Source: WASHINGTON STATE UNIVERSITY submitted to
GENOME DATABASE FOR ROSACEAE: EMPOWERING SPECIALTY CROP RESEARCH THROUGH BIG-DATA DRIVEN DISCOVERY AND APPLICATION IN BREEDING
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1005850
Grant No.
2014-51181-22376
Cumulative Award Amt.
$2,741,575.00
Proposal No.
2014-07929
Multistate No.
(N/A)
Project Start Date
Sep 1, 2014
Project End Date
Aug 31, 2019
Grant Year
2014
Program Code
[SCRI]- Specialty Crop Research Initiative
Recipient Organization
WASHINGTON STATE UNIVERSITY
240 FRENCH ADMINISTRATION BLDG
PULLMAN,WA 99164-0001
Performing Department
Horticulture
Non Technical Summary
This project will further expand the Genome Database for Rosaceae and provide scientists working on almond, apple, cherry, peach, pear, raspberry, strawberry and other members of this family with centralized access to all of the publicly available trait, genes and marker data as well as querying tools needed toenable their research. It will also further develop the generic database system tripal and provide educational resources for industry stakeholders and the public on research in this important family of crops.
Animal Health Component
40%
Research Effort Categories
Basic
40%
Applied
40%
Developmental
20%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011110108010%
2011110108110%
2011114108010%
2011114108110%
2011122108010%
2011122108110%
2011123108010%
2011123108110%
2011112108010%
2011112108110%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1114 - Peach; 1110 - Apple; 1112 - Cherry; 1122 - Strawberry; 1123 - Raspberry;

Field Of Science
1081 - Breeding; 1080 - Genetics;
Goals / Objectives
Objective 1: Collect, analyze, curate and integrate genomics, genetics and breeding data for Rosaceae to facilitate cross-species data utilization and translational discovery.Objective 2: Provide data-mining resources for basic scientists and breeders to facilitate knowledge discovery and expedite development of Rosaceae cultivarsObjective 3: Extend community outreach in genomics, genomics-assisted breeding, and crop management.
Project Methods
Objective 1: Collect, analyze, curate and integrate genomics, genetics and breeding data to facilitate cross-species data utilization and translational discovery.We will integrate the exponentially growing volume of Rosaceae "big data." These data include whole genome sequencing and annotation/re-annotation of several species, re-sequencing to find and score polymorphisms, RNA-seq for expression profiling or coding variant identification and small RNA sequencing. In addition, high throughput genotyping using SNP arrays and large-scale standardized phenotyping are also generating immense amounts of data. The recent advent of big data necessitates new ways of data storage, integration and presentation for the data to be readily utilized for further studies and applications. We (Main, Jung, Gasic, Blenda) will continue to collect, analyze, curate and integrate genomic, genetic and breeding data, developing appropriate strategies to integrate these new big data with existing data in GDR to maximize utility to the research community. Data collection will involve computational download, literature curation and direct submission from researchers. The approach and methods we will employ for collection, curation, and computational analysis of each type of data are described below.Objective 2: Provide data-mining resources for basic scientists and breeders to facilitate knowledge discovery and expedite development of cultivars.We will build a custom query builder to enable scientists to fully utilize genomic, genetic, genotypic and phenotypic data for fundamental biology research. The custom query builder will allow users to construct sophisticated queries and save them for future reference and use. Users will be able to download the files with the data types they select in addition to the predefined files.Objective 3: Extend community outreach in genomics, genomics-assisted breeding, and crop management.The Genome Database for Rosaceae (GDR) contains massive amounts of information being used to conduct research in Rosaceae crops around the world. However, the potential impact of this research and the success stories being afforded by the use of this information is not being advertised by those in the scientific community or with industry stakeholders. It is essential that these success stories are publicized and open communication is facilitated within the scientific community and to stakeholders.We will use a variety of communication platforms to disseminate information to the scientific community and to industry stakeholders. A newsletter will be established and disseminated to the GDR listserve, which is a collection of scientific community members, students and outreach specialists interested in Rosaceae genomics, genetics, and breeding. This newsletter will be published two times per year (January and June) in both .pdf format and in a digital format (Bluetoad Digital Publishing, Orlando, FL) for posting on the GDR website and distribution on the listserve. Popular press articles focusing on improved efficiencies in Rosaceae crop production and fruit/tree quality will be published in cooperation with fruit industry news magazines as project successes are published in peer-reviewed journals by members of the scientific community.We will additionally host webinars (1-2/year) focusing on how to utilize features of GDR including genome exploration, the Breeders' Toolbox and Cross Assist to increase usage of the database. Hands-on technical workshops and presentations on advances in GDR and Tripal database capabilities will be conducted at national and international scientific meetings to benefit the scientific and database community.

Progress 09/01/14 to 08/31/19

Outputs
Target Audience:The target audience is predominantly Rosaceae scientists, breeders, bioinformaticists, data scientists, database developers, both national and international, as well as, U.S. industry stakeholders. Scientists have been engaged through 7 peer-reviewed publications and 1in review, 2 training workshops and 2 webinars, 13 presentations at 5 scientific conferences and meetings, focus groups, emails to the GDR mailing list, and quarterly meetings of the community U.S. Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC), who serve as the GDR Steering Committee. Breeders have been engaged through hands-on training and use of the Breeding Information Management System and through a US breeding capacity survey, with program details made available through the NRSP10 site. Bioinformaticists, data scientists and database developers have been engaged through participation in monthly meetings on Tripal software, release of new versions of Tripal and extension modules, the tripal.info website, a two day in-person hackathon, monthly Agricultural Biological Database (AgBioData) group meetings, peer-reviewed publications, and presentations at conferences and meetings. Industry stakeholders are being engaged through presentations and interactions at commodity group meetings and advisory committee meetings. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training opportunities for undergraduate, graduate and postdoctoral researchers included participation in hackathons, presentations and participation at workshops, conferences, and meetings, and authorship on peer-reviewed publications. In addition, three developers attended the DrupalCon in Year 5 of this award. How have the results been disseminated to communities of interest?In year 5 outputs and activities updates were presented at one face-to-face and three online quarterly meetings. Regular updates to GDR were sent through the users mailing list and components of the GDR project were presented on 13 occasions at one local (Washington State Tree Fruit Association Annual Meeting), two national (2019 American Society of Horticultural Science Annual Conference, 2019 Annual RosBREED Meeting) and two international conferences (2019 Plant and Animal Genome Conference, 2019 Joint American Society Plant Biology) as well as seven published peer-reviewed publications in year 5 and 1more under review. An NRSP10 workshop was held at the Plant and Animal Genome Conference with over 60 participants as well as a one-day BIMS training workshop held for RosBREED breeders with 22 participants. Tripal database developer meetings were held as well as a 2 day in-person hackathon, support was provided to groups implementing Tripal databases and the Tripal website (tripal.info) kept current with new developments, and module releases. The team participated in: monthly AgBioData meetings; the AgBioData workshop at the Plant and Animal Genome Conference; monthly meta data ontology working group meetings; the AgBioData database booth at PAG and ASPB; and at the annual participants meeting of the SCRI RosBREED project. In year 5 of this SCRI project, GDR was accessed by 34,621 users from 164 countries during 81,893 visits, with 731,361 pages viewed. Of the 24,331 visitors, 12,807 were from the US with all US states and territories represented. The top ten states using GDR in year 5 of this project were NY, IL, CA, VA, WA, OR, PA, MI, FL and TX. According to google scholar metrics, GDR was cited in 193 publications in 2018 and 164 times in the first 10 months of 2018. Over the last 5 years of this project, 2,097,920 GDR pages have been viewed during 298,615 visits and GDR was cited in more than 1000 publications. