Abstract
BackgroundThe interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Their biological activity is well documented in several animal species, but their genetic variation and biological mechanism is less well understood, particularly in avian species.ResultsHere we report the complete sequence of the domestic chicken Gallus gallus IFITM locus from a wide variety of chicken breeds to examine the detailed pattern of genetic variation of the locus on chromosome 5, including the flanking genes ATHL1 and B4GALNT4. We have generated chIFITM sequences from commercial breeds (supermarket-derived chicken breasts), indigenous chickens from Nigeria (Nsukka) and Ethiopia, European breeds and inbred chicken lines from the Pirbright Institute, totalling of 206 chickens. Through mapping of genetic variants to the latest chIFITM consensus sequence our data reveal that the chIFITM locus does not show structural variation in the locus across the populations analysed, despite spanning diverse breeds from different geographic locations. However, single nucleotide variants (SNVs) in functionally important regions of the proteins within certain groups of chickens were detected, in particular the European breeds and indigenous birds from Ethiopia and Nigeria. In addition, we also found that two out of four SNVs located in the chIFITM1 (Ser36 and Arg77) and chIFITM3 (Val103) proteins were simultaneously under positive selection.ConclusionsTogether these data suggest that IFITM genetic variation may contribute to the capacities of different chicken populations to resist virus infection.
Highlights
The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity
Elucidation of the chicken IFITM (chIFITM) locus genetic variation can be achieved by comparing different chicken inbred lines that are being used for laboratory screening and kept under SPF conditions, commercial chickens and poultry populations kept in geographically-isolated villages in different areas of the world
The total number of variants were visualized on Integrative genome Visualization (IGV) by uploading the 40 kb consensus reference sequence we have previously characterized and the Variant call file (VCF) files generated by Genome Analysis Toolkit (GATK), for each set of the chicken groups
Summary
The interferon-induced transmembrane (IFITM) protein family comprises a class of restriction factors widely characterised in humans for their potent antiviral activity. Elucidation of the chIFITM locus genetic variation can be achieved by comparing different chicken inbred lines that are being used for laboratory screening and kept under SPF (specific-pathogen-free) conditions, commercial chickens and poultry populations kept in geographically-isolated villages in different areas of the world. These do represent distinct populations of chickens and reflect different indigenous pathogen exposures and husbandry considerations such as infection control measures and human selection for productivity and/or likeability traits. We hypothesize that genetic variation across diverse groups of birds will reveal genetic variants with enhanced adaptive antiviral functions
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