Genome-wide mapping and identification of genes controlling resistance to Marek's Disease virus infection in commercial layer chickens

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

Marek's Disease (MD) is caused by a highly contagious virus (MDV), which is a continuing threat to our global poultry industry and food security with estimated losses of £1-2 billion per year. These losses are associated with the cost of the disease, due to increased mortality, escalating vaccination costs and reduced egg production. It is therefore a disease that has an impact on our economy and ability to compete internationally, with additional concerns for animal health and welfare, and our global food security. Although it has been controlled by vaccination for over 40 years, there is growing evidence from researchers that intensive use of vaccines is driving the virus to have an increasing ability to kill poultry, with more aggressive strains of the disease continuing to emerge each year.

An alternative means to control this disease is being sought through breeding birds with enhanced resistance to MDV. Such differences were first reported nearly 80 years ago. Subsequently, genes associated with the major histocompatibility complex (MHC), which plays an important role in the immune system, were shown to contribute towards resistance to MDV. Despite this, other genes also have a strong influence on MDV resistance. This has been determined most effectively from studies using inbred strains of chickens that have identical MHC but still show differences in their susceptibility towards MDV.
Many chromosomal regions that control MDV resistance have been defined (quantitative trait loci, or QTL) but very few genes have been verified as controlling the host response towards this disease, which is typical for most complex traits. Those which have been identified include growth hormone (GH1), the cytokine SCYC1 and the cell surface marker on lymphocytes LY6E. Identifying genes involved in resistance (or susceptibility) to MDV and resolving their role is crucial to understanding this disease and why it appears to becoming more fatal. This knowledge is important; providng the means to control and reduce this threat to the poultry industry.

This proposal is extremely timely in that we now have at our disposal many new research tools which may enable us to identify genes involved in resistance to MD infection. These include QTL data, access to MDV challenge facilities, genomic sequences of chicken lines, a large QTL high resolution mapping population (now in its 6th generation) based on parents differing in their resistance to MDV and a panel of 600K SNPs (single nucleotide polymorphisms - genetic markers) which can be used together to fine map Marek's Disease QTL to high resolution to genomic regions containing around 25 genes. This, in conjunction with high throughput sequencing and bioinformatics approaches, will allow us to not only predict candidate genes for MD resistance but also possible causative mutations within these genes.

We also have available to us all the MDV proteins cloned into suitable vectors for testing in 'yeast-2-hybrid' experiments for direct protein/protein binding between viral and host proteins. In this way we will be able to identify genes which bind directly with viral proteins and then go on to test whether mutations within these genes alter any binding interactions.
In this proposal we aim to determine the chromosomal regions that play a role in MD resistance in commercial egg-layers, identify genetic variation within candidate genes, explore direct protein binding interactions between host and viral proteins, and examine the functional consequences of genetic variation in these genes.

The outcome of this project will be the identification and characterization of valuable genetic markers in commercial egg-layer lines for use in selective breeding programs within the poultry industry, which would result in large economic and health benefits. This comes at a time when there are renewed pressures on the poultry industry as the world population expands and concerns over food security increase.

Technical Summary

We will use a full-sib intercross line created for fine mapping QTL for MD. 1200 F6 animals, selected for high or low resistance from 2400 tested will be genotyped with 600K SNPs, expected to map QTL to regions of about 5cM. Genome sequences of 10 founder parents will be determined and used to impute the sequence of QTL containing regions (QTLR) in F6 animals.

We will annotate QTLR for genes based on Ensembl and RNAseq resources. Sequences will be examined for genetic variants, such as SNPs, indels, simple sequence repeats and CNV. Functional effects of variants on genes and other constrained sequences will be predicted using bioinformatics tools.

We will annotate variants that affect regulation of genes as shown by allele-specific-expression, based on unequal number of RNAseq reads mapped to alternate alleles. Gene regulation will be based on three comparisons: (i) macrophage LPS/control, (ii) macrophage MDV/control or (iii) spleen MDV/control. SNPs with a significant effect for any of these responses will be selected for further investigation.

Candidate host proteins will be tested for binding to MDV proteins via Y2H screens against a library of 100 MDV genes sub-cloned into pGADT7, and verified by co-immunoprecipitation in chicken splenocytes. Alternate alleles of host proteins may show altered binding to MDV proteins these will be tested by semi-quantitative co-immunoprecipitation.