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? (a) Impact of Project GDR is an up to date, curated and integrated, internationally recognized database resource for Rosaceae species. It includes crops such as almond, apple, apricot, blackberry, cherry, peach, pear, plum, rose, and strawberry, with an annual US value of production exceeding $15 B in 2017. With over 114,000 users from 186 countries, 2.1 M pages accessed since 2014, GDR is widely used and has been cited in over 1000 scientific publications. It serves the community as a source of genomics, genetics and breeding data and analysis tools, facilitating research discovery, translation and application for this economically and biologically important crop family. As one of the founding Tripal databases, the GDR team are proactive in leading developing and supporting adoption of this generic, open-source and resource-efficient database platform for genomics, genetics and breeding research. Over 150 databases are now using this platform, with 8 research groups actively collaborating, developing and sharing modules for new functionality. (b) Activities related to these accomplishments in year 5 are summarized as follows: New functionality and data added to GDR in Year 5 include: (1) Curation and addition of large scale genomic data - (a) 9 new genome assemblies and annotations and 1 new annotation added for almond, plum, flowering cherry, strawberry, apple and pear species: almond (Prunus dulcis Texas v2.0 and Prunus dulcis Lauranne v1.0), plum (Prunus domestica Draft Genome v1.0), flowering cherry (Prunus yedoensis v1.0, Cerasus x yedoensis Somei-Yoshino v1.0), strawberry (Fragaria x ananassa Camarosa v1.0, Fragaria vesca v4.0.a2), apple (Malus x domestica HFTH1 v1.0), and pear (Pyrus bretschneideri DangshanSuli v1.1, Pyrus communis Bartlett DH v2.0), all with GDR analyzed functional annotation available to, browse, search and download, (b) reference transcriptome for Rosa genus built and made available, transcriptome data of Rubus idaeus 'Heritage' fruit available, transposable Elements detected from six genome assembly data by RepetDB available to view from the genome browser and for download, (c) Conducted major synteny analysis across 18 major rosaceae genomes to include data from 9 new genome assemblies/annotations, added results to database and enabled visualization of syntenic blocks and orthologs in Synteny Viewer, (d) alignments of F. x ananassa 90K SNP to F. x ananassa genome v1.0 and F. vesca v2.0 and markers aligned to P. persica v2.0 available to download, search and in the genome browser and (e) added 596,970 genes and 673,747 mRNAs to database, aligned to respective genomes and made available to view in the genome browser, search and download from the gene/transcript search page. (2) Curation and addition of genetic data - (a) curated data from 32 publications, (b) added 89 genetic maps, (b) added 41 QTL/MTL and more trait ontology developed to describe traits for QTL, (c) added 147,358 markers and (d) collected and standardized accession names of the phenotype and genotype data of apple, peach, and strawberry from the RosBREED project. (3) Web interface and analysis pipeline development - (a) new MegaSearch, allowing users to customize dataset and fields to view and download for any type of data in GDR, (b) data template for genetic and breeding data loader includes columns to choose trait ontology to allow ontology association by breeders and data submitters, (c) QTL search results linked to the new Genetic Map Viewer to display QTLs in the entire map as well as in each linkage group along with the markers (related to Enhance Trait Locus Warehouse), (d) MapViewer being further developed to display genome data to enable users to go from QTLs in a genetic map to view polymorphism data in the genome viewer for new marker development (related to Enhance Marker Converter), (e) more functionality added to the Breeding Information Management System (BIMS) including loading/searching/downloading genotype data, searching crosses, searching data using custom categories, restricting datasets and then comparing trait statistics using various categories. (4) Outreach - (a) held one day BIMS training workshop to train Rosaceae breeders on use of BIMS and the Field Book App. It was attended by 22 people representing 12 Rosaceae breeding programs, (b) held 2 BIMS webinars for Rosaceae breeders, (c) presented the project through 7 peer-reviewed publications, 13 presentations at 5 conferences/meetings, and twelve brochures (d) actively participated in agricultural biological database (AgBioData) monthly and workshop meetings (e) actively participated in Tripal community developer meetings and (f) provided support for Tripal adoption and module development including several online training sessions. GDR by the numbers: By the end of year 5 of this project, GDR contained the following data: 31 genomes for 15 species; 1,125,860 genes and 1,259,321 mRNAs; 338 genetic maps; 3,421,788 markers; 3,941 trait loci; 11,189,181 genotypes; 389,191 phenotypes; 14,452 germplasm; 1,972 species, and 7,935 publications.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Jung, S., Lee, T., Chung, C-H., Buble, K., Zheng, P., Yu, J., Humann, J., Ficklin S.P., Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Evans, K., Peace, C., Olmstead, M., DeVetter, L.W., McFerson, J., Coe, M., Wegrzyn, J.L., Staton, M.E., Abbott, A.G., Main, D. (2018). 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Research, 41(D1):1137-1145.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T. Z., Birkett, C., Cannon, S., Carson, J., Bondon, B., Cooper, L., Dunn, N., Elsik, C.G., Farmer, A., Ficklin, S. P., Grant, D., Grau, E., Herndon, N., Hu, Z-L., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M-A., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C. J., Munoz-Torres, M. C., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L-A., Sen, T. Z., Staton, M., Subramaniam, S>, Tello-Ruiz, M. K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M., Yu, J., Main, D. (2018). AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database, bay088.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Wegrzyn, J.L., Staton, M.A., Street, N., Main, D., Grau, E., Herndon, N., Buehler, S., Falk, T., Zaman, S., Ramnath, R., Richter, P., Sun, L., Condon, B., Almsaeed, A., Chen, M., Mannapperuma C., Jung, S., Ficklin, S. (2019). Cyberinfrastructure to improve forest health and productivity: the role of tree databases in connecting genomes, phenomes, and the environment. Frontiers in Plant Science, 10, 813.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Spoor, S., Cheng, C-H., Sanderson, L-A., Condon, B., Almasaeed, A., Chen, M., Bretaudeau, A., Rasche, H., Jung, S., Main, D., Bett, K., Staton, M., Wegrzyn, J.L., Feltus, F.A., Ficklin, S.P. (2019). Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. Databases, baz077.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Peace, C. P., Bianco, L., Troggio, M., Van de Weg, E., Howard, N. P., Cornille, A., Durel, C-E., Myles, S., Migicovsky, Z., Schaffer, R.J., Costes,E., Fazio,G., Yamane, H., van Nocker, S., Gottschalk, C., Costa, F., Chagn�, D., Zhang, X., Patocchi, A., Gardiner, S.E., Hardner, C., Kumar, S., Laurens, F., Bucher, E., Main, D., Jung, S., Vanderzande, S. (2019). Apple whole genome sequences: recent advances and new prospects. Horticulture Research, 6(1), 59.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Aranzana, M.A., Decroocq, V., Dirlewanger, E., Eduardo, I., Gao, Z.H., Gasic, K., Iezzoni, A., Jung, S., Peace, C., Prieto, H., Tao, R., Verde, A., Abbott, A.G., Ar�s, P. (2019). Prunus genetics and applications after de novo genome sequencing: achievements and prospects. Horticulture Research, 6, 58.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Buble, K., Jung, S., Humann, J.L., Yu, J., Cheng, C-H., Lee, T., Ficklin, S.P., Hough, H., Condon, B., Staton, B., Wegrzyn, J., Main, D. (2019). Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps. Databases, baz100.
