ADVANCED TECHNOLOGIES FOR THE GENETIC IMPROVEMENT OF POULTRY (WAS NC-168)

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: TERMINATED
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1001693
• Project No.: ARZT-1370180-R50-115
• Multistate No.: NC-_old1170
• Project Start Date: Oct 22, 2013
• Project End Date: Sep 30, 2018

Project Director
McCarthy, FI, MA.

Recipient Organization
UNIVERSITY OF ARIZONA
888 N EUCLID AVE
TUCSON,AZ 85719-4824

Performing Department
Animal & Comparative Biomedical Sciences

Non Technical Summary
For the first time in history, biologists have access to technologies that enable them to rapidly generate enormous amounts of data about the genomes of our agricultural species. However, researchers using these technologies now face a major bottleneck in deriving knowledge from data to use it for improving agricultural productivity. Our goal is to enable researchers to accelerate knowledge delivery from research investments by giving them the tools to avoid the current bottleneck. We will do this by linking existing information about how genes work to biological data; developing novel and improved methods for predicting links between our existing knowledge and biological data; and by providing new tools for viewing how biological data relates to different species. The tools, training and resources that we develop are easily extended to other species. Not only will we provide data and tools but we also provide integrated, practical training for the next generation of US researchers. This training ensures that researchers are able to use the resources we provide. The outcome of this project is that researchers will be able to more effectively and efficiently convert the power of genomic research into gains foragriculture and consumer use. Overall, the impact of our work is the improved ability for researchers to benefit society through improved agricultural systems, renewable energy, aquaculture, human nutrition, food safety and biotechnology. The societal impact of our education initiative is recruitment of minorities to emerging areas of biology via novel education and training opportunities.

Animal Health Component

5%

Research Effort Categories

Basic

0%

Applied

10%

Developmental

90%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
304	3910	1040	100%

Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3910 - Cross-commodity research--multiple animal species;

Field Of Science
1040 - Molecular biology;

Keywords

chicken

gene expression

bioinformatics

genomics

Goals / Objectives
Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices.

Project Methods
(1) Chicken gene nomenclature will be assigned based upon the guidelines provided by the Chicken Gene Nomenclature Consortium. This in turn is based upon standards developed by international gene nomenclature groups such as the HGNC. (2) Functional annotation will be based upon providing both manual curation of published literature and by computational analysis of sequence. The data will be produced according to current Gene Ontology Consortium standards. Other functional annotation methods will also follow community curation standards. (3) Chicken Gene Expression data will be done by RNASeq analysis if mRNA and ncRNAs to identify expression at a transcriptional level and using proteomics and proteognomics mapping to identify expression at a translational level. All data will be submitted to public archives and final annotation files made available as gtf and/or gff files, as appropriate.

Progress 10/22/13 to 09/30/18

Outputs
Target Audience:The target audience for this project are US poultry researchers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest?Results have been disseminated to the community via scientific publications and presentations at scientific meetings. We also provide support to the community via our online resources (AgBase, Chickspress and CGNC). What do you plan to do during the next reporting period to accomplish the goals?Our planned work for next year includes: (1) Providing GO annotation for avian species (specifically chicken and turkey); these annotations will focus on novel protein coding transcripts and ncRNAs identified via FAANG projects. (2) Continued support to provide standardized gene nomenclature for chicken (3) Development of an automated workflow to do a rapid, first-pass functional annotation of genomic-scale transcriptomes.

