Source: IOWA STATE UNIVERSITY submitted to
NATIONAL ANIMAL GENOME RESEARCH PROGRAM
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
REVISED
Funding Source
HATCH
Reporting Frequency
Annual
Accession No.
1001816
Grant No.
(N/A)
Project No.
IOW05380
Proposal No.
(N/A)
Multistate No.
NRSP-8
Program Code
(N/A)
Project Start Date
Oct 30, 2013
Project End Date
Sep 30, 2018
Grant Year
(N/A)
Project Director
Tuggle, CH, K.
Recipient Organization
IOWA STATE UNIVERSITY
2229 Lincoln Way
AMES,IA 50011
Performing Department
Animal Science
Non Technical Summary
The NRSP-8 National Animal Genome Research Support Program has played a major role in enabling genomic discoveries in livestock animals and aquaculture species. As outlined in the Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017, infrastructure provides the critical foundation upon which genomics-oriented discovery science can be channeled into substantial advances in agricultural practices. Infrastructure, as defined by the Blueprint, includes genomic tools (e.g., maps, genome assemblies), integrative bioinformatics tools and databases, genetic resource populations, and education and training of students, scientists, and the public. The mission of NRSP-8 focuses on providing support for these crucial infrastructure components. Developed infrastructure is, in turn, used to leverage more substantial funding support for livestock genomics research from a variety of public and private sources. Our first objective is to advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. The annual NRSP-8 meetings provide the opportunity to communicate new results and develop core infrastructure and leadership discussions necessary for organizing these efforts, including sharing of DNA resources, collaborative use of computational power, and community-based annotation. Our second objective is to develop strategies to identify and exploit genes and genetic variants that contribute to economically relevant traits, in part through improving functional description of the genomes of our species. The tremendous power of genome-wide variant analysis is leading to the identification of markers linked to important production traits in agricultural animal species. NRSP-8 support is critical to developing powerful experimental strategies that rely on improved description and understanding of the genes and their structures within complex genomes. Our third objective is to facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by high-throughput sequencing. This bioinformatic capacity is a critical component of infrastructure support enabled by NRSP-8. NRSP-8-supported approaches in this area include continued expansion of the tools and capabilities of the bioinformatics coordination program (http://www.animalgenome.org/), development of community-wide common methodologies for variant analysis and curation, training of students, scientists, and stakeholders in high-throughput data analysis, and development of collaborative platforms that facilitate species-group level access to timely genomic data. Across all objectives, the NRSP-8 will continue providing enabling technologies and support activities, and to disseminate data/genetic material otherwise sorely lacking across the animal genomics community. The organizational structure of NRSP-8 serves to bring together domestic scientists within a given livestock/aquaculture group, and facilitate rapid transfer of successful approaches to commercial national and international stakeholders.
Animal Health Component
40%
Research Effort Categories
Basic
70%
Applied
30%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3013510104010%
3033299108010%
3033320108010%
3033410108010%
3033510108010%
3043299108010%
3043310108010%
3043410108010%
3043510108010%
3043721108010%
Knowledge Area
301 - Reproductive Performance of Animals; 303 - Genetic Improvement of Animals; 304 - Animal Genome;

Subject Of Investigation
3299 - Poultry, general/other; 3510 - Swine, live animal; 3721 - Marine shrimp; 3320 - Meat, beef cattle; 3310 - Beef cattle, live animal; 3410 - Dairy cattle, live animal;

Field Of Science
1080 - Genetics; 1040 - Molecular biology;
Goals / Objectives
Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest.
Project Methods
NRSP-8 will accomplish its mission by working with a structure that is organized by animal species and managed by species-specific coordinators. The 6 species coordinators for aquaculture, cattle, equine, poultry, sheep, and swine are joined by a bioinformatics coordinator. The coordinators communicate with the species sub-committee members to facilitate the availability of shared genomic resources (e.g., tools, reagents, samples, and data) to the species committee members, often by leveraging the limited resources of the coordinator with those available from federal (e.g., NIH, USDA AFRI), international, industry, and state sources. The coordinators, working with the members of their respective committees and among themselves, also help to develop, stimulate and coordinate new initiatives. Finally, NRSP-8 fosters communication among its members and stakeholders through, among other things, e-mail newsletters and participation in meetings and conferences. Species coordinators stimulate this communication and provide focal points for input from the committee members and other stakeholders. Coordinators will meet with their respective species committee members at least once each year at annual meetings (e.g., species workshop at PAG) and solicit ideas and plans for project development and resources to share. Coordinators will communicate by e-mail, newsletters, and other means to make resources known to community members and solicit input throughout the year. Coordinators will meet with the NAGRP Director and Administrative Advisors at least once each year and as needed through conference calls and e-mail communications. The processes used to evaluate the success of the project will include the attendance at the NRSP-8 Workshops, enumerating the publications and presentations by NRSP-8 members and the Coordinators in a variety of venues. We will also evaluate our progress through counting the downloads, visits and users of tools, software and data produced within NRSP-8 and provided via public websites. Finally, we will quantify the participation of industry representatives in meetings and in adoption of methods and data produced within NRSP-8.

