title: Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array.
abstract: BACKGROUND
  Toll-like receptors (TLR) are crucial in innate immunity for the recognition of a broad range of microbial pathogens and are expressed in multiple cell types. There are 10 TLR genes described in the pig genome.
  
  
  RESULTS
  With a twofold objective i.e. to catalogue genetic variants in porcine TLR genes and develop a genotyping array for genetic association studies on immune-related traits, we combined targeted sub-genome enrichment and high-throughput sequencing to sequence the 10 porcine TLR genes in 266 pigs from 10 breeds and wild boars using a DNA-pooling strategy. We identified 306 single nucleotide variants across the 10 TLR and 11 populations, 87 of which were novel. One hundred and forty-seven positions i.e. six stop-gains and 141 non-synonymous substitutions were predicted to alter the protein sequence. Three positions were unique to a single breed with alternative allele frequencies equal to or higher than 0.5. We designed a genotyping array for future applications in genetic association studies, with a selection of 126 variants based on their predicted impact on protein sequence. Since TLR4, TLR7 and TLR9 were underrepresented in this selection, we also included three variants that were located in the 3'UTR of these genes. We tested the array by genotyping 214 of the 266 sequenced pigs. We found that 93 variants that involved the 10 TLR genes were polymorphic in these animals. Twelve of these variants were novel. Furthermore, seven known variants that are associated with immune-related phenotypes are present on the array and can thus be used to test such associations in additional populations.
  
  
  CONCLUSIONS
  We identified genetic variations that potentially have an impact on the protein sequence of porcine TLR. A genotyping array with 80 non-synonymous, 10 synonymous and three 3'UTR polymorphisms in the 10 TLR genes is now available for association studies in swine populations with measures on immune-related traits.
authors.affiliation: Center for Research in Agricultural Genomics (CRAG) Consorci CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Catalonia, Spain. Alex.clop@cragenomica.es.
authors.forename: Alex
authors.identifier: http://orcid.org/0000-0001-9238-2728
authors.initials: A
authors.lastname: Clop
authors.affiliation: Hypor BV, Villa 'de Körver', Spoorstraat 69, 5831 CK, Boxmeer, The Netherlands.
authors.forename: Abe
authors.initials: A
authors.lastname: Huisman
authors.affiliation: Hendrix-Genetics, Villa 'de Körver', Spoorstraat 69, 5831 CK, Boxmeer, The Netherlands.
authors.forename: Pieter
authors.initials: P
authors.lastname: van As
authors.affiliation: Ain Shams University, Cairo, Egypt.
authors.forename: Abdoallah
authors.initials: A
authors.lastname: Sharaf
authors.affiliation: Centre Nacional d'Anàlisi Genòmica CNAG, Baldiri Reixac 4, 08028, Barcelona, Catalonia, Spain.
authors.forename: Sophia
authors.initials: S
authors.lastname: Derdak
authors.affiliation: Center for Research in Agricultural Genomics (CRAG) Consorci CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Catalonia, Spain.|Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain.
authors.forename: Armand
authors.initials: A
authors.lastname: Sanchez
mesh_terms: D000818:Animals; D005787:Gene Frequency / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques; D011110:Polymorphism, Genetic / Q000235:genetics*; D013552:Swine / Q000235:genetics*; D051193:Toll-Like Receptors / Q000235:genetics*
chemical_list: D051193:Toll-Like Receptors