Single nucleotide polymorphism in toll-like receptor genes in sus species

K. Darfour-Oduro, J. Ma, L.B. Schook
4th Annual Personal Genomes Meeting, September 30 – October 2, 2011, Cold Spring Harbor, New York


Toll-like receptors (TLRs) are pattern recognition receptors that mediate pathogen recognition and immune system activation.  Polymorphism in TLR genes may affect the recognition of pathogens and may alter human and livestock immune response. Studies carried out on livestock for TLRs have focused more on domesticated breeds. However, wild species suffer from multiple infections and variable environment and may display different polymorphism patterns as compared with domesticated breeds. A complete knowledge of polymorphism in TLRs of livestock will therefore require studies in wild species. Advances in comparative genomics have led to the discovery of single nucleotide polymorphisms (SNPs) by aligning sequence reads from animals to a reference genome. In this study, sequence reads from Sus Celebenesis, Sus Verrucosus, Phachoerus Africanus and Sus Barbatus were aligned to Sus Scrofa reference genome to investigate single nucleotide polymorphism in 9 toll-like receptor gene (TLR 1-10, except TLR 5) coding sequences of the four Sus species. TLR 7 showed no polymorphism in its coding sequence. Heterozygous snps for the 8 remaining TLR genes ranged from 12 to 41 with TLR 4 recording the highest number of snps and TLR 9 recording the lowest.  Relative frequencies of non synonymous to synonymous snps were highest in TLR 9.  Across genes, a high percentage (72%) of non-synonymous snp was found in LRR, the extracellular domain responsible for binding microbial products.  The distribution of non-synonymous snps in other domains were signal peptide (20.3%), signal peptide (3.9%), region of low complexity (2%) and transmembrane (1.3%).  Sus Celebenesis had the highest number of snps for TLR1, TLR6 and TLR8.  Sus Verucosus had the highest number of snps for TLR2, TLR3, TLR4 and TLR 9.  These differences may reflect the high pathogen diversity in the wild.