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

Outputs
Target Audience:Primary beneficiaries of NRSP-8 will be research scientists that are either engaged directly in animal genome research or utilize genomic data in complementary areas of animal science. Direct beneficiaries also include ever-increasing numbers of commercial animal breeders and producers who apply genomic data and related technologies to enhance aspects of animal health, welfare, productivity, and management, as well as, government agencies and breed organizations utilizing genomic methods for animal identification, disease surveillance, and regulatory monitoring. NRSP-8 will continue to be visible at national and international scientific meetings and workshops. A leading example is the annual International PAG Conference. NRSP-8 is showcased in species-specific and comparative genomics sessions, as well as through committee meetings where scientific presentations and reports are required from participating Experiment Stations. NRSP-8 has held its annual meeting jointly with PAG for >20 years, and NRSP-8 representatives play a major role in the organization and programming for this high profile international conference. Additionally the Swine Genome Coordinator publishes a newsletter that is read by a target audience that goes well beyond the actual members of NRSP, as it is circulated to over 3000 people who are scientists, students, and extension workers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?A PhD student, Haibo Liu, (ISU), was competitively awarded a Neil Jorgenson Travel scholarship supported by the Swine Genome Coordination funds. A PhD student, Jicai Jiang, (University of Maryland) was competitively awarded a Neil Jorgenson Travel scholarship supported by the Bioinformatics coordination funds. We also provided professional development to two researchers by partially supported their travel to speak at the 2017 Cattle/Swine Workshops at the PAG meeting: Alan Archibald, Roslin Institute/University of Edinburgh, and Vanmathy Kasimanickam, Washington State University. How have the results been disseminated to communities of interest?The Pig Genome Update was prepared and published once in the reporting period, #123 and #124. Three Bioinformatics/Database Updates were published and disseminated, 2016#3, 2017#1 and 2017#2.Plans are to publish the Pig Genome Update approximately 2 times per year and the Bioinformatics update 3 times per year, timed for major genome activities. These will include a February issue, with a Plant and Animal Genome (PAG) meeting summary and descriptions of summer meetings and research opportunities, and an October issue with PAG meeting announcements and reminders. The Pig Genome and Bioinformatics updates are emailed to over 3,000 recipients on the Angenmap mailing list. Both the Swine Genome and Bioinformatic Coordinators presented reports at the 2016 NRSP-8 Swine Subcommittee (January 14, 2017) as well as at the NRSP-Workshop on January 15, 2017, both coincided with the 2017 PAG meeting in San Diego, California. Cathy Ernst (Michigan State University) and Chris Tuggle (Iowa State University) reported on results from NRSP-8 seed funding projects at the PAG meeting in the Swine Workshop. The Angenmap mailing list is being maintained and is being actively used; 296 individual messages were submitted to angenmap@animalgenome.org in the reporting period. What do you plan to do during the next reporting period to accomplish the goals? Continue to provide funding for travel of Coordinators and NRSP-8 Swine Subcommittee members to relevant meetings; these will include in FY 2018: Plant and Animal Genome Meetings, Midwest ASAS meeting, International Society of Animal Genetics. Continue to offer funding for appropriate research projects involving more than one Station. Discuss use of NRSP-8 Coordination funds to increase collaboration across participating Stations. Report on activities at 2018 NRSP-8 meetings (January 2018). Continue to prepare Pig Genome and Bioinformatics Updates in FY 2018. Provide reports on funded seed projects to members of the NRSP-8 Swine Subcommittee. Discuss potential to provide new genotyping chip to NRSP-8 Committee members. Provide Bioinformatic training in FAANG related analyses.

