Bovine Innate Immune Genomics: Signatures of Selection and Association

We utilized a custom next-generation sequencing approach and allele-specific genotyping assays to detect and validate 280 biallelic variants across all 10 bovine TLR genes, including 71 nonsynonymous single nucleotide polymorphisms (SNPs) and one putative nonsense SNP.   Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and specialized beef and dairy breeds could not be differentiated despite an average polymorphism density of 1 marker/158 bp.  Polyphen and SIFT analyses of amino acid (AA) replacements encoded by bovine TLR SNPs indicated that up to 32% of the AA substitutions were likely to impact protein function.  Classical and newly developed tests of diversity provide strong support for balancing selection operating on TLR3 and TLR8, and purifying selection acting on TLR10.  An investigation of the persistence and continuity of linkage disequilibrium (r² ≥ 0.50) between adjacent variable sites also supported the presence of selection acting on TLR3 and TLR8.  A case-control study employing validated variants from bovine TLR genes recognizing bacterial ligands revealed six SNPs potentially eliciting small effects on susceptibility to Mycobacterium avium spp paratuberculosis infection in dairy cattle.  The results of this study will broadly impact domestic cattle research by providing the foundation to explore several avenues of bovine translational genomics, and the potential for marker-assisted vaccination.