Abstract
Functional polymorphisms in pattern recognition receptors (PRRs) modulate innate immunity and play a crucial role in resistance or susceptibility to diseases. The present study was carried out to explore polymorphic patterns in the coding sequences of PRR genes TLR3, TLR1LA (TLRs), MDA5, LGP2 (RLRs) and NOD1 (NLR) in chicken breeds of India, namely Ghagus (GH), Nicobari (NB) and the exotic White Leghorn (WLH) breed. Out of 209 SNPs observed in five genes among three breeds, 117 were synonymous (Syn) and 92 were non-synonymous (NS) SNPs. In TLR genes the highest polymorphism was observed in NB (16, 28) compared to GH (14, 16) and WLH (13, 19) breeds. In the MDA5 gene the highest polymorphism was observed in GH (12) compared to NB (eight) and WLH (four) breeds. However, an almost similar level of polymorphism was observed in the LGP2 gene among the three breeds. In the NOD1 gene, the highest polymorphism was observed in NB (27), followed by WLH (11) and GH (10) breeds. The overall highest number of SNPs was observed in NB (90), followed by GH (62) and the WLH (57) breed. With regard to variation in polymorphism among different classes of PRRs, the study revealed the highest polymorphism in TLRs compared to NOD1 and the RLR class of PRRs. Further, the domain locations of various Syn and NS SNPs in each PRR among the three breeds were identified. In silico analysis of NS SNPs revealed that most of them had a neutral effect on protein function. However, two each in TLR1LA and LGP2 and one in the MDA5 gene were predicted to be deleterious to protein function. The present study unravelled extensive polymorphism in the coding sequences of the TLR and NLR class of PRR genes, and the polymorphism was higher in indigenous chicken breeds.
Highlights
Pattern recognition receptors (PRRs) are highly conserved germ-line-encoded molecules which recognize pathogenassociated molecular patterns (PAMPs) that are an integral part of pathogens
Coding sequences of five genes belonging to three different classes of PRRs (TLRs, retinoic acid-inducible gene-I-like (RIG-I) receptors (RLRs) and nucleotide-binding and oligomerizationdomain-like receptors (NLRs)) were studied for functional polymorphisms in GH, NB and White Leghorn (WLH) breeds
Amino acid substitutions due to polymorphism in the leucine-rich repeats (LRR) domain of PRRs may affect the ability of receptors to recognize PAMPs, while those in the transmembrane domain may lead to defects in intracellular receptor transport
Summary
Pattern recognition receptors (PRRs) are highly conserved germ-line-encoded molecules which recognize pathogenassociated molecular patterns (PAMPs) that are an integral part of pathogens. Recognition of PAMPs by PRRs leads to activation of innate immune response by inducing type I interferons and pro-inflammatory cytokines. Three classes of PRRs, such as Toll-like receptors (TLRs), retinoic acid-inducible gene-I-like (RIG-I) receptors (RLRs), and nucleotide-binding and oligomerizationdomain-like receptors (NLRs), have been described (Chen et al, 2013). SNPs in the CDSs of PRR genes may alter the activity of PRRs and thereby affect the resistance or susceptibility to infectious diseases.
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