Impacts
What was accomplished under these goals? Overall impact statement: Genome sequence information has the potential for advancing knowledge relevant to human and animal health and for improved production efficiency and nutrient composition of animal-based food products. Through coordination the international cooperative effort to sequence the genes and genomes of agricultural animals, NRSP-8 provides critical support for developing powerful experimental strategies that rely on improved description and understanding of the genes and their structures within complex genomes. This project year, conferences were held at San Diego (PAG) and in Dublin (ISAG), and reports were made therein on outcomes of funding provided to NRSP-8 Stations, and described under the relevant Objective below. In the reporting period, several groups used seed funding to advance our understanding of genetic variation and annotate the structure of the genome and provide functional annotation of genes and gene expression variants. Finally, we worked with and on behalf of researchers in the U.S. to effectively share, combine, manage, manipulate, and analyze information from genomics/genetics studies. In the past year, 46 TB of curated quantitative trait loci (QTL) data were downloaded, accessed by over 15,026 unique users. This access to and distillation of data from hundreds of publications dramatically reduces and streamlines the work for these researchers. Obj 1. Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. C Ernst (MSU) with J. Dekkers (ISU) used NRSP-8 seed funding to evaluate a new genotyping tool the Affymetrix Axiom Pig HD Array work will be valuable for further annotation of the variation across US breeds and companies. A seed project (T. Smith, USDA-MARC) with C. Tuggle (ISU) was initiated in 2016 to analyze unique PacBio Isoseq data. Results were presented in 2017 at the PAG meeting by Dr. H. Liu (ISU). Dr. Liu described error-correction of PacBio Isoseq data using Illumina RNA sequence data and mapping of these RNA sequences to the developing new genome assembly. The annotation of the new pig genome assembly using these Isoseq data was announced in 2017 (http://www.ensembl.org/Sus_scrofa/Info/Annotation). Dr. Liu also used this Isoseq data to analyze a blood transcriptome assembly published in 2017. Obj 2. Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. Signatures of selection strategies have been applied to scan the whole genome, to detect candidate genes for pig disease resistance or resilience (Porcine Periweaning Failure to Thrive Syndrome, Porcine Epidemic Diarrhea and heart failure during transport), supported by RNA-seq data when available. Similar strategies, were applied to detect signature of selection of worldwide adaptation to different environments and breeding goals in a high representative number of goat breeds. Functional annotation will allow faster and more accurate genetic improvements, as well as help in further understanding of genomes as they relate to animal biology. However, because of the high cost in these assays, a major test is the organization and coordination of many interested research groups to share samples and protocols to efficiently produce such data. To that end, the Bioinformatics and Swine Genome Coordinators have made multiple important contributions to FAANG: a) We provided funds to H. Zhou, UC-Davis to sequence the small RNAs for all tissues funded by USDA-NIFA-AFRI, as well as add one tissue (small intestine). Further, the Coordinators paid for genome sequencing of the two pigs for which tissues were collected for the FAANG project. This sequencing data will be useful in mapping sequence-based assay data back to the pig genome. P. Ross (UCDavis) has been invited to present the current status of this research at the 2018 PAG meeting. b) Further work in 2017 on the previously funded seed project (T. Smith) et al. to analyze unique PacBio Isoseq data showed significant numbers of different isoforms are present in all tissues analyzed, with brain having a very high number of such isoforms. Progress on this work will be presented by H. Beiki (ISU) at the 2018 PAG meeting in San Diego c) USDA-NIFA requested that the NRSP-8 membership prepare to apply for funding to annotate the function of the Swine genome. C. Tuggle organized a discussion at the 2017 PAG meeting and invited all Swine Subcommittee members as well as other scientists. Several groups then applied for seed funding. Three projects were funded (MSU/USDA; ISU; and UNL). d) Leadership in FAANG project development: The Bioinformatics and Swine Genome Coordinators continue to have a major role in the development of the organizational infrastructure of FAANG. C. Tuggle continued service as Co-Chair of the FAANG Steering Committee and is Chair of the FAANG Communications Subcommittee. J. Reecy continued to serve as co-Chair of the FAANG Bioinformatics and Data Analysis subcommittee. e) In new efforts, J. Reecy and colleagues led efforts to organize workshops on High-throughput phenotyping and the USDA Genomics Blueprint for the community. f) Additional support for new FAANG related efforts: Recognizing that a bottleneck in the analysis of genomic data for the NRSP-8 project is bioinformatics expertise, a part-time postdoctoral position proposed in the last period was advertised and filled with H. Beiki. H. Beiki is tasked with analyzing PacBio IsoSeq data for nine tissues collected at USDA-MARC, and will be reporting on his results at the 2018 Swine Workshop at PAG- San Diego. Objective 3... Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest. During this reporting period, the NRSP-8 website (animalgenome.org) had 8,642,447 hits, by 625,282 unique users from 152 countries. The website supports internet discussion and information sharing in animal genome research (http://animalgenome.org/community/angenmap/). By the end of 2017 this group had over 2,985 members from 63 countries/regions of the world. One of our supported databases, the Animal QTLdb (http://www.animalgenome.org/QTLdb) has been accessed by 15,026 unique users from 125 countries where the downloaded of curated QTL data amounts to 46 TB. These numbers do not included users that access our curated data via NCBI, Ensembl, UCSC, or Reuters Data Citation Index. Throughout 2017, the NAGRP bioinformatics team has continued their efforts to make improvements and curate new data into the database. In 2017, a total of 41,093 new QTL/association data have been curated into the database. Currently, there are 26,076 curated porcine QTL, 108,040 curated bovine QTL, 8,363 curated chicken QTL, 1,304 curated horse QTL, 1,932 curated sheep QTL, and 127 curated rainbow trout QTL in the database (http://www.animalgenome.org/QTLdb/). All data have been ported to NCBI, Ensembl, and UCSC genome browser in a timely fashion. Users can fully utilize the browser and data mining tools at NCBI, Ensembl, and UCSC to explore animal QTL/association data. In addition, we have continued to improve existing and add new QTLdb curation tools and user portal tools. The new improvements include permanent record locators for authors to refer to their published data, to provide proof of evidence of data entry at the Animal QTLdb to journal editors/manuscript reviewers, gene-centric views and trait-centric views of QTL data to facilitate data track and analysis, and new functions that allow linking of QTL data to genetic/phenotypic correlation data housed in CorrDB through annotated common trait terms.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Huang, J., M. Schroyen, N. Gabler, J. Dekkers, and C. Tuggle, Combining transcriptome and epigenetic analysis of H3K36me3 and H3K4me3 marks to explore mechanisms of liver-specific gene expression in pigs.?2017. Proceedings of International Society of Animal Science meeting, Dublin, Ireland, #WT70 p.79.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Zhou, H., P. Ross, C. Kern, P. Saelao, Y. Wang, M. Halstead, K. Chanthavixay, I. Korf, M. Delany, H. Cheng, J. Medrano, A. Van Eenennaam, C. Tuggle, and C. Ernst. ? 2017. Identification of regulatory elements in livestock species.? Proceedings of International Society of Animal Science meeting, Dublin, Ireland, #WT58 p.78.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Vella, G., M. Schroyen, H. Beiki, C. L. Loving, and C. K. Tuggle. 2017. Porcine bloodomics: Identification of porcine neutrophil-specific genes through gene expression correlations to neutrophil abundance and comparative expression data.? Proceedings of International Society of Animal Science meeting, Dublin, Ireland, #MT164, p.55.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Kern C., Y. Wang, P. Saelao, K. Chanthavixay, I. Korf, C. K. Tuggle, C. Ernst, P. Ross, and H. Zhou, ?2017. Genome-wide analysis of H3K4me3 and H3K27me3 in three tissues in pigs.? Proceedings of International Society of Animal Science meeting, Dublin, Ireland, #MT10, p.41
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Beiki, H. M. Schroyen, A. Rakhshandeh, N. Gabler, J. Dekkers, and C. Tuggle. 2017. Rewiring of porcine mRNA and miRNA networks in response to selection for residual feed intake. Proceedings of International Society of Animal Science meeting, Dublin, Ireland, #MT275, p.65
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Liu, H., T.P.L. Smith, D.J. Nonneman, J.C.M. Dekkers, C.K. Tuggle 2017. A high-quality annotated transcriptome of swine peripheral blood. BMC Genomics 18:479. doi: 10.1186/s12864-017-3863-7.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kommadath, A., H. Bao, I. Choi, J.M. Reecy, J.E. Koltes, E. Fritz-Waters, C. J. Eisley, J. R. Grant, R.R.R. Rowland, C. K. Tuggle, J.C.M. Dekkers, J.K. Lunney, L.L. Guan, P. Stothard, and G.S. Plastow. 2017. Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection. Scientific Reports 7:46203. doi: 10.1038/srep46203
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Fleming, D., Weigend, S., Simianer, H., Weigend, A., Rothschild, M., Schmidt, C., Ashwell, C., Persia, M., Reecy, J., Lamont, S.J. 2017. Genomic comparison of indigenous African and Northern European chickens reveals putative mechanisms of stress tolerance related to environmental selection pressure. Genes, Genomes, Genetics doi: https://doi.org/10.1534/g3.117.041228
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Fleming, D.S., Koltes, J.E., Fritz-Waters, E.R., Rothschild, M.F., Schmidt, C.J., Ashwell, C.M., Persia, M.E., Fulton, J., Reecy, J.M., Lamont, S.J. 2016. Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences. BMC Genomics 17:812. DOI 10.1186/s12864-016-3147-7
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bertolini, F., J.C.S. Harding, B. Mote, A. Ladinig, G.S. Plastow, M.F. Rothschild. 2017. Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks. Animal Genetics 48:228-32.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Talenti, A., F. Bertolini, G. Pagnacco, F. Pilla, P. Ajmone-Marsan, M.F. Rothschild, P. Crepaldi, the Italian Goat Consortium. 2017. The Valdostana goat: a genome-wide investigation of the distinctiveness of its selective sweep regions. Mammalian Genome 28:114-28.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Bertolini, F., A. Elbeltagy, M.F. Rothschild. 2017. Evaluation of the application of bovine, ovine and caprine SNP chips to dromedary genotyping. Livestock Research for Rural Development 29:2
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Bertolini, F., T. Yang, Y. Huang, J. Harding, M.F. Rothschild, G.S. Plastow. 2017. A Genomic Investigation of Porcine Periweaning Failure to Thrive Syndrome (PFTS). Plant & Animal Genome XX, San Diego, California. Abstract #W915
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Bertolini, F., M.F. Rothschild, the ADAPTmap Consortium. 2017. Linkage Disequilibrium Analysis Across 126 Goat Breeds of the Adaptmap Consortium. Plant & Animal Genome XX, San Diego, California. Abstract #P1101
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Bertolini, F., E. Rochat, S. Joost, B. Servin, P. Crepaldi, A. Stella, M.F. Rothschild. 2017. A worldwide investigation of the effects of climate selection on goat genomes. 2017. 36th International Society for Animal Genetics Conference, Dublin, Ireland. Abstract #MT362
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Bertolini, F., K. Zurbrigg, T. van Dreumel, T. OSullivan, M.F. Rothschild. 2017. Investigating the genomic basis of pigs that have died in transit. 36th International Society for Animal Genetics Conference, Dublin, Ireland. Abstract #MT246
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Bertolini, F., S. Bovo, M.F. Rothschild, L. Fontanesi. 2017. Mining the European Sea Bass (Dicentrarchus labrax) genome for the characterization of tandem repeat variability. 36th International Society for Animal Genetics Conference, Dublin, Ireland. Abstract #WT83
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Huang, J., M. Schroyen, Y. Nguyen, N. Gabler, D. Nettleton, J.C.M. Dekkers, C.K. Tuggle. 2017. Identifying tissue specific gene expression using RNAseq data from multiple porcine tissues. 25h Plant and Animal Genomics Conference, 14-18 January, San Diego, CA, US. Abstract P1163.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Trakooljul, N., H. Zhou, P. Ross., I. Korf, M.E. Delany, H. Cheng, C.K. Tuggle, C.Ernst, S. Ponsuksili, K. Wimmers. 2017. Comparative DNA Methylome of the Chicken and Pig: An Evolutionary Bridge Between Avian and Mammalian 25h Plant and Animal Genomics Conference, 14-18 January, San Diego, CA, US. Abstract P0274.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Liu, H., N. Manchanda 1, D. Nonneman, T.P.L. Smith, C.K. Tuggle 2017. Cataloguing multi-tissue transcriptomes by PacBio IsoSeq and Illumina RNA-seq, and its application in annotating new-generation swine reference genome assemblies: Lessons learned from and recommendations given. 25h Plant and Animal Genomics Conference, 14-18 January, San Diego, CA, US. Abstract P1162.