Candidate functional SNPs for MD resistance will be tested for their utility in 8 pure-bred lines that serve as parental lines for Hy-Line layer crosses. This will be based on large numbers of males progeny tested for MD resistance within each line for the past 15 years. Tests for SNP-trait association will be in two stages. Stage-1 based on pooling resistant and susceptible individuals within each line and Stage-2 based on selective individual genotyping of SNPs that achieve suggestive statistical significance in Stage-1.

Planned Impact

The UK poultry industry faces numerous challenges in order to remain sustainable. These include the imminent move to more extensive rearing systems; the withdrawal of prophylactic and many therapeutic antibiotics, and other drugs such as anti-coccidials; resistance and residue problems with anti-helminthics. These challenges will all have an impact on poultry health and the potential to impact on human health. For example, with an increased incidence of zoonotic pathogens in chickens, there is the potential to lead to an increase in these diseases in human. It is important that poultry breeders are able to select for genetic improvement in performance when birds are reared in such environments. New and effective disease control requires detailed understanding of host-pathogen interactions.

Marek's Disease (MD) is caused by a highly contagious oncogenic alpha-herpesvirus which is a continuing threat to the world's poultry industry, with estimated losses of £1-2 billion per annum. Although it has been controlled by vaccination for over 40 years, there is growing evidence that intensive use of vaccines is driving the virus to increasing virulence and new, more virulent strains continue to emerge. An alternative means to control MD would be through the selection of birds with enhanced genetic resistance to the virus (MDV). Several potential MD resistance QTLs have been identified, but relatively few genes have been associated with the disease.

This project directly addresses this problem, and should result in a wealth of knowledge regarding pathways, genes and genetic mutations involved in MD disease resistance. It should also be possible to patent these candidates for use as selective markers in breeding programmes. Beneficiaries of this research include academics interested in the genetics of disease resistance, host-pathogen interactions and the innate immune system. Results will be published, when appropriate, in peer-reviewed scientific journals and presented atinternational conferences.

Results of this research will have potentially far-reaching social and economic consequences. A reduction in the incidence and losses caused by MD through selective breeding would have an important economic impact on the poultry industry in the UK and around the world. Selection could be done directly on genes, thus improving selection accuracy and decreasing the need for costly challenge studies and unnecessary loss of birds. Improvement in disease resistance at the primary breeder level will have a positive impact on the well-being of hundreds of millions of birds at the commercial production level. The health and well-being of farmed chickens would be greatly improved and a major source of human food production would be further secured.

Established contacts with companies such as Pfizer Animal Health, Aviagen and Hy-Line will ease this transfer of knowledge from the academic environment to industry. Markers will have been detected and tested in existing commercial lines and would therefore be ready for utility by poultry breeders. Effective uptake of the outcomes of our research is facilitated by close links with Biosciences KTN, who identified disease resistance and animal health as the top priorities for UK breeding industries. This work has the potential to impact on the sustainability of the poultry industry in the UK, and thus to inform DEFRA policy.

In scientific terms this project falls within the remit of the BBSRC 'Animal systems, health and wellbeing' Research Committee and matches the BBSRC scientific priority of 'Food Security' in terms of 'Animal Health' and 'Livestock Production'.
 
Description The aim was to detect genes and genetic markers for Marek's Disease Virus resistance in chickens. Over 100 loci were defined and 34 key candidate regions identified. In these regions we have found genes/DNA variants which show significant association with resistance for Marek's Disease.
Outputs:
-Genome sequence of birds susceptible and resistant to MDV
-Catalogue of 360k genetic variants between these birds
-Genotypes of 1200 F6 commercial birds selected for susceptibility/resistance
- A profile of the host response to MDV infection
-Genes differentially expressed between susceptible and resistant birds in response to viral challenge
-Strong genetic association between candidate genes/SNPs and MDV survival
-Identification of QTL regions, genes and variants which are significantly associated with MDV resistance and could be established as targets in selective breeding programmes
-Collaboration between industry (Hy-line) and academia (Roslin and HUJ)
-Publications in preparation
Exploitation Route Candidate genes can be functionally validated by knockout experiments etc. Genetic markers can be used to select for Marek's disease resistance in chickens.
Sectors Agriculture, Food and Drink

 
Description yes by academics and industry to perform genome wide selection of chicken traits
First Year Of Impact 2013
Sector Agriculture, Food and Drink
Impact Types Economic

