Abstract
BackgroundThe comparative analysis of genome sequences emerging for several avian species with the fully sequenced chicken genome enables the genome-wide investigation of selective processes in functionally important chicken genes. In particular, because of pathogenic challenges it is expected that genes involved in the chicken immune system are subject to particularly strong adaptive pressure. Signatures of selection detected by inter-species comparison may then be investigated at the population level in global chicken populations to highlight potentially relevant functional polymorphisms.ResultsComparative evolutionary analysis of chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genes identified interleukin 4 receptor alpha-chain (IL-4Rα), a key cytokine receptor as a candidate with a significant excess of substitutions at nonsynonymous sites, suggestive of adaptive evolution. Resequencing and detailed population genetic analysis of this gene in diverse village chickens from Asia and Africa, commercial broilers, and in outgroup species red jungle fowl (JF), grey JF, Ceylon JF, green JF, grey francolin and bamboo partridge, suggested elevated and balanced diversity across all populations at this gene, acting to preserve different high-frequency alleles at two nonsynonymous sites.ConclusionHaplotype networks indicate that red JF is the primary contributor of diversity at chicken IL-4Rα: the signature of variation observed here may be due to the effects of domestication, admixture and introgression, which produce high diversity. However, this gene is a key cytokine-binding receptor in the immune system, so balancing selection related to the host response to pathogens cannot be excluded.
Highlights
The comparative analysis of genome sequences emerging for several avian species with the fully sequenced chicken genome enables the genome-wide investigation of selective processes in functionally important chicken genes
interleukin-4 receptor alpha-chain gene (IL-4Rα) was selected for further analysis because of its critical function in the immune response, including an implicated role in the anti-viral response [1]
Another chicken immune gene identified by the pairwise comparison method (Progesterone-induced blocking factor) had a human ortholog that binds IL-4Rα
Summary
The comparative analysis of genome sequences emerging for several avian species with the fully sequenced chicken genome enables the genome-wide investigation of selective processes in functionally important chicken genes. The chicken represents one of our most important sources of food protein worldwide but remains a potential threat to human health as a reservoir for diseases and foodborne pathogens Emerging diseases such as avian influenza [1] provide a new impetus to investigate chicken immunity – in particular the relationship between population diversity and disease susceptibility. High allelic variation at this gene appeared to be balanced at two nonsynonymous SNP sites in particular This may enhance immune system variability in response to challenges by pathogens, a consequence of the complex domestication history of the chicken is that introgression, multiple origins and migration are likely to have altered the pattern of diversity at this locus, complicating selection signatures. Knowledge about the nature of selection acting on a gene can illuminate their evolutionary history and can provide insight into the complex relationship between diseases and genes [7]
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