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

Outputs
Target Audience:Primary beneficiaries of NRSP-8 will be research scientists that are either engaged directly in animal genome research or utilize genomic data in complementary areas of animal science. Direct beneficiaries also include ever-increasing numbers of commercial animal breeders and producers who apply genomic data and related technologies to enhance aspects of animal health, welfare, productivity, and management, as well as, government agencies and breed organizations utilizing genomic methods for animal identification, disease surveillance, and regulatory monitoring. NRSP-8 will continue to be visible at national and international scientific meetings and workshops. A leading example is the annual International PAG Conference. NRSP-8 is showcased in species-specific and comparative genomics sessions, as well as through committee meetings where scientific presentations and reports are required from participating Experiment Stations. NRSP-8 has held its annual meeting jointly with PAG for >20 years, and NRSP-8 representatives play a major role in the organization and programming for this high profile international conference. Additionally the Swine Genome Coordinator publishes a newsletter that is read by a target audience that goes well beyond the actual members of NRSP, as it is circulated to over 3000 people who are scientists, students, and extension workers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?A PhD student, Jeremy Howard, (North Carolina State University), was competitively awarded a Neil Jorgenson Travel scholarship supported by the Swine Genome Coordination funds. A PhD student, Asher Haug-Baltzell, University of Arizona) was competitively awarded a Neil Jorgenson Travel scholarship supported by the Bioinformatics coordination funds. We also provided professional development to four researchers by partially supported their travel to speak at the 2016 Cattle/Swine joint and Swine Workshops at the PAG meeting: Randy Prather, University of Missouri, and Bruce Whitelaw, Roslin Institute, Cattle/Swine Workshop Min-Kyeung Choi, Konkuk University, and Francisco Peñagaricano, University of Florida, Swine Workshop. How have the results been disseminated to communities of interest?The Pig Genome Update was prepared and published two times in the reporting period, #123 and #124. The plans are to publish the Pig Genome Update approximately 2 times per year, timed for major genome activities. These will include a February issue, with a Plant and Animal Genome (PAG) meeting summary and descriptions of summer meetings and research opportunities, and an October issue with PAG meeting announcements and reminders. The PGU is emailed to over 3,000 recipients on the Angenmap mailing list. Both the Swine Genome and Bioinformatic Coordinators presented reports at the 2016 NRSP-8 Swine Subcommittee (January 9, 2016) as well as at the NRSP-Workshop on January 11, 2016, both coincided with the 2016 PAG meeting in San Diego, California. Three scientists reported on results from NRSP-8 seed funding projects at the PAG meeting in the Swine Workshop (F. Bertolinini et al., 2016) or in other sessions (Smith et al., 2016; Zhou et al., 2016). The Angenmap mailing list is being maintained and is being actively used; 308 individual messages were submitted to angenmap@animalgenome.org in the reporting period. What do you plan to do during the next reporting period to accomplish the goals? Continue to provide funding for travel of Coordinators and NRSP-8 Swine Subcommittee members to relevant meetings; these will include in FY 2015: Plant and Animal Genome Meetings, Midwest ASAS meeting, International Society of Animal Genetics. Continue to offer funding for appropriate research projects involving more than one Station. Report on activities at 2017 NRSP-8 meetings (January 2017). Continue to prepare Pig Genome Updates in FY 2017. Provide reports on funded seed projects to members of the NRSP-8 Swine Subcommittee. Finalize plan to provide new genotyping chip to NRSP-8 Committee members.