Impacts
What was accomplished under these goals? Objective 1: Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. a. AgBase: supporting functional modeling in agricultural organisms.AgBase (http://www.agbase.msstate.edu) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. We provide 2,069,320 Gene Ontology (GO) annotations for 394,599 gene products from more than 50 agriculturally important species and their pathogens. During 2018 AgBase was moved to a new server system which will provide enhanced performance. We also partnered with Phoenix Bioinformatics, a non-profit organization, to implement a subscription-based funding model for AgBase tools and large-scale analyses, and this will go into effect during 2019. b. Standardized Gene Nomenclature.The Chicken Gene Nomenclature Consortium (CGNC;http://birdgenenames.org/cgnc) is the sole source globally for chicken gene nomenclature. During 2018 we mapped and updated gene names for the new Galgal5 release. This resulted in 817 obsolete records, 2,693 records with duplicated gene symbols and 1,111 records for manual review. c. Chickspress - developing a tissue specific compendium of gene expression for chicken gene products.The Chickspress resource (http://geneatlas.arl.arizona.edu) provides a detailed "atlas" of chicken gene expression, collating experimental information from Red Jungle Fowl and chicken gene expression studies. During 2018 we have completed remapping all expression data to the new Galgal5 annotations and the publication describing this resources have recently been provisionally accepted (pending minor revisions).

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Ammari M, McCarthy F, Nanduri B. Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome. Current Protocols in Bioinformatics. 2018 Mar;61(1):8-26.

Progress 10/01/16 to 09/30/17

Outputs
Target Audience:The target audience for this project is poultry researchers and students. We disseminate our results by making data freely and publicly accessible in our online databases and tools, and by presenting information about this data and how to use it at scientific conferences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The postdoc on this project presented her data at theTenth International Biocuration Conference, Stanford University USA, 26-29 March 2017. How have the results been disseminated to communities of interest?Data are made freely and publicly available via databases, and are disseminated to additional public databases (e.g. UniProt, NCBI, HGNC). Results are also presented at scientific conferences and published in scientific journals, including "how to" guides for using the data types. What do you plan to do during the next reporting period to accomplish the goals?Contingent upon funding, our planned work for next year includes: (1) providing GO annotation for avian species (specifically chicken and turkey); (2) continued support to provide standardized gene nomenclature for chicken (3) continued computational support for researchers to functional model their gene expression data sets.