  • Type: Journal Articles Status: Under Review Year Published: 2019 Citation: Liu, Z., Ma, H., Jung, S., Main, D., Guo, L. Developmental mechanisms of fleshy fruit diversity in Rosaceae. Annual Review of Plant Biology (in review).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: McFerson, J., Jung, S., Lee, T., Cheng, C-H., Hough, H., Gasic, K., Ficklin, S., Coe, M., Main, D. (2018). Genome Database for Rosaceae. Proceedings from the Washington State Tree Fruit Association Annual Meeting, December 3-5, 2018; Yakima, WA, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Zurn, J.D., Driskill, M., Jung, S., Main, D., Yin, M.H., Clark, M., Cheng, L., Clark, J.R., Worthington, M., Finn, C.E. and Bassil, N.V. (2019). Leveraging Synteny across Rosaceae to Identify Loci Controlling Fruit Sweetness in Blackberry. Proceedings of the ASHS Annual Conference; July 21-25, 2019; Las Vegas, NV, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Staton, M., Condon, B., Wegrzyn, J.L., Main, D., Ficklin, S.P. and Almsaeed, A. (2019). Data Federation in the Tripal Community and Beyond with Structured Cross-Site Searching. Proceedings of the International Plant and Animal Genome XXVII Conference, January 12-16, 2019; San Diego, CA, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Jung, S., Lee, T., Cheng, C.H., Gasic, K., Campbell, B.T. and Main, D. (2019). BIMS (Breeding Information Management System) in Tripal for Efficient Management and Analysis of Breeding Data. Proceedings of the International Plant and Animal Genome XXVII Conference, January 12-16, 2019; San Diego, CA, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Spoor, S., Wytko, C., Chen, M., Almsaeed, A., Condon, B., Hough, H., Herndon, N., Mills, N., Staton, M., Wegrzyn, J.L. and Feltus, A. (2019). Execution of Scientific Workflows for Tripal-Based Community Databases. Proceedings of the International Plant and Animal Genome XXVII Conference, January 12-16, 2019; San Diego, CA, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Iezzoni, A.F., Bassil, N., Coe, M., Finn, C.E., Gasic, K., Hokanson, S.C., Luby, J.J., Main, D., McFerson, J.R., Norelli, J. and Peace, C. (2019). RosBREED: Sustaining Success in DNA-Informed Breeding Impacts for Rosaceae. Proceedings of the ASHS Annual Conference; July 21-25, 2019; Las Vegas, NV, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Peace, C., Jung, S., Buble, K., Cheng, C.H., Hough, H., Humann, J.L., Zheng, P., Yu, J. and Main, D. (2019). Using NRSP10 Data and Tools for Translational Research. Proceedings of the International Plant and Animal Genome XXVII Conference, January 12-16, 2019; San Diego, CA, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Hardner, C., Peace, C., Jung, S., Lee, T. and Main, D. (2019). Global Performance Prediction Tool in Tripal BIMS. Proceedings of the International Plant and Animal Genome XXVII Conference, January 12-16, 2019; San Diego, CA, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Main, D., Jung, S., Peace, C., Bassil, N., Hardner, C.M., McFerson, J.R., Iezzoni, A.F., Lee, T., Cheng, C.H., Hough, H. and Luby, J.J. (2019). Data Access and Use: From Rosbreed Data Management to Genomic Prediction. Proceedings of the ASHS Annual Conference; July 21-25, 2019; Las Vegas, NV, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: Main, D., Jung, S., Ficklin, S.P., Staton, M., Wegrzyn, Crocker, E., Nelson, D., and Abbott, A.G. (2019). Enabling big-data driven discovery for tree crop research. Proceedings of the ASPB Annual Conference; Aug 3-7, 2019; San Jose, CA, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: AgBioData Brochure, ASHS Annual Conference, July 21-25, 2019; Las Vegas, NV, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: Genome Database for Rosaceae Brochure, ASPB Annual Conference AgBioData Booth, Aug 3-7, 2019; San Jose, CA, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: Tripal Brochure, ASPB Annual Conference AgBioData Booth, Aug 3-7, 2019; San Jose, CA, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: AgBioData Brochure, ASPB Annual Conference AgBioData Booth, Aug 3-7, 2019; San Jose, CA, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: AgBioData Brochure, International Plant and Animal Genome XXVII Conference AgBioData Booth, January 12-16, 2019; San Diego, CA, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: Genome Database for Rosaceae Brochure, International Plant and Animal Genome XXVII Conference AgBioData Booth, January 12-16, 2019; San Diego, CA, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: Breeding Information Management System (BIMS) Brochure, International Plant and Animal Genome XXVII Conference AgBioData Booth, January 12-16, 2019; San Diego, CA, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: Tripal Brochure, International Plant and Animal Genome XXVII Conference AgBioData Booth, January 12-16, 2019; San Diego, CA, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: Genome Database for Rosaceae Brochure, ASHS Annual Conference, July 21-25, 2019; Las Vegas, NV, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: Breeding Information Management System (BIMS) Brochure, ASHS Annual Conference, July 21-25, 2019; Las Vegas, NV, USA.
  • Type: Other Status: Published Year Published: 2019 Citation: Tripal Brochure, ASHS Annual Conference, July 21-25, 2019; Las Vegas, NV, USA.