Impacts
What was accomplished under these goals? IMPACT: Genome sequence information has the potential for advancing knowledge relevant to human and animal health and for improved production efficiency and nutrient composition of animal-based food products. Through coordination, conferences, a database and financial support of the international cooperative effort to sequence the genes and genomes of agricultural animals, we continued to provide critical support for developing powerful experimental strategies that rely on improved description and understanding of the genes and their structures within complex genomes. We worked with and on behalf of researchers in the U.S. to effectively share, combine, manage, manipulate, and analyze information from genomics/genetics studies. In the past year, 313 TB of curated QTL data (animal qualitative traits data) were downloaded, which was accessed by over 18,875 unique users, in 125 countries. This access to and distillation of data from hundreds of publications dramatically reduces and streamlines the work for these researchers. Objective 1... Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. We provided additional funds to Dr. Huaijun Zhou, UC-Davis to sequence the small RNAs for all tissues funded by USDA-NIFA-AFRI, as well as add one tissue (small intestine) to the total. Further, the Coordinators paid for genome sequencing of the two pigs for which tissues were collected for the FAANG project (Yorkshire pigs). This sequencing data will be useful in mapping sequence-based assay data back to the pig genome; most if not all assays being used for the FAANG genome annotation are sequence-based. Objective 2... Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. Functional annotation will allow faster and more accurate genetic improvements, and help in further understanding of genomes as they relate to animal biology. However, because of the high cost in functional annotation assays, a major test is the organization and coordination of many interested research groups to share samples and protocols to efficiently and effectively produce such functional genomics data. To that end, the Bioinformatics and Swine Genome Coordinators have made multiple important contributions to FAANG. The Bioinformatics and Swine Genome Coordinators continue to have a major and ongoing role in the reporting year in the development of the organizational infrastructure of FAANG. Dr. Tuggle continued service as Co-Chair of the FAANG Steering Committee and is Chair of the FAANG Communications Subcommittee. Dr. Reecy continued to serve as co-Chair of the FAANG Bioinformatics and Data Analysis subcommittee. A meeting of FAANG was held October 7-8, 2015; both USDA-NIFA-AFRI money as well as NSF-IOS funds supported this meeting, as well as funds from Iowa State University and the Poultry, Sheep and Swine Genome Coordinators. The outcomes of this conference have been reported as project IOW05448. 2. A Symposium on FAANG was chaired by Chris Tuggle and funded by the American Society of Animal Science (ASAS), as the FAANG Symposium was held on the last day of the 2016 Joint meeting of ASAS, CSAS and other animal science related societies (July 23, 2016). This day was also the first day of the 2016 International Society of Animal Genetics (ISAG) meeting. This was a unique opportunity to bring together both animal geneticists and animal scientists to highlight functional genome annotation. This Symposium was organized by an ad hoc group, with input from the ISAG Genome Sequencing Workshop Committee (GSWC) chaired by Dr. Reecy. The format of this Symposium was primarily full-length or short talks by scholars in the field of functional genomics, as well as short descriptions of the FAANG project (introductory or current progress summaries). The current progress summary was followed by a short business meeting where it was proposed that the name of the GSW be replaced with Genome Sequencing and Annotation Workshop, and that annotation reports be a regular component of the workshop. This proposal passed and was subsequently approved by ISAG. An impact of this decision was to make permanent a commitment by ISAG to provide a forum for FAANG reporting. Another important impact was the exposure to animal science communities of FAANG and its goals; this was successful as more than 400 attended the Symposium, and included many attendees from both ASAS and ISAG. Supporting new FAANG related efforts: Recognizing that a bottleneck in the analysis of genomic data for the NRSP-8 project is bioinformatics expertise, a part-time postdoctoral position was proposed. This postdoc will be tasked with bioinformatic analysis of the PacBio Isoseq/Illumina RNAseq data being created, to maximize the use of these data. Additional projects on analysis of data from multi-station projects are projected. The Advisory Committee approved all uses of funds, and a search for a qualified person to fill this position is underway. Objective 3... Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest. During this reporting period, the NRSP-8 website (animalgenome.org) had 45,486,097 hits, by 342,922 unique users from 152 countries. The website supports international internet discussion and information sharing in the broad fields of animal genome research (http://animalgenome.org/community/angenmap/) with active discussions and information exchanges. By the end of 2016 this group had over 3,000 members from 63 countries/regions of the world. One of our supported databases, the Animal QTLdb (http://www.animalgenome.org/QTLdb) has been accessed by 18,875 unique users from 125 countries where they downloaded 31 TB of curated QTL data. These accession numbers do not included users that access our curated data via NCBI, Ensembl, UCSC, or Reuters Data Citation Index. Throughout 2016, NAGRP bioinformatics team members have continued their efforts to make improvements and curate new data into the database. In 2016, a total of 57,229 new QTL/association data have been curated into the database, representing a 47% data increase from a year ago. Currently, there are 16,516 curated porcine QTL, 95,332 curated bovine QTL, 6,633 curated chicken QTL, 1,245 curated horse QTL, 1,412 curated sheep QTL, and 127 curated rainbow trout QTL in the database (http://www.animalgenome.org/QTLdb/). All data have been ported to NCBI, Ensembl, and UCSC genome browser in a timely fashion. Users can fully utilize the browser and data mining tools at NCBI, Ensembl, and UCSC to explore animal QTL/association data. In addition, we have continued to improve existing and add new QTLdb curation tools and user portal tools, e.g., accommodation of multiple genomes for QTL/association mapping, allowing the inclusion of "supplementary data" to QTL/association publications as part of the supporting evidence to curated data.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bertolini F., J. Harding, B. Mote, G.S. Plastow, and M.F. Rothschild. 2016. Genomic differences between pre-weaning survival and mortality of piglets following PEDV outbreaks. Plant & Animal Genome XXIV, San Diego, California. Abstract #W912
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Smith, T.P.L. S. Koren, A. Phillippy, D.M. Bickhart, B. D. Rosen, K. C. Worley, S. G. Schroeder, B. L. Sayre, I. Liachko, S. T. Sullivan, J. N. Burton, A. R. Hastie, T. S. Sonstegard, C. M. Kelley, A. L. Archibald, M. Watson, R. Green, J. Chin, D. Nonneman, G. A. Rohrer, C. K. Tuggle, H. Liu, 140. D.C. Ciobanu, J.F. Medrano, A. Zimin, S. J. Schultheiss, D. E. Hagen, C. G. Elsik, B. Dalrymple, J. W. Kijas, N. Cockett, and M. P. Heaton. Approaches Taken, Progress Made, and Enhanced Utility of Long Read-based Goat, Swine, Cattle and Sheep Reference Genomes Proceedings of Plant and Animal Genome XXIV. San Diego, CA, USA. Abstract #W635.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Tuggle, C.K., E. Giuffra, E., S.N. White, L. Clarke, H. Zhou, P.J. Ross, H. Acloque, J.M. Reecy, A. Archibald, R.R. Bellone, M. Boichard, A. Chamberlain, H. Cheng, R.P.M.A. Crooijmans, M.E. Delany, C.J. Finno, M.A.M. Groenen, B. Hayes, J.K. Lunney, J.L. Petersen, G.S. Plastow, C.J. Schmidt, J. Song, M. Watson. 2016. GO-FAANG: a Gathering On Functional Annotation of ANimal Genomes. Animal Genetics 47:528-33.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hu Z.L., Park C.A., Reecy J.M. 2016. Developmental progress and current status of the Animal QTLdb. Nucleic Acids Res 44(D1):D827-833.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Hu, Z.-H. C. Park, J.M. Reecy. 2016. Animal QTLdb: Towards a Comprehensive Database and Tool for Livestock Genome Research. Plant and Animal Genome meeting, San Diego, CA. Abstract #P0334


