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Biased distribution of single nucleotide polymorphisms (SNPs) in porcine Toll-like receptor 1 (TLR1), TLR2, TLR4, TLR5, and TLR6 genes

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Abstract

Toll-like receptors (TLRs) recognize various microbial components and induce immune responses. Polymorphisms in TLRs may influence their recognition of pathogen-derived molecules; swine TLRs are predicted to be associated with responses to infectious diseases such as pneumonia. In this study, we searched for single nucleotide polymorphisms (SNPs) in the coding sequences of porcine TLR1, TLR2, TLR4, TLR5, and TLR6 genes in 96 pigs from 11 breeds and elucidated 21, 11, 7, 13, and 11 SNPs, respectively, which caused amino acid substitutions in the respective TLRs. Distribution of these nonsynonymous SNPs was biased; many were located in the leucine-rich repeats, particularly in TLR1. These data demonstrated that the heterogeneity of TLR genes was preserved in various porcine breeds despite intensive breeding that was carried out for livestock improvement. It suggests that the heterogeneity in TLR genes is advantageous in increasing the possibility of survival in porcine populations.

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Fig. 1

Abbreviations

CDS:

coding sequence

LPS:

lipopolysaccharide

LRR:

leucine-rich repeat

RT:

reverse transcriptase

PCR:

polymerase chain reaction

SNP:

single nucleotide polymorphism

TIR:

Toll/interleukin-1 receptor

TLR:

Toll-like receptor

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Acknowledgements

We thank Dr. Takeshi Hayashi (NIAS) for the helpful discussions related to statistical analyses and Dr. Joan K. Lunney (APDL, ARS, USDA) for the critical reading of this manuscript. This work was supported by the Animal Genome Research Project of the Ministry of Agriculture, Forestry and Fisheries of Japan and by a Grant-in-Aid from the Japan Racing Association.

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Authors and Affiliations

  1. Second Research Division, STAFF-Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Hiroki Shinkai, Maiko Tanaka & Naohiko Okumura

  2. Animal Genome Research Program (NIAS/STAFF), 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan

    Hiroki Shinkai, Maiko Tanaka, Takeya Morozumi, Tomoko Eguchi-Ogawa, Naohiko Okumura, Takashi Awata & Hirohide Uenishi

  3. Department of Immunology, National Institute of Animal Health, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan

    Yoshihiro Muneta

  4. Animal Genome Laboratory, Genome Research Department, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

    Tomoko Eguchi-Ogawa, Takashi Awata & Hirohide Uenishi

Authors
  1. Hiroki Shinkai
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  2. Maiko Tanaka
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  3. Takeya Morozumi
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  4. Tomoko Eguchi-Ogawa
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  5. Naohiko Okumura
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  6. Yoshihiro Muneta
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  7. Takashi Awata
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Corresponding author

Correspondence to Hirohide Uenishi.

Electronic supplementary material

Below is the image is a link to a high resolution version.

Supplementary Fig. 1

Comparison of the deduced amino acid sequence of porcine TLR5 gene with those of its human and mouse counterparts. The amino acid sequences encoded by human and mouse TLR5 genes are derived from Swiss-Prot accession nos. O60602 and Q9JLF7, respectively. Asterisks, colons, and periods under the aligned sequences indicate complete matches, similar amino acids among the three species, and matches in two species among three, respectively. Boxes indicate the predicted signal peptide and the transmembrane domain (GIF 789 KB)

High resolution image file (EPS 3974 KB)

Supplementary Fig. S2

Expression of the TLR5 gene in eight porcine tissues, as analyzed by RT-PCR. Total RNAs from the colon, kidney, liver, lung, small intestine, spleen, stomach, and thymus were purified from a 1-month-old male pig. The CDS of porcine TLR5 was encoded using a single exon. RNase-freeDNase I (Takara Bio, Otsu, Japan) was used before the samples were subjected to reverse transcription to ensure the complete degradation of genomic DNA, which contaminates the RNA samples. Primer pairs,templates treated with (+) or without (−) reverse transcriptase, and PCR cycles are shown at the top of the (GIF 130 kb)

High resolution image file (EPS 114 KB)

Supplementary Fig. S3

Haplotypes of porcine TLR genes reconstructed by the expectation-maximization method (Excoffierand Slatkin 1995). Haplotypes are estimated using individuals whose genotypes of SNP loci are completely determined. Thebreeds in which the haplotypes cannot be determined are indicated as ND. Nonsynonymous SNP loci are indicated by redletters. Heterozygosity (HT) are calculated using the formula:\({\text{HT = }}{\sum {{\text{p}}^{2}_{{_{i} }} } }\) where p i is the observed frequencies of the ith haplotypes at each TLR gene. BS, Berkshire; CL, Clawn; DR, Duroc; HS,Hampshire; JH, Jinhua; LR, Landrace; LW, Large White; PB, Potbelly; MS, Meishan; MY, Middle Yorkshire; and WB,Japanese wild boar (GIF 575 kb)

High resolution image file (EPS 216 KB)

Supplementary Table 1

Primers for expression analysis of porcine TLR5 (DOC 25 kb)

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Shinkai, H., Tanaka, M., Morozumi, T. et al. Biased distribution of single nucleotide polymorphisms (SNPs) in porcine Toll-like receptor 1 (TLR1), TLR2, TLR4, TLR5, and TLR6 genes. Immunogenetics 58, 324–330 (2006). https://doi.org/10.1007/s00251-005-0068-z

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  • DOI: https://doi.org/10.1007/s00251-005-0068-z

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