Page 28 - L. Genetics and genomics

[L. Genetics and genomics-22]

Genetic characteristics and polymorphisms in the chicken

interferon-induced transmembrane protein (IFITM3) gene

Min-Ju Jeong¹˙², Byung-Hoon Jeong¹˙²

¹Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju 54896, South Korea, ²Korea

Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, South Korea

The interferon-induced transmembrane protein 3 (IFITM3) gene is classified as a small interferon-stimulated gene
and is associated with a broad spectrum of antiviral functions against several fatal enveloped viruses, including

influenza A viruses (IAVs). The rs12252 single nucleotide polymorphism (SNP) of the IFITM3 gene in humans was

associated with susceptibility to H1N1 influenza in a 2009 pandemic. In addition, overexpression of the IFITM3
protein potently inhibits the highly pathogenic avian influenza H5N1 virus in ducks and chickens. Although chickens
are a major host of influenza viruses and the IFITM3 gene participates in the host antiviral system, studies on

chicken IFITM3 gene are very rare. To investigate the genetic characteristics of the chicken IFITM3 gene, we
performed direct sequencing and alignment in 108 Dekalb White and 72 Ross breeds. We also investigated the

genotype and haplotype frequencies and linkage disequilibrium of the IFITM3 gene polymorphisms and evaluated
whether the non-synonymous SNPs are deleterious. We found significantly different genotype, allele and haplotypes

frequencies between two chicken breeds, Dekalb White and Ross. Furthermore, we compared and analyzed the
promoter structure of the chicken IFITM3 gene with that of several species. We found that birds have a long C-

terminal domain and inverted topology of the IFITM3 protein compared to mammals. We also identified fourteen
genetic polymorphisms in the chicken IFITM3 gene. L100 M and N125H were predicted as ‘probably damaging’ and

L100 M can alter the length of its conserved intracellular loop (CIL). Furthermore, chickens, but not mammals,
contain CpG islands (CGIs) in this promoter region.