Impacts
What was accomplished under these goals? 3.1 Objective 1: Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. a. AgBase: supporting functional modeling in agricultural organisms. AgBase (http://www.agbase.msstate.edu) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. We provide 1,833,993 Gene Ontology (GO) annotations for 354,329 gene products from more than 40 agriculturally important species and their pathogens. During 2017 we worked on moving the AgBase database to new servers, which will enable continued growth and maintenance of this resource. b. Standardized Gene Nomenclature. The Chicken Gene Nomenclature Consortium (CGNC; http://birdgenenames.org/cgnc) is the sole source globally for chicken gene nomenclature. During 2017 we mapped gene nomenclature to genes annotated for the new Galgal5 release to provide unambiguous nomenclature for a further 29,783 genes. c. Chickspress - developing a tissue specific compendium of gene expression for chicken gene products. The Chickspress resource (http://geneatlas.arl.arizona.edu) provides a detailed "atlas" of chicken gene expression, collating experimental information from Red Jungle Fowl and chicken gene expression studies. The Chickspress genome browser information now utilizes the CoGe genome browser, providing access to more comparative analysis tools and leveraging cyberinfrastructure supported by the NSF funded CyVerse project. During 2017 we have remapped all expression data to the new Galgal5 annotations. d. Host-Pathogen Interaction Database (HPIDB) - curation to support animal health data sets. During 2017 we continued manual biocuration of host-pathogen interaction data to support network modeling of animal health data sets as well as developing a set of predicted 75,323 "interologs" (developed in conjunction with Mississippi State). This includes curated and predicted interactions for Marek's Disease, Salmonella and Mycoplasma. 3.2 Objective 2: Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer. a. Chicken Phenotype annotation. During 2017 we added 1,774 avian anatomy terms to the avian ontology provided by Uberon. This project is finishing as we did not obtain funding for further work. 3.3 Objective 3: Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. a. Training workshops and community support via AgBase. We continue to provide training, outreach and support for poultry researchers via AgBase to ensure that they are able to better leverage their functional genomics data to understand key economic traits for poultry. During 2017, the AgBase resources were visited by 18,497 different researchers, with 28.7% of these visitors from the US (includes visitors from 48 states). AgBase was cited in 68 publications during 2017. 3.1 Objective 1: Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. a. AgBase: supporting functional modeling in agricultural organisms. AgBase (http://www.agbase.msstate.edu) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. We provide 1,833,993 Gene Ontology (GO) annotations for 354,329 gene products from more than 40 agriculturally important species and their pathogens. During 2017 we worked on moving the AgBase database to new servers, which will enable continued growth and maintenance of this resource. b. Standardized Gene Nomenclature. The Chicken Gene Nomenclature Consortium (CGNC; http://birdgenenames.org/cgnc) is the sole source globally for chicken gene nomenclature. During 2017 we mapped gene nomenclature to genes annotated for the new Galgal5 release to provide unambiguous nomenclature for a further 29,783 genes. c. Chickspress - developing a tissue specific compendium of gene expression for chicken gene products. The Chickspress resource (http://geneatlas.arl.arizona.edu) provides a detailed "atlas" of chicken gene expression, collating experimental information from Red Jungle Fowl and chicken gene expression studies. The Chickspress genome browser information now utilizes the CoGe genome browser, providing access to more comparative analysis tools and leveraging cyberinfrastructure supported by the NSF funded CyVerse project. During 2017 we have remapped all expression data to the new Galgal5 annotations. d. Host-Pathogen Interaction Database (HPIDB) - curation to support animal health data sets. During 2017 we continued manual biocuration of host-pathogen interaction data to support network modeling of animal health data sets as well as developing a set of predicted 75,323 "interologs" (developed in conjunction with Mississippi State). This includes curated and predicted interactions for Marek's Disease, Salmonella and Mycoplasma. 3.2 Objective 2: Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer. a. Chicken Phenotype annotation. During 2017 we added 1,774 avian anatomy terms to the avian ontology provided by Uberon. This project is finishing as we did not obtain funding for further work. 3.3 Objective 3: Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. a. Training workshops and community support via AgBase. We continue to provide training, outreach and support for poultry researchers via AgBase to ensure that they are able to better leverage their functional genomics data to understand key economic traits for poultry. During 2017, the AgBase resources were visited by 18,497 different researchers, with 28.7% of these visitors from the US (includes visitors from 48 states). AgBase was cited in 68 publications during 2017.

Publications

• Type: Journal Articles Status: Published Year Published: 2017 Citation: 1. Joyce BL, Haug-Baltzell AK, Hulvey JP, McCarthy FM, Devisetty UK, Lyons E. Leveraging CyVerse resources for de novo comparative transcriptomics of underserved (non-model) organisms. J Vis Exp. 2017 May 9;(123). doi:10.3791/55009. PMID: 28518075.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: McCarthy FM, Burgess SC, Nanduri B. Data Sustainability and Funding: AgBase. Data Sustainability and Funding Workshop, Plant & Animal Genome XXV, San Diego, January 13-18, 2017.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: McCarthy FM, Cooksey AM, Gresham CG, Pendarvis K, Burgess SC, Nanduri B. Beyond annotation: Assigning function to chicken ncRNAs. Poultry 2 Workshop, Plant & Animal Genome XXV, San Diego, January 13-18, 2017.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Ammari MG, Gresham CG, Manda P, McCarthy FM, Nanduri B. Host-Pathogen Interactome: Biocuration and Computational Prediction. The Tenth International Biocuration Conference, Stanford University USA, 26-29 March 2017.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Zhang J and McCarthy FM. Development of Avian Anatomy Ontology Annotation. The Tenth International Biocuration Conference, Stanford University USA, 26-29 March 2017.