Progress 09/01/17 to 08/31/18

Outputs
Target Audience:The target audience is predominantly scientists, bioinformaticists/data scientists, database developers/curators, both national and international, as well as, U.S. industry stakeholders. Scientists have been engaged through 3 peer-reviewed publications (3 more in review), 2 training workshops and 3 webinars, 22 presentations at 8 scientific conferences and meetings, a newsletter to the GDR mailing list, user surveys and focus groups, emails to the GDR mailing list, and quarterly meetings of the community U.S. Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC), who serve as the GDR Steering Committee. Bioinformaticists/data scientists and database developers have been engaged through participation in monthly meetings on Tripal software, release of new versions of Tripal and extension modules, the tripal.info website, a two day in-person hackathon, monthly Agricultural Biological Database (AgBioData) group meetings and work on a published white paper, peer-reviewed publications, and presentations at conferences and meetings. Industry stakeholders are being engaged through presentations and interactions at commodity group meetings Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Training opportunities for undergraduate, graduate and postdoctoral researchers included participation in hackathons, presentations and participation at workshops, conferences, and meetings, and authorship on peer-reviewed publications. How have the results been disseminated to communities of interest? Outputs and activities updates were presented at one face-to-face and three online quarterly meetings. A newsletter was sent out to the GDR users mailing list and components of the GDR project were presented on 22 occasions at one local (Washington State Tree Fruit Association Annual Meeting), three national (2017 and 2018 American Society of Horticultural Science Annual Conferences, and 2018 Bioinformatics Open Source Conference) and three international conferences (2018 Plant and Animal Genome Conference, 2018 Joint American Society Plant Biology and Canadian Plant Biology Conference, 2018 International Rosaceae Genomics Conference), as well as three published peer-reviewed publications in year 4 and 3 more in press or under review. A one-day BIMS training workshop was held for RosBREED breeders with over 25 participants, Tripal database developer meetings were held as well as a 2 day in-person hackathon, support was provided to groups implementing Tripal databases and the Tripal website (tripal.info) kept current with new developments, and module releases. The team participated in: monthly AgBioData meetings; the AgBioData workshop at the Plant and Animal Genome Conference; monthly meta data ontology working group meetings; the AgBioDat database booth at PAG and ASPB; and at the annual participants meeting of the SCRI RosBREED project. In year 4 of this SCRI project, GDR was accessed by 24,331 users from 156 countries during 66,591 visits, with 641,518 pages viewed. This is triple the number of pages served in year 3. Of the 24,331 visitors, 5,947 were from the US with all US states and territories represented. The top ten states using GDR in year 4 of this project were CA, NY, VA, MA, WA, MI, FL, TX, CT and MD. According to google scholar metrics, GDR was cited in 196 publications in 2017 and 144 times in the first 8 months of 2018. Over the last 4 years of this project, 1,366,559 GDR pages have been viewed during 216,722 visits and GDR was cited in 831 publications. What do you plan to do during the next reporting period to accomplish the goals? (1) Complete conversion of GDR to Tripal 3 (2) enable connectivity between GDR and other Tripal tree databases so users can cross query other databases from GDR to further enable comparative genomic opportunities (3) Release TripalMap v1.0 for use by the Tripal community (4) Release BIMS v1.0 continue for use by the Tripal community (5) Continue to develop BIMS (6) Implement a Tripal Expression module (6) continue to promote further use of the FieldBook App for more efficient collection of phenotype data by Rosaceae breeding programs and allied scientists (4) continue to add large scale genomic, genetic and breeding data as they become available (5) present GDR at relevant conferences and meetings; provide GDR webinars, continue providing Tripal support; continue actively participating in GGB database efforts at the national and international level.

Impacts
What was accomplished under these goals? Impact of Project GDR is an up to date, curated and integrated, internationally recogized database resource for Rosaceae species. It includescrops such as almond, apple, apricot, blackberry, cherry, peach, pear, plum, rose, and strawberry, with an annual US value of productionexceeding $15 B in 2016. With over 80,000users from 185 countries, 1.3 M pages accessed 2014, GDRis widely used and cited in 831 scientific publications as sources of genomics, genetics and breeding data and analysis tools facilitating research discovery, translation and application for this economically and biologically important crop family. As one of the founding Tripal databases, it is proactive in leading developingand supporting adoption of this generic, open-source and resource-efficient database platform for genomics, genetics and breeding research. Over 150 databases are now using this platform, with 8 research groups actively collaborating, developing and sharing modules for new functionality. Activities related to these accomplishments in year 4are summarized as follows: (1) Curation and addition of large scale genomic data- (a) 9 genome assemblies and annotations added for blackberry, rose, and strawberry species: blackberry (Rubus_occidentalis_v1.1 and Rubus_occidentalis_v3.0), rose (rosa_chinensis_v1.0, Rosa_chinensis_old_blush_homozygous_genome_v2.0, Rosa_chinensis_old_blush_Illumina_genome_v1.0, Rosa_multiflora_v1.0), and strawberry (Fragaria­_vesca_v2.0.a2, Fragaria_vesca__v4.0.a1, Potentilla_micrantha_v1.0 ), all with GDR analyzed functional annotation available to, browse, search and download (b) Conducted major synteny analysis across 8 major rosaceae genomes, added results to database and enabled visualization of syntenic blocks and orthologs in Synteny Viewer (c) added 243,0354 genes and 253,325 mRNAs to database, aligned to respective genomes and made available to view on JBrowse, search and download from the gene/transcript search page and (d) added 291,402 genotypic measurements. (2)Curation and addition of genetic data- (a) curated and added 89 genetic maps (b) added 1001 QTL/MTL for 72 agronomic traits (c) added over 8000 markers (d) added 291,402 genotypic measurements and (e) added sweet cherry phenotype and genotype data from RosBREED project. (3) Web interface and analysis pipeline development- (a) developed and implemented new Tripal MapViewer map visualization tool to view and compare genetic maps and associated features, with links into features detail pages. This replaces the GMOD CMap software that was inefficient to manage (b) developed and implemented a trait evaluation search tool (c) developed and implemented functionality to enable customizing of output from gene/transcript search page (d) implemented multivariant plugin for JBrowse genome viewer to enable visualization of resequencing data mapped to reference genomes (e) Tripal Breeding Information Management System (BIMS) made available for public breeding phenotype data (f) new and improved functionality added to BIMS as requested by breeders includes: (i) data archiving, (ii) viewing statistics of phenotypic data for each accession, (iii) configuration page to set column names for the phenotype file, (iv) new search/download function, (v) generate Field book input file' for progeny from a new cross, (vi) more columns can be added to the downloaded file, (vii) list of accessions generated by 'Search' function, (viii) mean/max/min/std and frequency were added in the downloaded file from search , (ix) Google Map embedded in BIMS to show the locations of the breeding program sites when coordinates provided, (x) frequency of each category displayed for categorical traits for a given dataset , (xi) order of traits in 'Trait' in 'Manage Breeding' section able to be changed by users in the configuration page, (xii) ability to compare trait statistics from different categories (year, cross, etc.), (xiii) Chart.js (javascript graphic library) was added to improve BIMS charts, and (xiv) user manual and FAQ available in BIMS. (4) Outreach - (a) held one day BIMS training workshop for Rosaceae breeders to train on using BIMS and Field Book App, attended by 25 people representing 11 Rosaceae breeding programs (b) held 3 BIMS webinars for Rosaceae breeders, (c) presented GDR through peer-reviewed publications, 22 presentations at 8 conferences/meetings, newsletters and brochures (d) actively participated in agricultural biological database (AgBioData) monthly and workshop meetings (e) actively participated in Tripal community developer meetings (f) provided support for Tripal adoption and module development including several online training sessions. GDR by the numbers: By the end of year 4 of this project, GDR contained the following data: 21 genomes for 14 species; 528890 genes and 585,574 mRNAs; 313 genetic maps; 3,286,882 markers; 3,799 trait loci; 10,787,946 genotypes; 389,191 phenotypes; 14,411 germplasm; 1,967 species, and 7,468 publications.

Publications

  • Type: Other Status: Published Year Published: 2018 Citation: Genome Database for Rosaceae Brochure, AgBioData Booth, ASPB Annual Conference; July 14-18, 2018, Montreal, Canada.
  • Type: Other Status: Published Year Published: 2018 Citation: Genome Database for Rosaceae Brochure, NRPS10 Workshop, ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C.
  • Type: Other Status: Published Year Published: 2017 Citation: Genome Database for Rosaceae Newsletter, October 1, 2017.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Jung, S., Lee, T., Cheng, CH., Humann, J., Yu, J., Ficklin, S.P. and Main, D. (2017). Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. Database, bax092
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Iezzoni A., Peace, C., Main, D., Bassil, N., Coe, M., Finn, C., Gasic, K., Luby, J., Hokanson, S., McFerson, J., Norelli, J., Olmstead, M., Whitaker, V., Yue, C. (2017). RosBREED 2: Progress and future plans to enable DNA-informed breeding in the Rosaceae. Acta Horticulturae, ActaHortic.2017.1172.20.2017.1172.20.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Falk, T., Herndon, N., Grau, E., Buehler, S., Richter, P., Zaman, S., Baker, E.M., Ramnath, R., Ficklin, S., Staton, M., Feltus, F.A., Jung, S., Main, D., Wegrzyn, J.L. (2018) Growing and cultivating the forest genomics database, TreeGenes. Database, bay084.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Jung, S., Cheng, C.H., Lee, T., Zheng, P., Gasic, K., Yu, J., Humann, J., Evans, K., Peace, C., DeVetter, L., Mcferson, J., Coe, M.I. and Main, D. Resources in the Genome Database for Rosaceae for Peach Research. Acta Horticulturae (in press).