 
Title Characterization of 360k SNPs between M and F Hy-line birds (MDV) 
Description Whole genome sequencing of birds susceptible or resistant to Marek's Disease Virus (MDV) allowed us to look for variants between phenotypically distinct birds. We characterized 360k SNPs between resistant male parents and susceptible female parents 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Identification of variants associated with resistance to MDV 
 
Title MDV challenge expt 
Description Spleen transcriptomes of birds susceptible and resistant to Marek's Disease Virus (MDV) 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Identification of genes differentially expressed between birds which are either susceptible or resistant to Marek's Disease Virus (MDV) 
 
Title WGS of founder parents_MDV_Hy-line 
Description Whole genome sequence of 10 Hy-line founder parental birds (males - resistant; females-susceptible) 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Identification of QTL for resistance to MDV. 
 
Description Hebrew University of Jerusalem 
Organisation Hebrew University of Jerusalem
Country Israel 
Sector Academic/University 
PI Contribution GWAS analysis carried out by Moshe Soller and Ehud Lipkin at the Hebrew University of Jerusalem resulted in the identification of many QTL regions (QTLR) associated with MDV resistance. Jacqueline Smith (Roslin) then used these data to identify candidate genes for MDV resistance. Jacqueline was also able to use WGS data to analyse SNPs in QTLR and identify candidate variants in genes of interest. Our colleagues at HUJ were then able to carry out association analysis using genotyping data from 10,000 Hyline birds which were genotyped for SNPs in these candidate regions
Collaborator Contribution Moshe Soller and Ehud Lipkin from the Hebrew University of Jerusalem carried out genetic analysis of chicken whole genome sequence data from Hy-line commercial birds to identify QTL regions involved in Marek's disease resistance. They also analysed genotyping data from candidate gene regions and identified significant associations with particular genes and variants. Genotyping was carried out across 10,000 Hy-line individuals.
Impact Identification of QTL regions, genes and variants associated with resistance to Marek's disease
Start Year 2013
 
Description International Avian RNA-Seq Consortium 
Organisation Agrocampus Ouest
Country France 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Arizona State University
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Centre for Genomic Regulation (CRG)
Country Spain 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation French National Institute of Agricultural Research
Department INRA Rennes Centre
Country France 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation French National Institute of Agricultural Research
Department INRA Toulouse
Country France 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation French National Institute of Agricultural Research
Country France 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Harvard University
Department Harvard Medical School
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Iowa State University
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Kenya Agriculture & Livestock Research Organization (KALRO)
Country Kenya 
Sector Private 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Medical Research Council (MRC)
Department Medical Research Council (MRC) Centre Cambridge
Country United Kingdom 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation National Institute of Allergy and Infectious Diseases (NIAID)
Country United States 
Sector Public 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation National Institute of Environmental Health Sciences
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Oregon State University
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Swedish University of Agricultural Sciences
Country Sweden 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of Arkansas
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of California, Davis
Department UC Davis Genome Cente
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of Delaware
Country United States 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of East Anglia
Country United Kingdom 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of Leipzig
Country Germany 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description International Avian RNA-Seq Consortium 
Organisation Weizmann Institute of Science
Country Israel 
Sector Academic/University 
PI Contribution I organised the 6th International chick meeting, Edinburgh (2011) and also formed at that event the International Avian RNA-Seq Consortium. The purpose was to collaborate with national and international labs to pool RNA-seq data for the chicken (and other avian genomes). This data would provide a rich source of data for gene annotation of the chicken genome. This was used subsequently to annotate the chicken genes by the ENSEMBL gene annotation team, as part of our BBSRC funded work. We provided the organisation, advice for submission of data, provided early storage of data, and we provided all our data (20+ libraries).
Collaborator Contribution Many labs joined (21+) and one output was a joint publication and yearly updates to chicken genome.
Impact Jacqueline Smith, Bronwen L. Aken, Perry J. Blackshear, Shane C. Burgess, Amanda M. Cooksey, Dirk-Jan de Konig, Ian C. Dunn, Mario Fasold, Laure Frésard, David P. Froman, Valerie Garceau, Olivier Hanotte, Julien Häsler, David A. Hume, Pete Kaiser, Darek Kedra, Stephen J. Kemp, Richard Kuo, Sandrine Lagarrigue, Susan J. Lamont, Fiona M. McCarthy, Heather A. McCormack, Stefan A. Muljo, Andrea Münsterberg, Cedric Notredame, Harry Noyes, Andrew J. Oler, Sheila C. Ommeh, Helio Pais, Frédérique Pitel, Douglas D. Rhoads, Carl J. Schmidt, Matt Schwartz, Steve M. Searle, Michael A. Skinner, Peter F. Stadler, Cliff J. Tabin, Igor Ulitsky, Ying Wang, Huaijun Zhou, David W. Burt. (2015). In: "Chicken Genes and Chromosomes, Third Report 2015 (Editors: Schmid M., Smith J., Burt D.W.). The Avian RNASeq Consortium: a community effort to annotate the chicken genome. Cytogenetic and Genome Research 145, 83-88; DOI: 10.1159/isbn.978-3-318-05569-6.
Start Year 2011
 