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

Outputs
Target Audience:Primary beneficiaries of NRSP-8 will be research scientists that are either engaged directly in animal genome research or utilize genomic data in complementary areas of animal science. Direct beneficiaries also include ever-increasing numbers of commercial animal breeders and producers who apply genomic data and related technologies to enhance aspects of animal health, welfare, productivity, and management, as well as, government agencies and breed organizations utilizing genomic methods for animal identification, disease surveillance, and regulatory monitoring. NRSP-8 will continue to be visible at national and international scientific meetings and workshops. A leading example is the annual International PAG Conference. NRSP-8 is showcased in species-specific and comparative genomics sessions, as well as through committee meetings where scientific presentations and reports are required from participating Experiment Stations. NRSP-8 has held its annual meeting jointly with PAG for >16 years, and NRSP-8 representatives play a major role in the organization and programming for this high profile international conference. Additionally, the Swine Genome Coordinator publishes a newsletter that is read by a target audience that goes well beyond the actual members of NRSP, as it is circulated to over 3000 people who are scientists, students, and extension workers. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Travel of several project scientists was partially funded to attend important pig genomics meetings in this reporting period, including the Midwest American Society of Animal Science meetings in Des Moines, IA (March 2015); GO-FAANG Workshop in Washington DC, and the Plant and Animal Genome meeting (January 2015). A MS student, Melanie Trenhaile (University of Nebraska-Lincoln), was competitively awarded a Neil Jorgenson Travel scholarship, which was supported by the Swine Genome Coordination funds. A PhD student, Asher Baltzel (University of Arizona) was competitively awarded a Neil Jorgenson Travel scholarship, which was supported by the Bioinformatics coordination funds. How have the results been disseminated to communities of interest?During this reporting period, the NRSP-8 website (animalgenome.org) had 13,263,199 hits, by 522,664 unique users from 162 countries. The website supports an international internet discussion and information sharing group, in the broad fields of animal genome research (animalgenome.org/community/angenmap/). There were 382 unique discussions. In addition, 13,613 unique users, in 109 countries accessed the Animal QTLdb, at animalgenome.org/QTLdb where they downloaded 21,251 GB of curated QTL data (animal qualitative traits data). The Pig Genome Update was prepared and published 3 times in the reporting period. This newsletter is published three times per year, timed for major genome activities. These include a February issue, with a PAG summary, a June issue describing summer meetings and research opportunities, and an October issue with PAG meeting announcements and reminders. Both the Swine Genome and Bioinformatic Coordinators presented reports at the 2015 NRSP-8 at the NRSP-Workshop on January 11, 2015, which coincided with the 2015 Plant and Animal Genome meeting in San Diego, California. The Swine Genome Coordination funds supported travel of Huaijun Zhou (UC-Davis) to travel to the Midwest American Society of Animal Science meetings in Des Moines, IA in March 2015 where he presented a talk on the NRSP-8 and National Pork Board supported FAANG project initation. The NRSP-8 "What's New" update was prepared and published 3 times in the reporting period. This newsletter is timed to occur every four months. These include a January issue, with PAG update, and a May and September issue with general announcements and reminders. What do you plan to do during the next reporting period to accomplish the goals? Continue to improve and develop an international website (faang.org) for the purposes of coordinating and facilitating the sharing of data internationally, and to establish an infrastructure for analysis of these data in order to accelerate identification of all functional elements in animal genomes. Continue to maintain and update project websites. Develop a plan to provide new genotyping chip to NRSP-8 committee members. Plan and organize a GO-FAANG meeting for October 2015. Provide funding for travel for attendance at NRSP-8 meetings January 2016 by project scientists and students. Continue to provide funding for travel of project coordinators and NRSP-8 Bioinformatics and Swine members to relevant meetings. Continue to offer to provide funding for appropriate research projects involving more than one Experimental Station. Report on activities at the 2016 NRSP-meetings. Continue to prepare Bioinformatics What's new and Pig Genome Updates in FY 2016.

