Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Steven R  Fiddaman; Christophe Klopp; Mathieu Charles; Philippe Bardou; Ophélie Lebrasseur; Martijn F. L. Derks; Jens  Schauer; Christian  Reimer; Johannes  Geibel; Almas Gheyas; Adrian L. Smith; Robert  Schnabel; Maria Luisa Martin  Cerezo; Masahide  Nishibori; Cyrill John P.  Godinez; John King N.  Layos; James M.  Alfieri; Heath Blackmon; Giridhar N.  Athrey; Greger Larson; Ismael  Ng’ang’a; William  Muir; Margaret  Lange; Dominic Wright; Hans H Cheng; Henner Simianer; Steffen Weigend; Wesley Warren; Richard P. M. A. Crooijmans; Olivier Hanotte; Jacqueline Smith; Michele Tixier-Boichard; Laurent Af Frantz

doi:10.1159/000529376

Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Steven R Fiddaman^*, Christophe Klopp, Mathieu Charles, Philippe Bardou, Ophélie Lebrasseur, Martijn F. L. Derks, Jens Schauer, Christian Reimer, Johannes Geibel, Almas Gheyas, Adrian L. Smith, Robert Schnabel, Maria Luisa Martin Cerezo, Masahide Nishibori, Cyrill John P. Godinez, John King N. Layos, James M. Alfieri, Heath Blackmon, Giridhar N. Athrey, Greger LarsonIsmael Ng’ang’a, William Muir, Margaret Lange, Dominic Wright, Hans H Cheng, Henner Simianer, Steffen Weigend, Wesley Warren, Richard P. M. A. Crooijmans, Olivier Hanotte, Jacqueline Smith, Michele Tixier-Boichard, Laurent Af Frantz^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	405-528
Journal	Cytogenetic and Genome Research
Volume	162
Issue number	8-9
Early online date	30 Jan 2023
DOIs	https://doi.org/10.1159/000529376
Publication status	Published - 1 Jul 2023

Access to Document

10.1159/000529376

FiddamanAccepted author manuscript, 747 KBLicence: Creative Commons: Attribution (CC-BY)

1 Active

Identifying the genomic basis of complex traits in farmed animals
Headon, D. (Principal Investigator)
1/04/23 → 31/03/28
Project: Research

1 Review article

Fourth Report on Chicken Genes and Chromosomes 2022
Smith, J., Alfieri, J. M., Anthony, N., Arensburger, P., Athrey, G. N., Balacco, J., Balic, A., Bardou, P., Barela, P., Bigot, Y., Blackmon, H., Borodin, P. M., Carroll, R., Casono, M. C., Charles, M., Cheng, H., Chiodi, M., Cigan, L., Coghill, L. M. & Crooijmans, R. & 104 others, Das, N., Davey, S., Davidian, A., Degalez, F., Dekkers, J. M., Derks, M., Diack, A. B., Djikeng, A., Drechsler, Y., Dyomin, A., Fedrigo, O., Fiddaman, S. R., Formenti, G., Frantz, L. A. F., Fulton, J. E., Gaginskaya, E., Galkina, S., Gallardo, R. A., Geibel, J., Gheyas, A., Godinez, C. J. P., Goodell, A., Graves, J. A. M., Griffin, D. K., Haase, B., Han, J.-L., Hanotte, O., Henderson, L. J., Hou, Z.-C., Howe, K., Huynh, L., Ilatsia, E., Jarvis, E., Johnson, S. M., Kaufman, J., Kelly, T., Kemp, S., Kern, C., Keroack, J. H., Klopp, C., Lagarrigue, S., Lamont, S. J., Lange, M., Lanke, A., Larkin, D. M., Larson, G., Layos, J. K. N., Lebrasseur, O., Malinovskaya, L. P., Martin, R. J., Martin Cerezo, M. L., Mason, A. S., McCarthy, F. M., McGrew, M. J., Mountcastle, J., Muhonja, C. K., Muir, W., Muret, K., Murphy, T., Ng'ang'a, I., Nishibori, M., O'Connor, R. E., Ogugo, M., Okimoto, R., Ouko, O., Patel, H. R., Perini, F., Pigozzi, M. I., Potter, K. C., Price, P. D., Reimer, C., Rice, E. S., Rocos, N., Rogers, T. F., Saelao, P., Schauer, J., Schnabel, R., Schneider, V., Simianer, H., Smith, A., Stevens, M. P., Stiers, K., Tiambo, C. K., Tixier-Boichard, M., Torgasheva, A. A., Tracey, A., Tregaskes, C. A., Vervelde, L., Wang, Y., Warren, W. C., Waters, P. D., Webb, D., Weigend, S., Wolc, A., Wright, A. E., Wright, D., Wu, Z., Yamagata, M., Yang, C., Yin, Z.-T., Young, M. C., Zhang, G., Zhao, B. & Zhou, H., 1 Jul 2023, In: Cytogenetic and Genome Research. 162, 8-9, p. 405-528
Research output: Contribution to journal › Review article › peer-review