Progress 10/01/15 to 09/30/16

Outputs
Target Audience:Our work provides fundamental annotation information (both structural and functional) that underpins functional modeling of genomic data sets. This enables poultry researchers to more accurately identify genes involved in the systems they are studying and translate long lists generated by functional genomics into a biological model that they can use to improve poultry production. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Provided professional development for a postdoctoral researcher. How have the results been disseminated to communities of interest?1. Publications of scientific papers. 2. Presentation of results at scientific meetings. 3. Public, freely accessible access via online databases and resources. What do you plan to do during the next reporting period to accomplish the goals?Our planned work for next year includes: (1) providing manual GO annotation for avian species (including chicken, turkey, zebra finch and quail) and complementary computational annotation to support these species; (2) continued biocuration of host-pathogen interactions for avian pathogens (3) continued support to provide standardized gene nomenclature for chicken (4) continued computational support for researchers to functional model their gene expression data sets.

Impacts
What was accomplished under these goals? Objective 1: Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. a. AgBase: supporting functional modeling in agricultural organisms. AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. During 2016 we continued to provide annotated gene function data to support NC1170 researchers. Via AgBase we provide 1,753,795 Gene Ontology (GO) annotations for 341,743 gene products across 531 species, including poultry species and their pathogens. b. Standardized Gene Nomenclature. During 2016 the Chicken Gene Nomenclature Committee (CGNC) biocurators worked closely with NCBI Entrez Curators to ensure that updated gene annotations had revised nomenclature. During 2016 we updated genes in line with the Galgal4 annotations and approved 1,454 chicken gene names. We currently provide standardized nomenclature for 27,237 chicken genes and have a pending grant application to support continued annotation of bird genes. We especially thank avian researchers that have contacted us about chicken gene nomenclature and worked with us to ensure that these names best represent our current understanding of gene function. c. Chickspress - developing a tissue specific compendium of gene expression for chicken gene products. The Chickspress resource (http://geneatlas.arl.arizona.edu/) provides a detailed "atlas" of chicken gene expression, collating experimental information from Red Jungle Fowl and chicken gene expression studies. The Chickspress genome browser information was also moved from GBrowse to the CoGe genome browser, providing access to more comparative analysis tools and leveraging cyberinfrastructure supported by the NSF funded CyVerse project. Expression information provided by this resource is publicly available and was used as part of the Galgal4 assembly and annotation. This data has also been utilized to investigate avian sex chromosomes. d. Host-Pathogen Interaction Database (HPIDB) - curation to support animal health data sets. During 2016 we also continued manual biocuration of host-pathogen interaction data to support network modeling of animal health data sets. The HPIDb now provides 3,733 manually curated molecular interactions, including host-pathogen interactions from 28 different livestock pathogens. These interactions have all been manually curated and pass international QC and curation standards. With collaborators at Mississippi State we are developing tools to support interaction prediction. Objective 3: Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. a. Chicken Phenotype annotation. Continuing work on the chicken anatomy ontology is based upon UA biocurator funds, with work focusing on adding adult chicken anatomy terms to the avian ontology provided by Uberon. The avian subset of the Uberon ontology contains >15,000 anatomy terms, with 1,774 terms added by the UA biocuration group. Since this ontology will be required for the Functional Annotation of Animal Genomes (FAANG) Funding is pending to support a full-time biocurator to complete this ontology. b. Training workshops and community support via AgBase. We continue to provide training, outreach and support for poultry researchers via AgBase to ensure that they are able to better leverage their functional genomics data to understand key economic traits for poultry. During 2016, the AgBase resources were visited by 18,506 different researchers, with 30.2% of these visitors from the US (includes visitors from 48 states). AgBase was cited in 65 publications during 2016, and in more than 600 publications overall.

