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.

Evaluation of the intragenic patterns of LD across all 31 breeds of cattle via 95% confidence intervals constructed for D' [32, 33] , application of the four gamete rule [32] , and estimates of recombination between adjacent variable sites [34, 35] revealed one or more blocks of strong LD within each of the 10 bovine TLR genes. Statistical evidence for historical recombination was detected within TLR2, TLR3, and TLR6, resulting in at least two detectable LD blocks within each gene. All other genes exhibited a single block of strong LD spanning either all, or the majority of all validated intragenic SNPs and indels, as supported by the majority rule of all three analyses [32] [33] [34] [35] . A comparison of average intragenic r 2 values calculated between adjacent variable sites across all 10 genes revealed a dynamic range of LD (0.09-0.70; all cattle, 31 breeds; Table 2 ). Discrete regions of high and low LD, the latter due to historical recombination, were also detected using the general model for varying recombination rate [31, 34, 35] . Cumulatively, four adjacent SNP sites [TLR2 (1), TLR3 (2), and TLR6 (1)] produced estimates of median recombination rates that exceeded the background rate () [31, 34, 35] by a factor of at least 2.5. The highest median estimate of recombination rate was observed in TLR3 (between SNP positions rs42851925, rs55617222; rs55617241, rs55617451, Table S2 ), and exceeded the background rate by a factor of at least 5.2. Analyses to identify tagSNPs/Indels which predictively captured 100% of the variation at 280 validated variable sites within all 10 genes for all cattle yielded 160 tagSNPs and 2 tagIndels (Table S3) . Similar analyses restricted to the B. t. taurus breeds demonstrated that only 118 tagSNPs and 1 tagIndel were predicted to capture 100% of the variation at 235 variable sites (Table S3) . Interestingly, the cumulative tagging efficiency (total tags predicted/total number of validated variable sites) was similar for both analyses (all cattle vs B. t. taurus), with this result largely due to the preponderance of taurine cattle in the total sample (94.4%), and the significant sharing of SNPs, indels, and haplotypes among the subspecific lineages.