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Harper, L., Campbell, J., Cannon, E., Jung, S., Poelchau, M., Walls, R.L., Andorf, C.M., Arnaud, E., Berardini, T., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C., Farmer, A., Ficklin, S.P., Grant, D., Grau, E., Herndon, N., Hu, Z-L., Humann, J.L., Jaiswal, J., Jonquet, C., Laporte, M.A., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C., Munoz-Torres, M., Naithani, S., Nelson, R., Nesdill, D., Park C., Reecy, J., Reiser, L., Sanderson, L-A., Sen, T.Z., Staton, M., Subramaniam, S., Tello-Ruiz, M.K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J.L., Williams, J., Woodhouse, M., Main, D. (2018). AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture. Database, bay088.
  • Type: Journal Articles Status: Under Review Year Published: 2018 Citation: Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Yu, J., Humann, J.L., Ficklin, S.P., Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Evans, K., Peace, P., DeVetter, L., McFerson, J., Coe, M., Wegrzyn, J.L., Staton, M., Main D. 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acid Research (Under Review).
  • Type: Journal Articles Status: Under Review Year Published: 2018 Citation: Wegrzyn, J.L., Staton, M.A., Street, N., Main, D., Grau, E., Herndon, N., Buehler, S., Falk, T., Zaman, S., Ramnath, R., Richter, P., Sun, L., Condon, B., Almsaeed, A., Chen, M., Mannapperuma C., Jung, S., Ficklin, S. Cyberinfrastructure to improve forest health and productivity: the role of tree databases in connecting genomes, phenomes, and the environment. Frontiers in Plant Science (Under Review)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: McFerson, J., Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., Gasic, K., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M., Kahn, M. and Main, D. (2017) GDR and Big Data. Oral presentation at the Washington State Tree Fruit Association Annual Meeting; December 4-6, 2017, Pasco, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Staton, M., Chen, M., Almsaeed, A., Condon, B., Yu, J., Henry, W., Wegrzyn J.L., Main, D., Ficklin, S.P. (2017) Using Tripal As a Project Database: The Hardwood Genomics Project. Proceedings of the ASHS Annual Conference; September 19-22, 2017, Waikoloa, HI.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Bassil, N., Jung, S., Cheng, C-H., Lee, T., Zheng, P., and Main, D. (2017) Database Resources for Small Fruit Research. Proceedings of the ASHS Annual Conference; September 19-22, 2017, Waikoloa, HI Gasic, K., Lee, T., Jung, S., Main, D. (2017) A Breeders Perspective on using the Breeding Information Management System for Fruit Breeding. Proceedings of the ASHS Annual Conference; September 19-22, 2017, Waikoloa, HI.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Peace, C., Vanderzande, S., Iezzoni, A., Jung, S., and Main, D. (2017) Database Resources for Translational Tree Fruit Research. Proceedings of the ASHS Annual Conference; September 19-22, 2017, Waikoloa, HI.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Jung, S., Lee, T., Cheng, C-H., Ficklin, S.P., Yu, J., Humann, J., Main, D. (2018) Mainlab Chado Module, a Tripal Module for Loading Map, Marker, QTL, Genotype, Phenotype and Germplasm Data. Proceedings of the International Plant & Animal Genome Conference XXVI; January 13-17, 2018, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Buble, K., Jung, S., Humann, J., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J., Main, D. (2018) TripalMap Mapviewer 1.0. Proceedings of the International Plant & Animal Genome Conference XXVI; January 13-17, 2018, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Main, D., Buble, K., Lee, T., Jung, S., Humann, J., Yu, M., Ficklin, S.P., Gasic, K., Campbell, B.T. (2018) Updates on Tripal Mapviewer and the Tripal Breeding Information Management System (BIMS). Proceedings of the International Plant & Animal Genome Conference XXVI; January 13-17, 2018, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Jung, S., Lee, T., Cheng, C-H., Zheng, P., Yu, J., Humann, J., Gasic, K., Frank, M., Scott, K., Evans, K.M., Peace, C., Devetter, L., McFerson, J., Kahn, M., Main, D. (2018) Using GDR for Translational Research. Proceedings of the International Plant & Animal Genome Conference XXVI; January 13-17, 2018, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Jung, S., Lee, T., Cheng, C-H., Gasic, K., Campbell B.T., Main, D. (2018) Using the Tripal Breeding Information Management System (BIMS) to Enable Efficient Management of Phenotypic and Genotypic Data. Proceedings of the International Plant & Animal Genome Conference XXVI; January 13-17, 2018, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Ficklin, S.P., Cheng, C-H., Spoor, S., Chen, M., Almsaeed, A., Mills, N., Watts, N., Wytko, C., Grau, E., Herndon, N., Soto, B., Wang, K-C., Feltus, A., Staton, M., Wegrzyn, J., Jung, S., Main, D. (2018) The Tripal Gateway Project: Supporting Exchange, Transfer and Analysis of Large-Scale Data for Online Biological Databases. Proceedings of the International Plant & Animal Genome Conference XXVI; January 13-17, 2018, San Diego, CA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Buehler S., Falk T., Grau E.S., Herndon N., Zaman S., Main D., Jung S., Ficklin F., Staton M., Wegrzyn J.L. (2018). Tripal Sequence Similarity Search provides efficient protein sequence similarity search for Tripal sites. Proceedings of the Bioinformatics Open Source Conference; June 25-30. 2018, Portland, OR.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Yu, J., Humann, J.L., Ficklin, S.P., Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Evans, K., Peace, P., DeVetter, L., McFerson, J., Coe, M., Wegrzyn, J.L., Staton, M., Main D. (2018) Genome Database for Rosaceae: A Resource for Genomic, Genetic and Breeding Research. Proceedings of the 9th International Genomics Conference; June 26-30, 2018. Nanjing, China.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Hardner, C., Satish, K., Main, D., Hayes, B., Peace, C. (2018) Global Genomic Prediction of Performance. Proceedings of the 9th International Genomics Conference; June 26-30, 2018. Nanjing, China.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Yu, J., Humann, J.L.,Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Evans, K., Peace, P., DeVetter, L., McFerson, J., Coe, M., Main D. (2018) Genome Database for Rosaceae: resource for genomic, genetic and breeding research. ?July, 2018, Chungbuk National University, Cheongju, South Korea.
  • Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2018 Citation: Main, D., Harper, L., Jung, S., Campbell, J.D., Cannon, E., Poelchau, M., Walls, R. (2018) AgBioData Visioning and Implementation. Proceedings of the ASPB Annual Conference; July 14-18, 2018, Montreal, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Staton, M., Ficklin, S.P., Cheng, C-H., Spoor, S., Chen, M., Condon, B., Almsaeed, A., Mills, N., Watts, N., Wytko, C., Grau, E., Herndon, N., Soto, B., Wang, K-C., Feltus, A., Wegrzyn, J., Jung, S., Main, D. (2018) Tripal v3, the Collaborative Online Database Platform Supporting an International Community of Plant Genome Databases. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Yu, J., Humann, J.L.,Gasic, K., Scott, K., Frank, M., Ru, S., Hough, H., Crabb J., Evans, K., Peace, P., DeVetter, L., McFerson, J., Coe, M., Jahn, M., Main D. (2018) New Data and Functionality in NRSP10 Databases. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Rife, T., Poland, J.A. (2018) Integrating Free Mobile Apps into Specialty Crop Breeding and Horticultural Programs. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2018 Citation: Peace, C., Hardner, C., Lee, T., Jung S., Main, D. (2018) Extending the Tripal Breeding Information System to Combine International Data for Global Performance Predictions. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C.
  • Type: Other Status: Published Year Published: 2017 Citation: Genome Database for Rosaceae Brochure, NRPS10 Workshop, ASHS Annual Conference; September 19-22, 2017, Waikoloa, HI.
  • Type: Other Status: Published Year Published: 2018 Citation: Genome Database for Rosaceae Brochure, AgBioData Booth, International Plant & Animal Genome Conference XXVI; January 13-17, 2018, San Diego, CA.


Progress 09/01/16 to 08/31/17

Outputs
Target Audience:The target audience is predominantly scientists, bioinformaticists, database developers/curators, both national and international, as well as, U.S. industry stakeholders. Scientists have been engaged through peer-reviewed publications, workshops, presentations at scientific conferences and meetings, biannual newsletters to the GDR mailing list, an online survey of users, emails about the website, and quarterly meetings of the community U.S. Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC), which serves as the GDR Advisory Panel. Bioinformaticists and database developers have been engaged through participation in monthly meetings on Tripal software, release of new versions of Tripal, the tripal.info website, a one day in-person hackathon, monthly Agricultural Biological Database (AgBioData) group meetings, peer-reviewed publications, and presentations at conferences and meetings. Industry stakeholders are being engaged through presentations and interactions at commodity group meetings. In year 3 of this SCRI project, GDR was accessed by 21,515 users from 153 countries, with 275,117 pages viewed over 56,338 visits. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training opportunities for undergraduate, graduate and postdoctoral researchers included participation and presentation at workshops, conferences and meetings. How have the results been disseminated to communities of interest?Outputs and activities updates were presented at quarterly web-based meetings of the USRosEXEC. A newsletter was sent out to the GDR users mailing list and components of the GDR project were presented on 14 occasions at two local, one national (ASPB) and four international meetings (International Peach Symposium, PAG, PAG ASIA, South Korea Plant Breeding and Genetics Symposium) as well as two peer-reviewed publications in year 3. A GDR training workshop was held at PAG with over 60 participants, Tripal database developer meetings were held as well as a 1.5 day hackathon, support was provided to groups implementing Tripal databases and the Tripal website (tripal.info) kept current with new developments, and module releases. The team participated in: monthly AgBioData meetings; the AgBioData workshop at the Plant and Animal Genome Conference; monthly meta data ontology working group meetings; the plant database booth at PAG; and at the annual participants meeting of the SCRI RosBREED project. In year 3 of this SCRI project, GDR was accessed by 21,515 users from 153 countries, with 275,117 pages viewed over 56,338 visits. What do you plan to do during the next reporting period to accomplish the goals?(1) Upgrade GDR to Tripal 3 (2) enable connectivity between GDR and other Tripal tree databases so users can cross query other databases from GDR to further enable comparative genomic opportunities (3) complete v2 of the Tripal breeding information management system (BIMS) (4) continue promoting further use of the FieldBook App for more efficient collection of phenotype data by Rosaceae breeding programs and allied scientists (4) continue to add large scale genomic, genetic and breeding data as they become available (5) present GDR at relevant conferences and meetings; continue providing Tripal support; continue actively participating in GGB database efforts at the national and international level including release of a white paper on Agricultural Biological Database data, code and communication sharing opportunities.

Impacts
What was accomplished under these goals? (1) Curation and addition of large scale genomic data- (a) 3 genome assemblies and annotations added: sweet cherry (v1.0.a1), peach (v2.0.a1), apple (GDDH13 v1.1), with GDR analyzed functional annotation available to, browse, search and download (b) Developed RubusCyc and updated the PeachCyc, FragariaCyc and AppleCyc databases (c) Reference transcriptomes (v1.0) generated from 9.6 billion RNASeq reads for apple, cherry, peach, strawberry and Rubus (v2.0). RefTrans are annotated and available to browse, search and download, and mapped to the genome sequence where available (d) over 900,000 markers added (e) 10,496,544 million SNP genotype measurement added to chado (previously available just to download as a file on GDR) (f) NCBI genes for Rosaceae aligned to respective genomes and made available on genome browsers (2)Curation and addition of genetic data- (a) All QTL updated using the standardized Riosaceae Trait Ontology (b) added 57 genetic maps and293 QTL/MTL added from 25 publications (c) added Rosbreed genotype and phenotype data from several programs. (3) Web interface and analysis pipeline development- (a) implemented new Tripal BLAST+ module that provides direct hyperlinks from the BLAST results to the database (b) developed and implemented a SNP marker search tool (c) developed and implemented a search by trait tool (d) implemented access to the IASMA Pathway Inspector tool though GDR. This embedded tool allows researchers to identify differentially expressed genes and provides a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad-hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology (e) completed and released three Tripal extension modules for data loading, search and display for sequence, map, marker, QTL, genotype, phenotype, germplasm (f) Identified sequences for a new 9K cherry array (g) Continued development of the Tripal Breeding Information Management System, all Clemson peach breeding program data added, currently being tested by the breeder. (4) Outreach - (a) promoted use of the FieldBook App for collection of phenotype data in field and laboratory experiments (b) presented GDR through peer-reviewed publications, presentations, specific GDR training workshop at PAG (followed by survey), newsletters and brochures (c) implemented suggestions from survey in GDR (d) actively participated in agricultural biological database (AgBioData) meetings including organizing a face-to-face workshop in Salt Lake City with over 40 scientists participated in developing a whitepaper on agricultural databases best practices (e) actively participated in Tripal community developer meetings (f) provided support for Tripal adoption and module development including several online training sessions. GDR by the numbers: By the end of year 3 of this project, GDR contained the following data: 14 genomes for 10 species; 285,855 genes and 332,249 mRNAs; 3,278,826 markers; 224 genetic maps; 2,901 trait Loci; 10,514,383 genotypes; 845,467 phenotypes; 18,700 germplasm; 1,967 species, and 7,062 publications.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2017 Citation: Jung, S., Lee, T., Cheng, CH., Humann, J., Yu, J., Ficklin, S.P. and Main, D. (2017). Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. Database (Oxford) (in press)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Gasic, K., Jung, S., Cheng, C.H., Lee, T., Zheng, P., Yu, J., Humann, J., Evans, K., Peace, C., DeVetter, L., Mcferson, J., Coe, M.I. and Main, D. (2017). Resources in the Genome Database for Rosaceae for Peach Research. Acta Horticulturae (in press).