Evolution of the Bovine TLR Gene Family and Member Associations with Mycobacterium avium Subspecies paratuberculosis Infection

Fisher, Colleen A.; Bhattarai, Eric K.; Osterstock, Jason B.; Dowd, Scot E.; Seabury, Paul M.; Vikram, Meenu; Whitlock, Robert H.; Schukken, Ynte H.; Schnabel, Robert D.; Taylor, Jeremy F.; Womack, James E.; Seabury, Christopher M.

Unphased diploid genotypes for a subset of the validated SNPs and indels (n = 35; nonsynonymous, putative nonsense, 5' upstream regions, and introns) within bovine TLR genes either known or postulated to primarily recognize bacterial ligands (TLR1, TLR2, TLR4, TLR5, TLR6, TLR9, TLR10) were tested for associations with bacterial culture status for MAP (fecal and/or tissue) in three Holstein dairy herds (n = 68 cases, 270 controls). All nonsynonymous TLR SNPs previously associated with MAP infection [19] (TLR1, TLR2, TLR4) were monomorphic in our samples (n = 549; 31 breeds). Conditional logistic regression models were constructed for each of 35 variable sites meeting our selection criteria (see methods) to estimate the relative odds of MAP infection given the defined diagnostic criteria adjusted for the effects of herd and age. Collectively, six SNPs produced suggestive associations, as evidenced by uncorrected P-values (Table 5) . Interestingly, three SNPs in TLR2 and one in TLR6 were associated with increased odds of MAP infection in animals with 1 or more copies of the minor allele (Table 5) . Two SNP loci, 1 in TLR4 and 1 in TLR10, were associated with decreased odds of infection given increasing copies of the minor allele (Table 5) . Following locus-specific correction of the P-values using the FDR method (http://sdmproject.com/utilities/? show=FDR) [45] , two SNPs (TLR6-rs43702941; TLR10-rs55617325) remained significant (P#0.05), and three SNPs (TLR2-rs68268245, ss470256479, rs43706433) displayed P-values (P#0.053) that were suggestive of a potential recessive genetic association with MAP infection ( Table 5 ). Two of these SNPs (TLR2-ss470256479, rs43706433)