ADVANCED TECHNOLOGIES FOR THE GENETIC IMPROVEMENT OF POULTRY

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1016841
• Multistate No.: NC-_old1170
• Project Start Date: Oct 1, 2018
• Project End Date: Sep 30, 2023
• Program Code: [(N/A)]- (N/A)

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
The poultry industry in the United States underpins the global food system providing an efficient, economical and nutritioussource of animal-based protein (meat and eggs). The industry foundation consists of breeding companies andgrowers/producers distributed throughout the nation (and the world) with a heavy concentration in states from which themembers of Multistate Research Project NC1170 are drawn (e.g., Arkansas, California, Delaware, Georgia, Iowa, Minnesota,North Carolina, Virginia). The USDA Economic Research Service reports that the U.S. poultry industry is the world's largestproducer and second-largest exporter of poultry meat and a major egg producer. The USDA National Agricultural StatisticsService reported that the combined value of production from broilers, eggs, and turkeys in 2015 was $47.9 billion. Many alliedindustries support and are impacted by the poultry industry, e.g., from grain producers and distributors to housing/cagemanufacturers. Thus, the economic impact of the poultry industry to the financial health of the U.S. is enormous. Theinteractions of the poultry researchers involved in NC1170 with their stakeholders takes place via a variety of formats andopportunities so as to integrate our expertise with their needs and goals. These formats include, but are not limited to,organized informal meetings, workshops, and conferences (e.g., Poultry workshop at annual International Plant and AnimalGenome meetings, annual National Breeders Roundtable, annual Poultry Science Association meeting), listserves, web basedtools/utilities useful to the industry, as well as collaborative ventures among research institutions and poultry industrybusinesses. Many NC1170 members have leveraged USDA-AFRI or other federal grants and have substantive collaborationswith poultry breeders and producers. It is noteworthy that many NC1170 researchers not only utilize specialized poultry geneticlines for experimental analysis but also routinely employ commercially-selected foundational lines and crosses in their work.

Animal Health Component

0%

Research Effort Categories

Basic

50%

Applied

0%

Developmental

50%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
304	3299	1080	100%

Knowledge Area
304 - Animal Genome;

Subject Of Investigation
3299 - Poultry, general/other;

Field Of Science
1080 - Genetics;

Keywords

chicken

turkey

annotation

ontology

Goals / Objectives
Create and share data and technology to enhance the development and application of genomics, epigenomics, and systems biology in poultry.

Project Methods
Functional annotation will be done using Gene Ontology (GO) Consortium approved methods for literature curation and using existing functional prediction workflows for protein coding genes. We will also develop functional prediction workflows for noncoding RNAs and predicted GO annotations will be appropriately labelled with evidence codes.Gene nomeclature will be done based upon manual curation (following established HGNC and CGNC guidelines) and in consultation with the poultry community.

Progress 10/01/19 to 09/30/20

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?Undergraduate students involved in this research had the opportunity to develop bioinformatics and communication skills. 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?Objective 1: Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. AgBase: supporting functional modeling in agricultural organisms. During 2021 we will seek funding to support AgBase's continued maintenance and the development of high-throughput functional annotation workflows. Standardized Chicken Gene Nomenclature. During 2021 we will complete error corrections flagged as part of the Galgal6 annotation updates. We are working with HGNC collaborators on specific gene families that requires extensive manual curation (e. g., ORs, CYP450s, GSTs). Functionally annotating novel chicken transcripts: We will pull any publicly available FAANG transcript data to identify and provide GO annotation for novel chicken transcripts. 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. Nothing to report. Objective 3: Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. Proteomics of chicken muscle: Functional analysis of Red Jungle Fowl, Heritage and Modern breast muscle proteins is complete and the manuscript is in process.

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. AgBase: supporting functional modeling in agricultural organisms. During 2020 we updated gene product and GO annotation data in AgBase. We also translated our genome-scale functional annotation workflows into biocontainers & made these available via CyVerse resources, complete with readthedocs documentation on how to install and use. Standardized Chicken Gene Nomenclature. During 2020 we continued working to provide updated nomenclature for the latest gene release (based on assembly GRCg6a). We co-ordinate with NCBI, HGNC and VGNC to ensure consistent gene nomenclature between vertebrate groups. Functionally annotating novel chicken transcripts: Efforts to provide GO annotation for novel transcripts identified by the Chicken FAANG group was delayed because of problems identifying and accessing this data. 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. Nothing to report. Objective 3: Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. Identifying chicken blood antigens: During 2020 we provided proteomics & bioinformatics support for a Hy-line -WVU collaboration to identify chicken red blood cell antigens. This work is ongoing. Proteomics of chicken muscle: We identified proteins expressed in Red Jungle Fowl, Heritage and Modern breast muscle and examined functional differences that occurred during domestication and selection.