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: McFerson, J., Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., Gasic, K., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M., Kahn, M. and Main, D. (2017). GDR and Big Data. Oral presentation at the Washington State Tree Fruit Association Annual Meeting; December 4-6, 2017; Pasco, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Main, D., Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., Gasic, K., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M. and Kahn, M. (2017). GDR: New Data and New Functionality. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., Gasic, K., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M., Kahn, M and Main, D. (2017). Using GDR: An Overview. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., Gasic, K., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M., Kahn, M and Main, D. (2017). Using GDR: An Overview. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., Gasic, K., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M., Kahn, M and Main, D. (2017). Newly Designed Genome Database for Rosaceae (GDR). Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Campbell, J.D., Campbell, E., Jung, S., Main, D., Poelchau, M., Walls, R. and Harper, L.S. (2017) AgBioData: A Consortium of Agricultural Biological Databases. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Buble, K., Jung, S., Humann, J.L., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J. and Main, D. (2017) Development of TripalMap. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Lin, Q., Herndon, N., Grau, E., Ficklin. S.P., Staton, M., Jung, S., Main, D., Feltus, A. and Wegrzyn, J.L. (2017) A Novel Tripal Database Module and Workflow to Facilitate Variant Mapping and Detection in Non-Model Plant Species. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Ficklin, S.P., Cheng, C.H., Watts, N., Chen, M., Wytko, W., Soto, B., Sanderson, L.A., Jung, S., Wang, K-H., Staton, M., Main D., Feltus, A. and Wegrzyn, J.L. (2017). Tripal Introduction and Core Development Efforts. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jung, S., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J., Humann, J.L. and Main, D. (2017) Mainlab Chado Loader, Chado Data Display and Chado Search for Sequence, Map, Marker, QTL, Genotype, Phenotype and Germplasm Data. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Gasic, K., Jung, S., Lee, T., Cheng, C-H., Yu, J., Campbell, T., Evans, K.M., Peace, C. and Main, D. (2016). Use of FieldBook and BIMS for Rosaceae Breeding. RosBREED Participants Meeting; March 6-8, 2017; East Lansing, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jung, S., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J., Humann, J.L. and Main, D. (2017) Development of Database Resources and Tools for Crop Genomics, Genetics and Breeding Research. Abstracts of the International Plant and Animal Genome Asia Conference XXV; May 29-30, 2017; Seoul, Korea
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Jung, S., Cheng, C-H., Lee, T., Ficklin, S.P., Yu, J., Humann, J.L. and Main, D. (2017) Development of Database Resources and Tools for Crop Genomics, Genetics and Breeding Research. Abstracts of the 2017 Plant and Breeding Symposium; June 3-4, 2017; Seoul, South Korea
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Gasic, K., Jung, S., Lee, T., Cheng, C-H., Zheng, P., Humann, J.L., Ru, S., Scott, K., Frank, M., Yu, J., McFerson, J., Evans, K.M., Peace, C.P., DeVetter, L., Coe, M., Kahn, M. and Main, D., (2017). Peach Resources in the Genome Database for Rosaceae. Proceedings of the IX International Peach Symposium; July 2-6, 2017; Bucharest, Romania


Progress 09/01/15 to 08/31/16

Outputs
Target Audience:The target audience is predominantly scientists, bioinformaticists, database developers/curators, both national and international, as well as, U.S. industry stakeholders. Scientists have been engaged through peer-reviewed publications, workshops, presentations at scientific conferences and meetings, biannual newsletters to the GDR mailing list, an online survey of users, emails about the website, and quarterly meetings of the community U.S. Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC), which serves as the GDR Advisory Panel. Bioinformaticists and database developers have been engaged through participation in monthly meetings on Tripal software, release of new versions of Tripal, the tripal.info website, a one day in-person hackathon, monthly Agricultural Biological Database (AgBioData) group meetings, peer-reviewed publications, and presentations at conferences and meetings. Industry stakeholders are being engaged through presentations and interactions at commodity group meetings. In year 2 of this SCRI project, GDR was accessed by 20,435 users from 147 countries, with 240,527 pages viewed. Changes/Problems:Dr. Mercy Olmstead left the University of Florida (UF) during Year 2 of this grant, relocated to California, and is no longer in an academic position. Activities originally proposed to be conducted at UF pertain to sub-objective 3d (Effective scientific communication). With Dr. Olmstead's departure, this project lacks the appropriate personnel and expertise at UF to fully achieve sub-objective 3d. From year 3 forward we propose to remove the general public component of sub-objective 3d and focus more effort on effective scientific communication with the project's primary stakeholders: the research community and industry stakeholders. These activities will include surveys, focus groups and outreach material generation under the direction of a replacement Co-PI, Dr. Jim McFerson, with support by Dr. Michael Coe, a consultant on this project. Dr. McFerson, former manager of the Washington Tree Fruit Research Commission and now Professor of Horticulture and Director of the Washington State University Tree Fruit Research and Extension Center, Wenatchee WA, has signficant extension respsonsiblities in his new position. Further, he has a strong academic background in plant breeding and genetics, brings highly relevant experience engaging industry stakeholders across the U.S. and internationally, and has been active in both RosEXEC and the SCRI project RosBREED. We feel that this amended goal and the personnel change will allow us to achieve the project's objectives effectively and comply with SCRI intent. To this end we propose to redirect all unspent funds from the UF subcontract back to WSU. What opportunities for training and professional development has the project provided?Training opportunities for undergraduate,graduate and postdoctoral researchers included attendance and presentation at several conferences and meetings. How have the results been disseminated to communities of interest?Outputs and activities updates were presented at quarterly web-based meetings of the USRosEXEC. Two newsletters was sent out to the GDR users mailing list and components of the GDR project were presented on 18 occasions at one local, three national (ASHS, CSSA, and SCRI Program Stakeholders advisory meeting and three international meetings (RGC8, 4th International Strawberry Symposium, PAG) as well as four peer-reviewed publications in year 2. Tripal database developer meetings were held as well as a one day hackathon, support was provided to groups implementing Tripal databases and the Tripal website (tripal.info) kept current with new developments, and module releases. The team participated in: monthly AgBioData meetings; the AgBioData workshop at the Plant and Animal Genome Conference; monthly meta data ontology working group meetings; the plant database booth at PAG; and at the annual participants meeting of the SCRI RosBREED project. In year 2 of the SCRI project, GDR was accessed by 19,069 users from 147 countries with 227,741 pages viewed. What do you plan to do during the next reporting period to accomplish the goals?Activities include: Add reference transcriptomes for all major Rosaceae species using our new Tripal RefTrans analysis pipeline; continue to add genetic, genomic and breeding data as it becomes publicly available; release the Mainlab Chado loader, search and display modules for sequence, map, marker, QTL, genotype, phenotype and germplasm; continue development of a Tripal comprehensive breeding information management system (BIMS); promote further use of the FieldBook App for more efficient collection of phenotype data by Rosaceae breeding programs and allied scientists; present GDR at relevant conferences and meetings; continue actively participating in GGB database efforts at the national and international level, including helping to organize and fund a two day AgBioData conference for the database community to develop a white paper on Agricultural Biological Database data, code and communication sharing opportunities.

