title: Contrasting evolution of diversity at two disease-associated chicken genes.
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-gamma and interleukin 1-beta) 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-gamma 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-beta 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.
authors.affiliation: Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland.
authors.forename: Tim
authors.initials: T
authors.lastname: Downing
authors.forename: David J
authors.initials: DJ
authors.lastname: Lynn
authors.forename: Sarah
authors.initials: S
authors.lastname: Connell
authors.forename: Andrew T
authors.initials: AT
authors.lastname: Lloyd
authors.forename: A K Fazlul Haque
authors.initials: AK
authors.lastname: Bhuiyan
authors.forename: Pradeepa
authors.initials: P
authors.lastname: Silva
authors.forename: Arifa N
authors.initials: AN
authors.lastname: Naqvi
authors.forename: Rahamame
authors.initials: R
authors.lastname: Sanfo
authors.forename: Racine-Samba
authors.initials: RS
authors.lastname: Sow
authors.forename: Baitsi
authors.initials: B
authors.lastname: Podisi
authors.forename: Cliona
authors.initials: C
authors.lastname: O'Farrelly
authors.forename: Olivier
authors.initials: O
authors.lastname: Hanotte
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Bradley
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics* / Q000276:immunology*; D014644:Genetic Variation; D007371:Interferon-gamma / Q000235:genetics* / Q000276:immunology; D053583:Interleukin-1beta / Q000235:genetics* / Q000276:immunology; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic
chemical_list: D053583:Interleukin-1beta; D007371:Interferon-gamma