Publications

• Type: Journal Articles Status: Published Year Published: 2016 Citation: MG Ammari, CR Gresham, FM McCarthy, B Nanduri. HPIDB 2.0: a curated database for hostpathogen interactions Database 2016, baw103.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Donald L Mykles, Karen G Burnett, David S Durica, Blake L Joyce, Fiona M McCarthy, Carl J Schmidt, Jonathon H Stillman. Resources and recommendations for using transcriptomics to address grand challenges in comparative biology Integrative and comparative biology, icw083.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: JE Koltes, JM Reecy, E Lyons, F McCarthy, MW Vaughn, JP Carson, E Fritz-Waters, J Williams. Bioinformatics resources for animal genomics using CyVerse cyberinfrastructure. Journal of Animal Science 94 (7supplement4), 33-34.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Ammari MG, Gresham CR, McCarthy FM and Nanduri B. HPIDB 2.0: current updates in database content, interface and computational prediction of host pathogen interactions. MidSouth Computational Biology and Bioinformatics Society. Memphis, TN, Mar 3-5, 2016. (Poster presentation).
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Ammari MG, Gresham CR, McCarthy FM and Nanduri B. HPIDB: a curated database for host-pathogen interactions. International Plant and Animal Genome XXIV Conference, San Diego, CA Jan 8-13, 2016. (Oral Presentation)
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Fiona McCarthy, Amanda Cooksey, Cathy Gresham, Ken Pendarvis, Shane Burgess. "Genome-wide Expression in Chicken". Invited presentation at Poultry Workshop, Plant and Animal Genome XXIV Conference, 8-13 January 2016. San Diego, CA.
• Type: Conference Papers and Presentations Status: Other Year Published: 2016 Citation: Ammari MG, Gresham CR, McCarthy FM and Nanduri B. HPIDB: a curated database for host-pathogen interaction. Biocuration 2016, The Ninth International Biocuration Conference, Geneva, Switzerland, Apr 10-14, 2016.

Progress 10/01/14 to 09/30/15

Outputs
Target Audience:The target audience for this project is poultry researchers working with functional genomics or animal health data. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest?All of the data and bioinformatics tools are freely available and our databases are freely and publicly available. What do you plan to do during the next reporting period to accomplish the goals?Objective 1. Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. a. AgBase: During 2016 we will continue our functional annotation efforts, focusing on key livestock and aquaculture species. We will also do regular updates to integrate new data from external resources. b. HPIDB: During 2016 we will continue to add curated host-pathogen interaction data. We will also continue the development of a host-pathogen interaction prediction tool. c. Chicken Gene Nomenclature Committee (CGNC): During 2016 we will continue our gene nomenclature annotation for chicken genes. We will be updating and reviewing nomenclature as the new chicken sequence and annotation data is released. d. Chickspress: During 2016 we will continue our analysis of ncRNAs and correlating mRNA expression with protein expression. Objective 2. Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer. a. Avian anatomy ontology: During 2016 we will continue to focus on adding adult chicken anatomy terms and integrating these terms with Uberon. b. VERVE Net: During 2016 we will continue to develop virus ecology research protocols on this forum.