Impacts
What was accomplished under these goals? Partial and complete DNA sequencing of agricultural animals is underway internationally. Genome sequence information has the potential for advancing knowledge relevant to human and animal health and for improved nutrient composition of animal-based food products. NRSP-8 provides critical support for developing powerful experimental strategies that rely on improved description and understanding of the genes and their structures within complex genomes. This project year, we provided partial matching funding ($13,000) for a new initiative to better understand the functioning of genomes: the Functional Annotation of Animal Genomes (FAANG) project. The project was approved and funded at $500,000 from USDA-NIFA. We organized support from the National Pork Board for this project, which provided an additional $30,000. This newly funded and initiated NIFA project lays the foundation for the U.S. to become a leader in functional annotation, which will facilitate faster and more accurate genetic improvements in agricultural animals. In this project year, we also provided needed funding for important animal research on PEDV genetic resistance which is underway, and for the validation of a promising new genotyping tool. Additionally, we worked with and on behalf of researchers in the U.S. to effectively share, combine, manage, manipulate, and analyze information from genomics/genetics studies. In the past year, 21,251 GB of curated QTL data (animal qualitative traits data) were downloaded, which was accessed by over 13,613 unique users, in 109 countries. Objective 1) Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals. We reviewed and approved a proposal submitted by Jack Dekkers, Iowa State University, in collaboration with partners at Michigan State University's USDA Molecular Genetics Laboratory, to validate the new Affymetrix 650K Genechip (a new high density genotyping tool) using U.S. breeds, and provide initial data on integration with 60K genotype data. When completed, the study will provide relevant and needed information to the U.S. animal science industry regarding this new research tool. We reviewed and approved a proposal by Tim Smith and Dan Nonneman at the U.S. Meat Animal Research Center (USMARC) in Nebraska, in collaboration with Chris Tuggle, Iowa State University, to add additional tissues to a PacBio IsoSeq project for functional annotation of the genome of the animal whose genome is being sequenced at USMARC. This will provide more detailed and specific information on long sequences for major tissues in the adult pig and provide more accurate assembly of gene sequences. This is a new partnership between Iowa State University and a USDA government lab. Objective 2) Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. The tremendous power of genome-wide variant analysis is leading to the identification of markers linked to important traits in agricultural animal species. NRSP-8 support is critical to developing powerful experimental strategies that rely on improved description and understanding of the genes and their structures within complex genomes. However, an important component of such research is understanding the function of the many variants found to be associated with such important traits. Functional annotation will allow faster and more accurate genetic improvements; yet a major test is the organization and coordination of many interested research groups to share samples and protocols to efficiently and effectively produce such functional genomics data on the same or similar samples. To that end, the Bioinformatics and Swine Genome Coordinators are well-positioned to help such coordination efforts, and have made multiple important contributions to FAANG. Supporting new FAANG related projects: This project year, the Swine Genome Coordinators provided matching funding for a new initiative to better understand the functioning of genomes: the Functional Annotation of Animal Genomes (FAANG) project. The project was approved and funded at $500,000 from USDA-NIFA. The National Pork Board provided an additional $30,000. The international project was initiated at UC-Davis during this project reporting period. This newly funded NIFA project lays the foundation for the U.S. to become a leader in functional annotation. Leadership in FAANG project development: The Bioinformatics and Swine Genome Coordinators have a major and ongoing role in the reporting year in the development of the organizational infrastructure of FAANG. They both played a significant role in publishing the FAANG white paper in 2015; Dr. Tuggle was a co-corresponding author. Dr. Tuggle serves as Co-Chair of the FAANG Steering Committee and is Chair of the FAANG Communications Subcommittee. Dr. Reecy is co-Chair of the FAANG Bioinformatics and Data Analysis subcommittee. Dr. Tuggle organized a meeting of FAANG at the 2015 Plant and Animal Genome meetings in which over 50 scientists attended, and submitted and obtained funding from National Science Foundation and USDA-NIFA-AFRI to organize a meeting of FAANG to be held in October 2015. Objective 3) Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest. During this reporting period, the NRSP-8 website (animalgenome.org) had 13,263,199 hits, by 522,664 unique users from 162 countries. The website supports an international internet discussion and information sharing group, in the broad fields of animal genome research (animalgenome.org/community/angenmap/). There were 382 unique discussions. In addition, 13,613 unique users, in 109 countries accessed the Animal QTLdb, at animalgenome.org/QTLdb where they downloaded 21,251 GB of curated QTL data (animal qualitative traits data). Throughout 2015, the NAGRP bioinformatics team has continued their efforts to make improvements to the database. The team facilitated the addition of gene network analysis data and improved search tools and data analysis tools. The QTL database numbers noted above, include the Pig Genome Database numbers. It also continues to receive considerable updating through the work of the Bioinformatics team. The PigQTLLdb (http://www.animalgenome.org/QTLdb/pig) is an excellent resource for sharing QTL (animal qualitative trait data) and for making comparisons within and between species. To date, there have been 14,479 pig QTLs from 507 publications curated into the database, a four percent increase from the last report period. The QTLs represent 592 different traits.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Smedley, D, S Haider, S Durinck, L Pandini, P Provero, J Allen, O Arnaiz, MH Awedh, P Baldock, G Barbiera, et al: The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Elisabetta Giuffra. 2015. Update on the Functional Annotation of ANimal Genomes (FAANG) initiative. Presented at Science Animale Paris Saclay (SAPS), Jouy-en-Josas, France, July 10, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Huaijun Zhou. 2015. Annotation of Functional Regulatory Elements in Livestock Species. Presented at the ASAS Midwest Convention at Des Moines, IA, USA, Mar. 17, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Elisabetta Giuffra, 2015. The Functional Annotation of the Animal Genomes (FAANG) initiative. Presented at the Plant and Animal Genome conference at San Diego, CA, USA, Jan. 10-14, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Tixier Boichard. 2015. A national infrastructure project to connect Biological Resource Centers for domestic animals. Presented at FR-AgENCODE kick off, Paris, France, Feb. 6, 2015.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: The FAANG Consortium. 2015. Coordinated International Action to Accelerate Genome to Phenome, The Functional Annotation of Animal Genomes (FAANG) Project. Genome Biology 2015, 15:57.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bickhard DM, JL Hutchinson, RD Schnabel, JF Taylor, JM Reecy, S Schroeder, CP Van Tassel, TS Sonsstegard, GE Liu. 2015. RAPTR-SV: a hybrid method for the detection of structural variants. Bioinformatics 2015, Jul 1;31(13):2084-90.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Laura Clarke. 2015. FAANG: Data Management Opportunities, Challenges and Connections to the Pilot Projects. Presented at FR-AgENCODE kick off, Paris, France, Feb. 6, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Thomas Derrien. 2015. Non-coding RNAs in the human ENCODE project: perspectives for "non-model" organisms. Presented at FR-AgENCODE kick off, Paris, France, Feb. 6, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Ian Streeter, David Richardson, et al. 2015. The FAANG project's commitment to data standards, annotation and sharing. Poster presented at: International Symposium on Animal Functional Genomics, Piacenza, Italy, July 27-29 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Laura Clarke, Alan Archibald, et al. 2015. The Functional Annotation of Animal Genomes: Data Standards, Annotation and Sharing. Poster presented at: Plant and Animal Genome conference at San Diego, CA, USA, Jan. 10-14, 2015.
  • Type: Websites Status: Published Year Published: 2013 Citation: Hu et al. 2013 (on-going). National Animal Genome Research Program website. http://www.animalgenome.org (See http://www.animalgenome.org/default/info.html for USDA acknowledgement.)