Open Access
File

Cite this

Fiddaman, S. R., Klopp, C., Charles, M., Bardou, P., Lebrasseur, O., Derks, M. F. L., Schauer, J., Reimer, C., Geibel, J., Gheyas, A., Smith, A. L., Schnabel, R., Cerezo, M. L. M., Nishibori, M., Godinez, C. J. P., Layos, J. K. N., Alfieri, J. M., Blackmon, H., Athrey, G. N., ... Frantz, L. A. (2023). Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens. Cytogenetic and Genome Research, 162(8-9), 405-528. https://doi.org/10.1159/000529376

@article{7320d340f4f145d3a4c43a7d5f25e0b0,

title = "Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens",

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. ",

author = "Fiddaman, {Steven R} and Christophe Klopp and Mathieu Charles and Philippe Bardou and Oph{\'e}lie Lebrasseur and Derks, {Martijn F. L.} and Jens Schauer and Christian Reimer and Johannes Geibel and Almas Gheyas and Smith, {Adrian L.} and Robert Schnabel and Cerezo, {Maria Luisa Martin} and Masahide Nishibori and Godinez, {Cyrill John P.} and Layos, {John King N.} and Alfieri, {James M.} and Heath Blackmon and Athrey, {Giridhar N.} and Greger Larson and Ismael Ng{\textquoteright}ang{\textquoteright}a and William Muir and Margaret Lange and Dominic Wright and Cheng, {Hans H} and Henner Simianer and Steffen Weigend and Wesley Warren and Crooijmans, {Richard P. M. A.} and Olivier Hanotte and Jacqueline Smith and Michele Tixier-Boichard and Frantz, {Laurent Af}",

year = "2023",

month = jul,

day = "1",

doi = "10.1159/000529376",

language = "English",

volume = "162",

pages = "405--528",

journal = "Cytogenetic and Genome Research",

issn = "1424-8581",

publisher = "S. Karger AG",

number = "8-9",

}

Fiddaman, SR, Klopp, C, Charles, M, Bardou, P, Lebrasseur, O, Derks, MFL, Schauer, J, Reimer, C, Geibel, J, Gheyas, A, Smith, AL, Schnabel, R, Cerezo, MLM, Nishibori, M, Godinez, CJP, Layos, JKN, Alfieri, JM, Blackmon, H, Athrey, GN, Larson, G, Ng’ang’a, I, Muir, W, Lange, M, Wright, D, Cheng, HH, Simianer, H, Weigend, S, Warren, W, Crooijmans, RPMA, Hanotte, O, Smith, J, Tixier-Boichard, M & Frantz, LA 2023, 'Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens', Cytogenetic and Genome Research, vol. 162, no. 8-9, pp. 405-528. https://doi.org/10.1159/000529376

TY - JOUR

T1 - Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

AU - Fiddaman, Steven R

AU - Klopp, Christophe

AU - Charles, Mathieu

AU - Bardou, Philippe

AU - Lebrasseur, Ophélie

AU - Derks, Martijn F. L.

AU - Schauer, Jens

AU - Reimer, Christian

AU - Geibel, Johannes

AU - Gheyas, Almas

AU - Smith, Adrian L.

AU - Schnabel, Robert

AU - Cerezo, Maria Luisa Martin

AU - Nishibori, Masahide

AU - Godinez, Cyrill John P.

AU - Layos, John King N.

AU - Alfieri, James M.

AU - Blackmon, Heath

AU - Athrey, Giridhar N.

AU - Larson, Greger

AU - Ng’ang’a, Ismael

AU - Muir, William

AU - Lange, Margaret

AU - Wright, Dominic

AU - Cheng, Hans H

AU - Simianer, Henner

AU - Weigend, Steffen

AU - Warren, Wesley

AU - Crooijmans, Richard P. M. A.

AU - Hanotte, Olivier

AU - Smith, Jacqueline

AU - Tixier-Boichard, Michele

AU - Frantz, Laurent Af

PY - 2023/7/1

Y1 - 2023/7/1

N2 - 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.

AB - 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.

U2 - 10.1159/000529376

DO - 10.1159/000529376

M3 - Article

SN - 1424-8581

VL - 162

SP - 405

EP - 528

JO - Cytogenetic and Genome Research

JF - Cytogenetic and Genome Research

IS - 8-9

ER -

Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Abstract

Access to Document

Fingerprint

Projects

Identifying the genomic basis of complex traits in farmed animals

Research output

Fourth Report on Chicken Genes and Chromosomes 2022

Cite this