Toll-like receptors (TLRs) play important roles in innate immunity and developmental processes. Due to their nature as molecular pattern recognition receptors, their genetic diversity may reflect the effects of various pathogen pressures. Here, the extent of variability in the TLR1-6-10 gene cluster in three geographically and historically distinct breeds of horses was analysed. A genetically diverse group of representatives of 14 other horse breeds provided additional information on the variability of this gene cluster in the domestic horse. Altogether, 25 SNPs were identified in the TLR6-1-10 gene cluster across the 4 equine breed groups studied, of which 7 were synonymous and 18 non-synonymous. Twenty-eight inferred SNPs and 22 in silico translated amino acid haplotypes were identified. A predominant major haplotype present in all breed groups along with several group-specific haplotypes were identified. Strong linkage disequilibrium was detected for several SNPs, as well as effects of pervasive, site-specific selection. The existence of a major haplotype suggests it may confer a selective advantage across breeds. Less frequent breed-specific haplotypes may represent variability required or beneficial for responses to local pathogen pressures. Purifying site-specific selection was detected in the TIR domain and its vicinity in TLR6, whereas AA sites under diversifying selection were located in LRR domains and/or their surroundings in TLR1. Population structure models based on immune-related TLR6-1-10 markers did not distinguish between breed groups, whereas in models based on neutral microsatellite markers, breed groups clustered separately. This supports the assumption that the diversity of the TLR6-1-10 cluster is of adaptive value. The TLR6-1-10 alleles and haplotypes identified represent potential candidate markers for disease association studies.

• Keywords
• equine, haplotype, innate immunity, toll‐like receptor,
• MeSH
• Genetic Variation * MeSH
• Haplotypes MeSH
• Polymorphism, Single Nucleotide MeSH
• Horses genetics   immunology   MeSH
• Multigene Family MeSH
• Immunity, Innate * genetics   MeSH
• Toll-Like Receptor 6 * genetics   MeSH
• Toll-Like Receptors * genetics   metabolism   MeSH
• Linkage Disequilibrium MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Toll-Like Receptor 6 * MeSH
• Toll-Like Receptors * MeSH

Toll-like receptors (TLRs) represent an important part of the innate immune system. While human and murine TLRs have been intensively studied, little is known about TLRs in non-model species. The order Perissodactyla comprises a variety of free-living and domesticated species exposed to different pathogens in different habitats and is therefore suitable for analyzing the diversity and evolution of immunity-related genes. We analyzed TLR genes in the order Perissodactyla with a focus on the family Equidae. Twelve TLRs were identified by bioinformatic analyses of online genomic resources; their sequences were confirmed in equids by genomic DNA re-sequencing of a panel of nine species. The expression of TLR11 and TLR12 was confirmed in the domestic horse by cDNA sequencing. Phylogenetic reconstruction of the TLR gene family in Perissodactyla identified six sub-families. TLR4 clustered together with TLR5; the TLR1-6-10 subfamily showed a high degree of sequence identity. The average estimated evolutionary divergence of all twelve TLRs studied was 0.3% among the Equidae; the most divergent CDS were those of Equus caballus and Equus hemionus kulan (1.34%) in the TLR3, and Equus africanus somaliensis and Equus quagga antiquorum (2.1%) in the TLR1 protein. In each TLR gene, there were haplotypes shared between equid species, most extensively in TLR3 and TLR9 CDS, and TLR6 amino acid sequence. All twelve TLR genes were under strong negative overall selection. Signatures of diversifying selection in specific codon sites were detected in all TLRs except TLR8. Differences in the selection patterns between virus-sensing and non-viral TLRs were observed.

• Keywords
• Equid, Innate immunity, Odd-toe ungulates, Toll-like receptor, Transpecies haplotype sharing,
• MeSH
• Equidae MeSH
• Phylogeny MeSH
• Genomics MeSH
• Horses genetics   MeSH
• Humans MeSH
• Mice MeSH
• Perissodactyla metabolism   MeSH
• Toll-Like Receptor 1 * genetics   MeSH
• Toll-Like Receptor 3 * MeSH
• Toll-Like Receptors genetics   metabolism   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Mice MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Toll-Like Receptor 1 * MeSH
• Toll-Like Receptor 3 * MeSH
• Toll-Like Receptors MeSH

The West Nile virus (WNV) is a mosquito-borne flavivirus causing meningoencephalitis in humans and animals. Due to their particular susceptibility to WNV infection, horses serve as a sentinel species. In a population of Romanian semi-feral horses living in the Danube delta region, we have analyzed the distribution of candidate polymorphic genetic markers between anti WNV-IgG seropositive and seronegative horses. Thirty-six SNPs located in 28 immunity-related genes and 26 microsatellites located in the MHC and LY49 complex genomic regions were genotyped in 57 seropositive and 32 seronegative horses. The most significant association (pcorr < 0.0002) was found for genotypes composed of markers of the SLC11A1 and TLR4 genes. Markers of five other candidate genes (ADAM17, CXCR3, IL12A, MAVS, TNFA), along with 5 MHC class I and LY49-linked microsatellites were also associated with the WNV antibody status in this model horse population. The OAS1 gene, previously associated with WNV-induced clinical disease, was not associated with the presence of anti-WNV antibodies.

• Keywords
• Horse, MHC, Microsatellite, NKR, Polymorphism, Restriction fragment length polymorphism, SLC11A1, TLR4, West Nile virus,
• MeSH
• Enzyme-Linked Immunosorbent Assay MeSH
• Polymorphism, Single Nucleotide genetics   MeSH
• Horses blood   genetics   immunology   MeSH
• Microsatellite Repeats genetics   MeSH
• Polymorphism, Restriction Fragment Length MeSH
• Antibodies, Viral analysis   blood   MeSH
• Sentinel Species MeSH
• West Nile virus pathogenicity   MeSH
• West Nile Fever genetics   immunology   veterinary   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Romania MeSH
• Names of Substances
• Antibodies, Viral MeSH