, and flanking regions of 24 cows revealed 442 variants (388 SNPs and 54 InDels) including 116 previously unknown variants. We detected three novel non-synonymous variants leading to the derived amino acid exchanges, i.e. CYP3A4 p.Gly197Ser, CYP3A4 p.Ile388Val, and CYP2R1 p.Val11Ala. The newly identified SNP 25:36589922 T > C (ss11846100002) is positioned in the splice site of CYP3A4, but showed no impact on the binding score of the splice enzymes. The CYP2R1 and TLR5 genes presented 11 SNPs in the 5'- and 3'-UTR, partly influencing transcription factor binding or microRNA target sites. Associations between polymorphisms and constructed haplotypes with infection traits were analysed via (generalized) linear mixed models including further potential confounders. In total, 109 variants in CYP3A4, 37 variants in CYP2R1, and 18 variants in TLR5 were significantly associated with F. hepatica and rumen fluke infections, and with SCC. The CYP2R1 and TLR5 variants were mostly linked to SCC, indicating the genes' roles in immune responses to bacterial infections. Haplotype analysis revealed significant associations between specific CYP3A4 haplotypes and F. hepatica worm count and faecal egg counts. This study revealed significant insights into gene polymorphisms related to vitamin D metabolism and immune response, which seem to play a role in helminth and udder infections.