Description Janet - Hy-line 
Organisation Hy-line International
Country United States 
Sector Private 
PI Contribution We carried out whole genome sequence analysis and RNAseq analysis on the samples provided by Hy-line. This enabled us to identify QTL, genes and variants associated with MDV resistance.
Collaborator Contribution Hy-line supplied all the chicken samples which made this project possible: -DNA from 10 founder parents (males resistant to MDV; females susceptible) -DNA from 1200 F6 commercial birds, with full phenotypic trait information relating to MDV survival -Spleen tissue from MDV challenged birds and control birds -Genotyping of DNA from 10,000 sire pedigreed Hy-line birds
Impact Identification of candidate genes for resistance to Marek's Disease Virus (MDV)
Start Year 2013
 
Description Animal and Plant Health in the UK 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact working group at Animal and Plant Health in the UK (2014): an assessment of future national capability, emerging technologies, 14 Feb 2014, BIS Conference Centre, London, UK
Year(s) Of Engagement Activity 2014
 
Description Avian genome evolution and the origins of species diversity. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited lecture: Avian genome evolution and the origins of species diversity. In "Molecular evolution of avian species", SMBE2016, Queensland's Gold Coast, Australia, 3-7 July, 2016.
Year(s) Of Engagement Activity 2016
 
Description CSH 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Keynote lecture: 'Chicken genome - 10 years on'. Presented at: Avian Model Systems - the 8th International Meeting, Cold Spring Harbour, USA, 4-8th March 2014.
Year(s) Of Engagement Activity 2016
 
Description From Sequences to Consequences 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact talk and meet industry at "21st Century Genomics for Animal Breeding and Animal Health. In "From Sequences to Consequences: What The Roslin Institute can do for you in the livestock sector", Industry Day. The Roslin Institute Building, Edinburgh, 18th March 2016."
Year(s) Of Engagement Activity 2016
 
Description ISAG talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Talk title: Mapping QTLs affecting Marek's disease by selective DNA pooling in eight lines across 15 generations
Year(s) Of Engagement Activity 2017
 
Description New tools and prospects for chicken genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at Genetics Society of Australia (GSA), July 2015, University of Adelaide, Australia
Year(s) Of Engagement Activity 2015
 
Description Past, Present and Future of Genomics in Poultry Breeding. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk: Past, Present and Future of Genomics in Poultry Breeding. 25th World's Poultry Congress, Beijing, 5-9 September, 2016.
Year(s) Of Engagement Activity 2016
 
Description Poultry beyond 2020 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Poultry Genome (2014): Implications for Immunity, Poultry Productivity and Health, Poultry beyond 2020, 13-17th April, Queenstown, New Zealand.
Year(s) Of Engagement Activity 2014
 
Description The Chicken and other Avian Genomes: new insights and opportunities for all from high throughput sequencing and bioinformatics. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk: the Chicken and other Avian Genomes: new insights and opportunities for all from high throughput sequencing and bioinformatics. In "Avian Model Systems 9: a new integrative platform", Taipei, Taiwan, 38 March to 3 April, 2016.
Year(s) Of Engagement Activity 2016
 
Description WGALP talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Talk entitled 'QTLs mapped by selective DNA pooling explain substantial proportion of phenotypic and genetic variation in MD mortality in chicken layer lines' presented at WGALP in Auckland, Feb 2018
Year(s) Of Engagement Activity 2018
 
Description • UK-Brazil Animal Health Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact UK-Brazil Animal Health Workshop, Edinburgh University UK, 3-5 Dec, 2014
Year(s) Of Engagement Activity 2016