Impacts
What was accomplished under these goals? Impact: The impact of this research is measured by the ability of poultry researchers to better translate their genomics data sets into products to reduce, alleviate or eliminate poultry disease. While in many cases the economic impact of individual disease agents is well characterized, the overall cost of disease in animal and aquaculture systems is not well defined. The direct economic impact of this project will be realized by enabling researchers to more readily translate genomics information about livestock and aquaculture disease into vaccines, immunotherapeutics and strategies to reduce the economic burden of disease in production systems. In addition to the economic impact, strategies to reduce or eliminate the severity animal disease will also broadly impact society. Societal benefits include reduced pathogens in the food supply, improved production efficiency and improved animal welfare. Objective 1. Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. a. AgBase: AgBase (http://www.agbase.msstate.edu/) provided 392,101 GO annotations for 57,589 avian gene products, 96% of which are associated with chicken and turkey. During 2015 manual biocuration focused on extending detailed, literature-based functional annotations to well studied genes in additional livestock and aquaculture species, including turkey. b. HPIDB: In 2015 the Host-Pathogen Interaction Database (HPIDb) provided 2,478 manually curated molecular interactions, including host-pathogen interactions from 28 different livestock pathogen strains. Future work with collaborators at Mississippi State focuses on developing tools to support interaction prediction. c. Chicken Gene Nomenclature Committee (CGNC): During 2015 CGNC reviewed and updated 2, 735 genes. CGNC currently provides standardized nomenclature for 22,172 chicken genes and there is a pending grant application to support continued annotation of bird genes. d. Chickspress: The Chickspress resource (http://geneatlas.arl.arizona.edu/) provides a detailed "atlas" of chicken gene expression, collating experimental information from Red Jungle Fowl and chicken gene expression studies. Initial mRNA analysis identified 66,309 transcripts, of which 35% differ from current gene models provided by NCBI or Ensembl; most represent alternate transcripts from predicted gene models. Also identified from these same tissues were 16,496 miRNAs, including15,291 novel miRNAs. Target prediction is complete for these novel miRNAs. Likewise proteomics was used to identify 16,003 NCBI and Ensembl proteins from these same tissues, as well as 77,418 peptides that are not supported by current chicken protein sequences. An ongoing collaboration with INRA researchers (lead by Elisabetta Giuffra) is investigating miRNA an lcnRNA expression. Objective 2. Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer. a. Avian anatomy ontology: Continuing work on the chicken anatomy ontology is based upon UA biocurator funds, with work focusing on adding adult chicken anatomy terms to the avian ontology provided by Uberon. The avian subset of the Uberon ontology contains 15,300 anatomy terms, with 1,774 terms added by the UA biocuration group. Since this ontology will be required for the Functional Annotation of Animal Genomes (FAANG) Funding is pending to support a full-time biocurator to complete this ontology. b. VERVE Net: VERVE Net is a virus ecology research and virtual exchange network (http://vervenet.us) collaboration with Dr Bonnie Hurwitz (U Azriona). VERVE Net is funded by the Gordon Betty Moore Foundation to develop a forum for virus ecology research. As part of this effort and in partnership with Protocols.io, a forum for groups share, discuss, and adapt protocols was developed. Initially the platform only supported molecular biology protocols, but was recently updated to include support for bioinformatics protocols. Drs. Hurwitz and McCarthy have partnered to begin to develop a similar forum specific to poultry research and breeding that uses the same software platform.

Publications

Progress 10/22/13 to 09/30/14

Outputs
Target Audience: The target audience for this project is animal health researchers, particularly those who are generating large and/or complex data sets. We expect to work with a diverse range of animal health researchers, including both livestock and aquaculture researchers and encompassing graduate students, postdoctoral associates, project leaders and new investigators. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? This project provided biocuration training with the EMBL-EBI IntAct database for a postdoctoral associate and research experience projects for three undergraduate and one graduate student. How have the results been disseminated to communities of interest? All curated data is freely and publicly available via the AgBase database, tools are available via AgBase and the iPlant/iAnimal Collaborative. What do you plan to do during the next reporting period to accomplish the goals? Our planned work for next year includes: (1) providing manual GO annotation for additional agricultural species (including turkey, sheep, pig, salmon and trout) based upon our eGIFT literature evaluation and complementary computational annotation to support these species; (2) continued development of mapping files that link poultry 'informative terms' (iTerms) to other ontology terms, providing organized data to support additional functional analysis of poultry functional genomics data sets; (3) addition of new functional annotation tools in the iPlant Discovery Environment to support functional modeling of large data sets (e.g. RNA-Seq data); (4) developing a chicken reference gene set for annotation and comparative analysis; (5) continued analysis of RNA and protein expression in chicken to provide updated information about chicken gene expression, including tissue and sex specific expression and allele specific expression patterns.

