Additional file 3. Number of gDNA samples included in each library pool and the corresponding sequencing read depth at each position (DP). Large White, Landrace, Duroc, Pietrain samples were merged in two library pools each according to their commercial origin. The numbers between brackets indicate the number of animals in each of the pools for these four breeds

Abdoallah Sharaf (3446327)

Abe Huisman (650541)

Alex Clop (235992)

Armand Sanchez (168473)

Pieter As (3570626)

Sophia Derdak (642670)

Genetics Selection Evolution

PubMed

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MOESM3 of Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array

Alex Clop

Abe Huisman

Pieter van As

Abdoallah Sharaf

Sophia Derdak

Armand Sanchez

Springer - Publisher Connector

Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array

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. 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. 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. The online version of this article (doi:10.1186/s12711-016-0206-0) contains supplementary material, which is available to authorized users

Clop, Alex

Huisman, Abe

van As, Pieter

Sharaf, Abdoallah

Derdak, Sophia

Sánchez Bonastre, Armando

Diposit Digital de Documents de la UAB

Crossref

[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.This work was funded by Grants from the Spanish Ministry of Science and Innovation (Project AGL2010-22358-C02-01) and the Spanish Ministry of Economy and Competitiveness (AGL2013-44978-R; CSD2007-00036, IPT-2012-0378-060000). A Clop acknowledges the Ramon y Cajal Fellowship program from the Spanish Ministry of Economy and Competitiveness (RYC-2011-07763). S Derdak is supported by the Parc Científic de Barcelona through the Torres Quevedo subprogram (MICINN) under Grant agreement PTQ-12-05391.Peer reviewe

As, Pieter van

Sánchez, Armand

Digital.CSIC

English

Additional file 2. Target TLR genomic regions. The coordinates correspond to the Sscrofa10.2 genome assembly. The column “portion without sequence information (bp)” indicates the number of bp that were sequenced to a depth of less than 1000. The column “cds and UTR content” indicates whether that genomic portion correspond to coding sequence or/and to UTR. The column “cause of missing sequence information” indicates the reason for lack of sequence information for the corresponding segment. There are two legends: “missing capture baits” indicate that Agilent capture baits that cover this segment could not be designed; “homologous region in the swine genome” indicates that although the baits were designed and the segment was sequenced, the corresponding sequence reads could not be unambiguously mapped to that region

MOESM2 of Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array

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MOESM3 of Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array

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