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Contrasting evolution of diversity at two disease-associated chicken genes

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An Erratum to this article was published on 20 March 2009

Abstract

There have been significant evolutionary pressures on the chicken during both its speciation and its subsequent domestication by man. Infectious diseases are expected to have exerted strong selective pressures during these processes. Consequently, it is likely that genes associated with disease susceptibility or resistance have been subject to some form of selection. Two genes involved in the immune response (interferon-γ and interleukin 1-β) were selected for sequencing in diverse chicken populations from Pakistan, Sri Lanka, Bangladesh, Kenya, Senegal, Burkina Faso and Botswana, as well as six outgroup samples (grey, green, red and Ceylon jungle fowl and grey francolin and bamboo partridge). Haplotype frequencies, tests of neutrality, summary statistics, coalescent simulations and phylogenetic analysis by maximum likelihood were used to determine the population genetic characteristics of the genes. Networks indicate that these chicken genes are most closely related to the red jungle fowl. Interferon-γ had lower diversity and considerable coding sequence conservation, which is consistent with its function as a key inflammatory cytokine of the immune response. In contrast, the pleiotropic cytokine interleukin 1-β had higher diversity and showed signals of balancing selection moderated by recombination, yielding high numbers of diverse alleles, possibly reflecting broader functionality and potential roles in more diseases in different environments.

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Acknowledgements

This work is supported by Government of Ireland Department of Agriculture FIRM grant 04/R + D/D/295. We would like to thank the Department of Ornithology and Mammalogy, Californian Academy of Sciences (San Francisco, USA) and Donal Campion, Wallslough Farm (Co. Kilkenny, Ireland) for bird samples and Karsten Hokamp (Trinity College, University of Dublin) for help in implementing LDhat.

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Authors and Affiliations

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

    Tim Downing, Sarah Connell & Daniel G. Bradley

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

    David J. Lynn

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

    Andrew T. Lloyd & Cliona O’Farrelly

  4. Bangladesh Agricultural University, Mymensingh, Bangladesh

    AK Fazlul Haque Bhuiyan

  5. University of Peradeniya, Peradeniya, Sri Lanka

    Pradeepa Silva

  6. PARC, Islamabad, Pakistan

    Arifa N. Naqvi

  7. INERA, Ouagadougou, Burkina Faso

    Rahamame Sanfo

  8. ISRA, Dakar, Senegal

    Racine-Samba Sow

  9. Department of Agricultural Research, Gaborone, Botswana

    Baitsi Podisi

  10. International Livestock Research Institute, Nairobi, Kenya

    Olivier Hanotte

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An erratum to this article can be found at http://dx.doi.org/10.1007/s00251-009-0367-x

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Downing, T., Lynn, D.J., Connell, S. et al. Contrasting evolution of diversity at two disease-associated chicken genes. Immunogenetics 61, 303–314 (2009). https://doi.org/10.1007/s00251-009-0359-x

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