Chicken genomic diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Authors: FIDDAMAN, STEVEN - University Of Oxford; KLOPP, CHRISTOPHE - Inrae; CHARLES, MATHIEU - Université Paris-Saclay; BARDOU, PHILIPPE - University Of Toulouse; LEBRASSEUR, OPHELIE - National Institute Of Anthropology And Latin American Thought; DERKS, MARTIJN - Wageningen University And Research Center; SCHAUER, JENS - Goettingen University; REIMER, CHRISTIAN - Wageningen University And Research Center; GEIBEL, JOHANNES - Goettingen University; GHEYAS, ALMAS - Roslin Institute; SMITH, ADRIAN - Oxford University; SCHNABEL, ROBERT - University Of Missouri; MARTIN CEREZO, MARIA LUISA - Linköping University; NISHIBORI, MASAHIDE - University Of Hiroshima; GODINEZ, CYRILL JOHN - Visayas State University; LAYOS, JOHN KING - Capiz State University; LARSON, GREGER - University Of Oxford; NG'ANG'A, ISMAEL - Queen Mary University Of London; MUIR, WILLIAM - Purdue University; LANGE, MARGARET - University Of Missouri; WRIGHT, DOMINIC - Linköping University; SIMIANER, HENNER - Goettingen University; Cheng, Hans; WEIGEND, STEFFEN - Goettingen University; WARREN, WESLEY - University Of Missouri; CROOIJMANS, RICHARD - Wageningen University And Research Center; HANOTTE, OLIVIER - University Of Nottingham; SMITH, JACQUELINE - Roslin Institute; TIXIER-BOICHARD, MICHELE - Université Paris-Saclay; FRANTZ, LAURENT - Queen Mary University Of London

Submitted to: Cytogenetics and Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/24/2023
Publication Date: 6/26/2023
Citation: Fiddaman, S., Klopp, C., Charles, M., Bardou, P., Lebrasseur, O., Derks, M., Schauer, J., Reimer, C., Geibel, J., Gheyas, A., Smith, A., Schnabel, R., Martin Cerezo, M., Nishibori, M., Godinez, C.P., Layos, J.N., Larson, G., Ng'Ang'A, I., Muir, W., Lange, M., Wright, D., Simianer, H., Cheng, H.H., Weigend, S., Warren, W., Crooijmans, R., Hanotte, O., Smith, J., Tixier-Boichard, M., Frantz, L. 2023. Chicken genomic diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens. Cytogenetics and Genome Research. https://doi.org/10.1159/000529376.
DOI: https://doi.org/10.1159/000529376

Interpretive Summary: With major advances in DNA sequencing, it is technically and economically feasible to determine the genome sequence of almost any species including chicken. To harness the power of the rapidly increasing number of sequenced chicken genomes, a worldwide consortium has been formed to address a number of fundamental and applied questions especially on connecting genotypic variation to phenotypic variation. The establishment of this consortium and the open access to the data and results greatly enhances the ability of both academic and applied scientists to understand the genetic basis of chicken biology, especially those controlling complex traits such as disease resistance.

Technical Abstract: On October 25-26, 2019, a satellite meeting devoted to the preparation of a Chicken Genome Diversity Consortium was organised after the 11th European Symposium of Poultry Genetics in Prague. Researchers involved in chicken genomics from Europe, Africa and China, discussed the objectives of such a consortium with some presenting their data. However, the technical aspects of how to share and jointly analyse the data were not finalized, nor was the funding model for the cost of data storage and computation. In 2021, an opportunity arose with the call for projects of the SuperMUC computing cluster of the Leibniz-Rechenzentrum in Germany. A new consortium of scientists re-launched the discussion to establish a project with the aim to explore how the high-throughput genomics age can be harnessed to answer evolutionary questions surrounding the chicken. The FARMGENOMIC project (23826) was accepted for funding in autumn 2021, gathering around 20 members from 10 institutions in Europe, North America and Africa. This newly-formed Chicken Genomic Diversity consortium brings together members from a variety of disciplines, including genomics, palaeogenetics, animal breeding, immunology, organismal biology, evolutionary biology, and archaeology. Central to the consortium are the concepts of inclusivity and openness – all data are to be made available to all members of the consortium, and later distributed to the wider community, and collaborations between groups are fostered and actively encouraged. It is hoped this state-of-the-art resource, curated in-house by bioinformaticians, will enable the community to answer previously intractable questions in chicken evolution.