Research article

Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus

Tim Downing¹ , David J Lynn² , Sarah Connell¹ , Andrew T Lloyd³ , A K Bhuiyan⁴ , Pradeepa Silva⁵ , A N Naqvi⁶ , Rahamame Sanfo⁷ , Racine-Samba Sow⁸ , Baitsi Podisi⁹ , Olivier Hanotte^10,11 , Cliona O'Farrelly³ and Daniel G Bradley¹

¹Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland

²Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada

³School of Biochemistry and Immunology, Trinity College, University of Dublin, Dublin, Ireland

⁴Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh

⁵Department of Animal Science, University of Peradeniya, Peradeniya, Sri Lanka

⁶PARC, Animal Sciences Division, Islamabad, Pakistan

⁷INERA, Department of Agriculture and Environment, Ouagadougou, Burkina Faso

⁸Institut Sénégalais de Recherches Agricoles, Dakar, Senegal

⁹Department of Agricultural Research, CTA, Gaborone, Botswana

¹⁰International Livestock Research Institute (ILRI), PO Box 30709, Nairobi 00100, Kenya

¹¹School of Biology, University of Nottingham, Nottingham, NG7 2RD, UK

author email corresponding author email

BMC Evolutionary Biology 2009, 9:136doi:10.1186/1471-2148-9-136

Published:	15 June 2009

Abstract

Background

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. 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.

Results

Comparative 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.

Conclusion

Haplotype 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.