Publications

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:The target audience for this project are poultry researchers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Undergraduate students involved in this research had the opportunity to develop bioinformatics and communication skills by presenting their results at undergraduate research days. 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?Objective 1: Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. AgBase: supporting functional modeling in agricultural organisms. During 2020 we will complete the update (the first time UA personnel have completed this process) and work towards streamlining this process for the future. We will also complete alpha testing of the functional annotation workflows and directly link them to AgBase using a user-friendly graphical interface. Standardized Chicken Gene Nomenclature. During 2020 we will complete error corrections flagged as part of the Galgal5 annotation updates. We anticipate the need for manual review of MHC genes as part of this process, which may take additional time. Functionally annotating novel chicken transcripts: We will pull any publicly available FAANG transcript data to identify and provide GO annotation for novel chicken transcripts. We are also identifying novel miRNAS (and their targets) from FAANG data sets to investigate functional prediction. 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. Nothing to report. Objective 3: Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. Identifying chicken blood antigens: During 2020 we anticipate receiving RBC samples for proteomic analysis. Proteomics of chicken muscle: Functional analysis of Red Jungle Fowl, Heritage and Modern breast muscle proteins is complete and the manuscript is in process.

Impacts
What was accomplished under these goals? (a) Major goals of the project: Objective 1: Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. 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. Objective 3: Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. (b) What was accomplished under these goals? Impact (non-technical): The University of Arizona contribution provides poultry researchers with the ability to effectively translate genomics data into knowledge that can be applied to agricultural systems. A search of the CRIS database identifies almost 260 actively funded genomics projects; this represents millions of dollars of investment in animal production. The direct economic impact of our research is to enable this investment to be more readily applied to production systems. In addition to the economic impact, strategies to reduce or eliminate the severity animal disease will also broadly impact society. List accomplishments by goal: Objective 1: Create and share data and technology to enhance the development and application of genomics and systems biology in poultry. AgBase: supporting functional modeling in agricultural organisms. AgBase is now located on servers at the University of Arizona. During 2019, we implemented a subscription-based funding model to meet database maintenance costs, and this was done in partnership with Phoenix Bioinformatics, a non-profit organization. We also started the first update of data with UA personnel, and built genome-scale functional annotation workflows using CyVerse resources. Standardized Chicken Gene Nomenclature. During 2019 we continued working through error corrections flagged as part of the Galgal5 annotation updates. We also co-ordinated with NCBI, HGNC and VGNC to implement and use a single JIRA tracking system for nomenclature issues; this has improved communication & response between nomenclature groups. Chickspress - developing a tissue specific compendium of gene expression for chicken gene products. Data in this resource has been remapped to Galgal5 annotations, and in 2019 the Chickspress manuscript describing this work and how to use this resource was published. Functionally annotating novel chicken transcripts: Efforts to provide GO annotation for novel transcripts identified by the Chicken FAANG group was delayed because of problems identifying and accessing this data. 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. Nothing to report. Objective 3: Elucidate genetic mechanisms that underlie economic traits and develop new methods to apply that knowledge to poultry breeding practices. Identifying chicken blood antigens: During 2019 we provided proteomics support for a Hy-line -WVU collaboration to identify chicken red blood cell antigens. This work is ongoing. Proteomics of chicken muscle: We identified proteins expressed in Red Jungle Fowl, Heritage and Modern breast muscle and examined functional differences that occurred during domestication and selection.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: McCarthy FM, Pendarvis K, Cooksey AM, Gresham CR, Bomhoff M, Davey S, Lyons E, Sonstegard TS, Bridges SM, Burgess SC. Chickspress: a resource for chicken gene expression. Database. 2019 Jan 1;2019.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Neerukonda SN, Tavlarides-Hontz P, McCarthy F, Pendarvis K, Parcells MS. Comparison of the Transcriptomes and Proteomes of Serum Exosomes from Mareks Disease Virus-Vaccinated and Protected and Lymphoma-Bearing Chickens. Genes. 2019 Feb;10(2):116.
• Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Nanduri B, Gresham CR, McCarthy FM. HPIDB: A Database for Host-Pathogen Interactions. InPlant and Animal Genome XXVII Conference (January 12-16, 2019) 2019 Jan 12. PAG.