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

Outputs
Target Audience:Primary beneficiaries of NRSP-8 will be research scientists that are either engaged directly in animal genome research or utilize genomic data in complementary areas of animal science. Direct beneficiaries also include ever-increasing numbers of commercial animal breeders and producers who apply genomic data and related technologies to enhance aspects of animal health, welfare, productivity, and management, as well as, government agencies and breed organizations utilizing genomic methods for animal identification, disease surveillance, and regulatory monitoring. NRSP-8 will continue to be visible at national and international scientific meetings and workshops. A leading example is the annual International PAG Conference. NRSP-8 is showcased in species-specific and comparative genomics sessions, as well as through committee meetings where scientific presentations and reports are required from participating Experiment Stations. NRSP-8 has held its annual meeting jointly with PAG for >16 years, and NRSP-8 representatives play a major role in the organization and programming for this high profile international conference. Additionally the Swine Genome Coordinator publishes a newsletter that is read by a target audience that goes well beyond the actual members of NRSP, as it is circulated to over 3000 people who are scientists, students, and extension workers. 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?The Pig Genome Update was prepared and published two times in the reporting period, #119 and #120. The plans are to publish the Pig Genome Update approximately 3 times per year, timed for major genome activities. These will include a February issue, with a PAG summary, a June issue describing summer meetings and research opportunities, and an October issue with PAG meeting announcements and reminders. Both the Swine Genome and Bioinformatic Coordinators presented reports at the 2014 NRSP-8 Swine Subcommittee (January 11, 2014) as well as at the NRSP-Workshop on January 12, 2014, both coincided with the 2014 Plant and Animal Genome meeting in San Diego, California. The Angenmap mailing list is being maintained and is being actively used; 283 individual messages were submitted to angenmap@animalgenome.org in the reporting period. What do you plan to do during the next reporting period to accomplish the goals?Continue to provide funding for travel of Coordinators and NRSP-8 Swine Subcommittee members to relevant meetings; these will include in FY 2015: International PRRS meeting, Plant and Animal Genome Meetings, Midwest ASAS meeting, International Symposium on Animal Functional Genomics. Continue to offer funding for appropriate research projects involving more than one Station. Report on activities at 2015 NRSP-8 meetings (January 2015). Continue to prepare Pig Genome Updates in FY 2015. Develop plan to provide new genotyping chip to NRSP-8 Committee members.

Impacts
What was accomplished under these goals? Impact statement: Iowa scientists in the NRSP-8 Program have played a major role in enabling genomic discoveries in livestock animals. We have developed human resources through transitioning to new researchers in the Swine Genome Coordinatorship, and improved our policy-making through developing an external advisory committee. We have increased communication of animal genome research data by providing support for members of NRSP-8 to travel to important genetics and genomics meetings to present results and learn of research by others. We have expanded the research on genomics thorugh providing funding to initiate new research on surviviability to porcine viral infection and on collecting functional genomics data on a set of tissues. We have increased the availability of genomic information through continued upgrading of on-line genome databases. Details of these impacts and project are provided below under specific NRSP-8 Goals. Across all objectives, the NRSP-8 provides technologies and support to enable genomic research, and to disseminate data and genetic samples to advance animal genomics research. Goal (1) Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals An important impact of NRSP-8 efforts is the development of human resources, and the Swine Genome Coordinatorship transitioned from Dr. Max Rothschild (Iowa State University, ISU) to Dr. Christopher K. Tuggle (ISU) and Dr. Catherine Ernst (Michigan State University). As well, the annual NRSP-8 meetings provide the opportunity to communicate new results and develop core infrastructure and leadership discussions necessary for organizing these efforts, including sharing of DNA resources, collaborative use of computational power, and community-based annotation. Travel funding has been provided to encourage new membership, and attendance by existing members, as well as support presentations on new results by scientists at the NRSP-8 Workshop. For example, travel was partially funded to attend the 2014 NRSP8 pig genomics meeting. These included: Melissa Merrill, NRSP8 Swine Genome Subcommittee new member; Chris Eisley, 2014 Neal Jorgenson Travel Award winner, and Joan Lunney, 2014 Distinguished Lecturer NRSP-8 Workshop. Goal (2) Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. The tremendous power of genome-wide variant analysis is leading to the identification of markers linked to important production traits in agricultural animal species. NRSP-8 support is critical to developing powerful experimental strategies that rely on improved description and understanding of the genes and their structures within complex genomes. A major way NRSP-8 funds are used is to support community activities to find associations with many different traits. One of the first accomplishments under the new swine genome leadership was to develop more formal policy advising through development of an Advisory Committee, which will provide guidance on policy as well as help evaluate requests for funding. The members of this Advisory Committee represent the swine industry, swine genomics and biotechnology researchers, NRSP-8 Stations and participating USDA labs. The members are: Jack Dekkers (ISU), Chris Hostetler (National Pork Board), Joan Lunney (USDA-BARC), Randy Prather (U. Missouri), and Juan P. Steibel (MSU). In 2014, a policy was developed and approved by the Advisory Committee that for swine genomics projects to be eligible for NRSP8 Coordination support, the project must materially involve two or more NRSP8 member groups (university or ARS research locations) and that substantial funding will only be provided for projects that have matching funding from another agency. In FY 2014 one project was approved to work toward a genetic analysis of PEDV resistance, and another was guaranteed matching funding for a USDA-AFRI proposal to work on functional annotation of the swine genome. Goal (3) Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest. This bioinformatic capacity is a critical component of infrastructure support enabled by NRSP-8. The Pig Genome Database continues to receive considerable updating through the work of the Bioinformatics team. The PigQTLdb (http://www.animalgenome.org/QTLdb/pig) is an excellent repository for QTL and candidate gene association results. As of Sept 30, 2014, in the Animal QTLdb there are >10,000 pig QTLs from >350 publications curated into the database. Throughout 2014, the NAGRP bioinformatics team has continued their efforts to make improvements to the Animal QTLdb, which includes a new mirror site in China, facilitate the addition of gene network analysis data, improved search tools and data analysis tools. Users are encouraged to register an account to enter new QTL data. Details are available from http://www.animalgenome.org/QTLdb. In addition, the pig genome build 10.2 annotations are continuing to be updated in the BioMart (http://www.animalgenome.org:8181) and for the Animal QTLdb.

Publications