Impacts
What was accomplished under these goals? 3.1 Objective 1: Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. a. AgBase: supporting functional modeling in agricultural organisms. AgBase (http://www.agbase.msstate.edu/) provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. We currently (21 November 2014) provide 1,808,007 Gene Ontology (GO) annotations for 383,527 gene products across 77 species, including agriculturally important species and their pathogens. This information includes GO annotations for 54,446 chicken and 2,958 turkey gene products, respectively. To more efficiently identify functional information in the published literature and extend our manual biocuration effort to additional species (including turkey, sheep and salmon) we collaborate with researchers at the University of Delaware to complete text mining of published literature and identify (a) papers likely to contain GO terms for agricultural species; and (b) additional 'informative terms' (iTerms) or functional information described in the literature. We used the latter information to link iTerms to functional terms from other, existing ontologies (such as the cell ontology and anatomy ontologies), creating an ontology mapping files for this literature. During 2014 we also started manual biocuration of host-pathogen interaction data to support network modeling of animal health data sets. Via the Host-Pathogen Interaction Database (HPIDb) we submitted 1,829 molecular interactions to the EMBL European Bioinformatics Institute (EBI) IntAct database. With collaborators at Mississippi State we will continue to develop the HPIDb, adding interaction data and developing tools to support interaction prediction. As part of the USDA funded iAnimal Project we also worked with the iPlant Collaborative to develop functional analysis pipelines within iPlant. During 2014 we added tools to support (a) functional annotation of large scale transcript data and (b) GO and pathways enrichment analyses of differentially expressed data. b. Standardized Gene Nomenclature. During 2014 the Chicken Gene Nomenclature Committee (CGNC) updated data reporting to support the use of this data by both NCBI and Ensembl. We currently provide standardized nomenclature for 16,422 genes and this data is now routinely distributed to both NCBI Entrez and Ensembl. During 2014 funding to support chicken gene nomenclature was provided by NIH NIGMS Project number 5R24GM079326-02 and during 2015 we will be seeking continued competitive funds for this project. To facilitate future nomenclature efforts, including sharing data with other vertebrate species (such as turkey), we are also developing a chicken reference gene set. The chicken reference gene set will be the focus of future annotation efforts and will facilitate comparative analysis with other species. The initial cattle gene nomenclature was provided by the Bovine Genome Database and we updated this information to assign standardized gene nomenclature for 9,910 Bos taurus genes (http://www.animalgenome.org/genetics_glossaries/bovgene). We are also working with HGNC to support the development and use of standardized gene nomenclature for livestock species. 3.2 Objective 2: Facilitate the creation and sharing of poultry research populations and the collection and analysis of relevant new phenotypes including those produced by gene transfer. a. Chicken Phenotype annotation. Continuing work on the chicken anatomy ontology is based upon UA biocurator funds, with work focusing on (1) linking adult chicken anatomy terms with the Uberon ontology (of generic anatomical terms) and (2) adding developmental terms provided by Professor Burt's group at the Roslin Institute. Currently the chicken anatomy ontology contains 14,627 terms, cross-referenced with the Uberon ontology (and other related anatomy ontologies). Since this ontology will be required for the Functional Annotation of Animal Genomes (FAANG) Project, during 2015 we will seek competitive funding for a full-time biocurator to complete this ontology. 3.3 Objective 3: Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. a. Training workshops and community support via AgBase. We continue to provide training, outreach and support for poultry researchers via AgBase to ensure that they are able to better leverage their functional genomics data to understand key economic traits for poultry. We have funding to provide on-site training for researchers who are interested in learning how to functional model their 'omics' data sets and will be seeking to contact researchers who would be interested in hosting such a workshop during 2015. During 2014 researchers from the US, Canada, Japan, India, China, France, Germany, Portugal, Brazil, the Russian Federation, and an additional 113 countries accessed AgBase. We provided direct support for researchers studying crow, zebra finch, Botrytis cinerea (a grape pathogen), pear, Reniform, Coregonus clupeaformis (lake whitefish), Japanese quail, Psophocarpus tetragonolobus (Winged Bean), Ciona intestinalis (sea squirt) and soil metatranscriptome data. During 2014 AgBase had 23,311 visitors, including researchers from 48 US states (who made up 19% of the total researchers using AgBase).

Publications

• Type: Journal Articles Status: Accepted Year Published: 2014 Citation: 1. Sun L, Lamont S, Cooksey A, McCarthy F, Tudor C, Shanker K-V, Derita R, Rothschild M, Ashwell C, Persia M and Schmidt, C (2014). Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line. Poultry Sci. Accepted.