CTLGH poultry genomics program

Permanent URI for this collectionhttps://hdl.handle.net/10568/74305

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    West Africa training on stem cell, assisted reproductive and surrogate technologies for conservation and improvement of indigenous chicken genetic resources
    (Report, 2024-05-30) Tiambo, Christian K.; Muhonja, Christine Kamidi; Dayo, Charles Guiguigbaza-Kossigan
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    Biobanking African poultry breeds for the future
    (Brief, 2021-10-30) Tiambo, Christian K.; McGrew, M.
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    Functional evolution of the colony‐stimulating factor 1 receptor (CSF1R) and its ligands in birds
    (Journal Article, 2020-02-01) Hume, D.A.; Gutowska‐Ding, M.W.; Garcia‐Morales, C.; Kebede, A.; Bamidele, Oladeji; Trujillo, A.V.; Gheyas, Almas A.; Smith, J.
    Macrophage colony-stimulating factor (CSF1 or M-CSF) and interleukin 34 (IL34) are secreted cytokines that control macrophage survival and differentiation. Both act through the CSF1 receptor (CSF1R), a type III transmembrane receptor tyrosine kinase. The functions of CSF1R and both ligands are conserved in birds. We have analyzed protein-coding sequence divergence among avian species. The intracellular tyrosine kinase domain of CSF1R was highly conserved in bird species as in mammals but the extracellular domain of avian CSF1R was more divergent in birds with multiple positively selected amino acids. Based upon crystal structures of the mammalian CSF1/IL34 receptor-ligand interfaces and structure-based alignments, we identified amino acids involved in avian receptor-ligand interactions. The contact amino acids in both CSF1 and CSF1R diverged among avian species. Ligand-binding domain swaps between chicken and zebra finch CSF1 confirmed the function of variants that confer species specificity on the interaction of CSF1 with CSF1R. Based upon genomic sequence analysis, we identified prevalent amino acid changes in the extracellular domain of CSF1R even within the chicken species that distinguished commercial broilers and layers and tropically adapted breeds. The rapid evolution in the extracellular domain of avian CSF1R suggests that at least in birds this ligand-receptor interaction is subjected to pathogen selection. We discuss this finding in the context of expression of CSF1R in antigen-sampling and antigen-presenting cells.
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    Whole-genome resequencing of red junglefowl and indigenous village chicken reveal new insights on the genome dynamics of the species
    (Journal Article, 2018) Lawal, R.A.; Al-Atiyat, R.M.; Aljumaah, R.S.; Silva, P.; Mwacharo, Joram M.; Hanotte, Olivier H.
    The red junglefowl Gallus gallus is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic control for production traits have been well studied in commercial chicken, but the selection pressures underlying unique adaptation and production to local environments remain largely unknown in indigenous village chicken. Likewise, the genome regions under positive selection in the wild red junglefowl remain untapped. Here, using the pool heterozygosity approach, we analysed indigenous village chicken populations from Ethiopia, Saudi Arabia, and Sri Lanka, alongside six red junglefowl, for signatures of positive selection across the autosomes. Two red junglefowl candidate selected regions were shared with all domestic chicken populations. Four candidates sweep regions, unique to and shared among all indigenous domestic chicken, were detected. Only one region includes annotated genes (TSHR and GTF2A1). Candidate regions that were unique to each domestic chicken population with functions relating to adaptation to temperature gradient, production, reproduction and immunity were identified. Our results provide new insights on the consequence of the selection pressures that followed domestication on the genome landscape of the domestic village chicken.
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