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.

Several studies have demonstrated that some naturally occurring TLR variants enhance the risk of severe infections in humans, mice, and domestic cattle, including the potential for increased susceptibility to Johne's disease, a debilitating and economically important disease of ruminants caused by infection with Mycobacterium avium spp paratuberculosis (MAP) (for review see [17] [18] [19] [20] [21] [22] ). Furthermore, several important bovine health-related QTL have also been localized to genomic regions either proximal to or directly overlapping one or more TLR loci (for review see [8, [23] [24] [25] [26] [27] ). Therefore, we utilized massively parallel pyrosequencing of a pooled TLR amplicon library (TLRs 1-10) to comprehensively evaluate nucleotide variation and haplotype structure for 31 cattle breeds representing Bos taurus taurus, Bos taurus indicus, and their subspecific hybrids (composites). Overall, 276 single nucleotide polymorphisms (SNPs) and 4 insertion-deletion (indel) mutations were detected and validated. Bovine TLR SNPs and indels leveraged from the pyrosequencing study were used in a casecontrol analysis to identify risk factors underlying differential susceptibility to MAP in U.S. dairy cattle. In addition, we also comprehensively report on bovine TLR haplotype structure, the extent of haplotype sharing among specialized breeds and subspecific lineages, and provide median joining networks as putative representations of bovine TLR haplotype evolution [28] . Finally, we provide computational evidence for several bovine TLR genes evolving under disparate modes of non-neutral evolution, thereby underscoring their potential importance to bovine innate immunity and health-related traits. The results of this study will enable bovine translational genomics, QTL refinement, and ultimately, genome-assisted methods for animal selection to develop cattle populations with enhanced disease resistance and favorable vaccine response.