Impacts
What was accomplished under these goals? New functionality and dataadded toGDR in Year 2 include the following: Curation and addition of large scale genomic data- (a) first Rubus genome (black raspberry, VanBuren et al. 2016) with GDR analyzed functional annotation available to, browse, search and download (b) Genome assembly of Malus x domestica v3.0.a1 pseudomolecules and Malus x domestica v3.0.a1 contigs available in JBrowse (c) Fragaria vesca v2.0.a2 added as a track in the Fragaria v2.0 JBrowse (d) Genome assembly of F. x ananassa and four wild species v1.0 available in JBrowse (e) 480K SNP array data for Malus x domestica (Bianco et al. 2016) available for download (f) Over 15 million SNP genotype data points added from the RosBREED peach and sweet cherry and FruitBreedomics peach projects available for download (g) New Rosaceae genes and mRNAs, downloaded and curated from NCBI non redundant database made available for searching and download (h) updated and released the PeachCyc, FragariaCyc and AppleCyc databases (i) conducted synteny analysis between Malus, Prunus, Fragaria, and Pyrus reference genomes and made available on GBrowse-Syn (j) developed an annotated Rubus Reference Transcriptome (Rubus RefTRans v1.0) from published RNASeq and EST data and made available to browse, search and download (k) Mapped the MDP genes from the apple genome assembly to the NCBI annotated LOC genes and made available as a downloadable excel file. (l) Loaded SNP data to the genome browser JBrowse as tracks (Apple 480K toM. x domesticagenome v3.0, IRSC Cherry 6K toP. persicagenome v2.0 and Strawberry 90K toF. vescav1.1); (2)Curation and addition of genetic data- (a) Trait ontology developed and implemented for major Rosaceae species (b) 18 maps, 3912 markers, 241 QTL and 45 MTL added from 25 publications; (3) Web interface and analysis pipeline development- (a) converted GDR to Tripal2 and Drupal 7 (b) redesigned and released GDR to make it easier for users to find data and tools (c) added dynamically generated data overview page (d) added germplasm image search functionality (e) added maps search functionality (f) redesigned the search sequences functionality (g) redesigned the search gene page and implemented as a search gene and transcript page (h) added SSR and SNP genotype search page (i) added new pages for NCBI Short Read Archive RNASeq and GBS data for all Rosaceae species (j) developed a Chado data loader (k) created publications dataset pages (l) conducted online voting for annual RosEXEC committee members election. (4) Outreach - (a) promoted use of the FieldBook App for collection of phenotype data in field and laboratory experiments (b) presented GDR through peer-reviewed publications, presentations, training workshops, newsletters and brochures (c) conducted an online survey of users and implemented most suggestions in the GDR redesign (d) actively participated in agricultural biological database (AgBioData) meetings (e) actively participated in Tripal community developer meetings (f) provided support for Tripal adoption and module development (g) secured funding to host a two day workshop for the AgBioData community to write a white paper on Agricultural Biological Database data, code and communication sharing opportunities. GDR by the numbers: By the end of year 2 of this project, GDR contained the following data: 16 genomes for 10 species; 241,590 genes and 331,639 mRNAs; 2,345,949 markers; 167 genetic maps; 3,338 trait Loci; 392,473 genotypes; 845,467 phenotypes; 17,386 germplasm; 1,899 species, and 6,820 publications by the Rosaceae community stored in the database.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Shin SS. Zheng P, Fazio G, Mazzola M, Main D, Zhu Y (2016) Transcriptome changes specifically associated with apple (Malus domestica) root defense response during Pythium ultimum infection. Physiological and Molecular Plant Pathology 94(April 2016):16-26
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ru S, Hardner C, Carter P, Evans K, Main D, Peace C. (2016) Modeling of genetic gain from marker-assisted seedling selection in clonally propagated crops. Horticulture Research (Online) 3, 16015.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Jung S, Bassett C, Bielenberg DG, Dardick C, Main D, Meisel L, Slovin J, Troggio M, Schaffer RJ (2015) A standard nomenclature for gene designation in the Rosaceae. Tree Genetics and Genomes 11(108)
  • Type: Other Status: Published Year Published: 2015 Citation: Jung M, Lee T, Ficklin S, Yu J, Main D (2015) Storing Genomic, Genetic, Phenotypic and Genotypic Data Using Chado. Research presentation at the AgBioData Monthly Meeting; September 2, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Main D, Jung S, Ficklin SP, Cheng C-H, Lee T, Zheng P, Humann P, Yu J, Blenda A, Scott K, Byrd M, Hough H, Wasko DeVetter L, Evans K, Peace C, Gasic K, Olmstead M, Cai L, Coe M (2015) Genome Database for Rosaceae  Utilizing Tripal, an Open-Source Database Platform for Genomics, Genetics and Breeding Research. Abstracts of the Crop Science Society of America/American Society of Agronomy/ Soil Society of America Annual Meeting; November 15-18, 2015; Minneapolis, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Main D, Jung S, Cheng C-H, Lee T, Zheng P , Ficklin SP, Humann JL, Yu J, Blenda A, Scott K, Byrd M, DeVetter L, Peace C, Evans KM, Gasic K, Olmstead M, Coe M, Abbott AG (2016) Genome Database for Rosaceae: Updates and New Directions. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Jung S, Cheng C-H, Lee T, Ficklin SP, Blenda A, Yu J, Scott, K, Byrd M, Ru S, Zheng P, Humann JL, DeVetter L, Peace C, Evans KM, Gasic K, Olmstead M, Coe M, Abbott AG, Main D (2016) GDR, the Genome Database for Rosaceae: New Data and Functionality. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Grau E, Demurijan SA, Vasquez-Gross H, Gessler D, Staton M, Jung S, Feltus A, Main D, Ficklin SP, Neale D, Wegrzyn J (2016) TreeGenes: Enabling Visualization and Analysis in Forest Tree Genomics. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Jung S, Lee T, Cheng C-H, Yu J, Gasi K, Campbell BT, Evans KM, Peace C, Main D (2016) TripalBIMS: the Breeding Information Management System in Tripal. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Ficklin SP, Sanderson L-A, Cheng C-H, Soto B, Wytko C, Jung S, Feltus A, Bett K, Main D (2016) Deliver Searchable Genomic, Genetic and Related Data Online Using Tripal. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Ficklin SP, Sanderson L-A, Cheng C-H, Wytko C, Soto B, Clytus M, Bett K, Main D (2016) The Future of Tripal: intuitive content creation, flexible data storage and web services. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Sanderson L-A, Ficklin SP, Main D, Bett K (2016) Tripal v2: An Overview. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA.
  • Type: Other Status: Published Year Published: 2016 Citation: Jung S, Lee T, Cheng C-H, Yu J, Gasic K, C Evans KM, Peace C, Main D (2016) Development of TripalBIMS: a Breeding Information Management System in Tripal. RosBREED Participants Meeting; March 7-9, 2016; East Lansing, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Main D, Jung S, Cheng C-H, Lee T, Ficklin SP, Blenda A, Yu J, Scott, K, Byrd M, Ru S, Zheng P, Humann JL, DeVetter L, Peace C, Evans KM, Gasic K, Olmstead M, Coe M, Abbott AG (2016) Introduction to RGC8 GDR Workshop. Abstracts of the 8th International Rosaceae Genomics Conference; June 21-24, 2016; Angers, France.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Jung S, Lee T, Chen C-H, Gasic K, Campbell BT, Evans KM, Peace C, Main D (2016) GDR Breeding Information Management Systems. Abstracts of the 8th International Rosaceae Genomics Conference; June 21-24, 2016; Angers, France.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Gasic K, Rife T, Poland JA, Jung S, Evans KM, Oraguzie N, DeVetter LW, Peace C, Olmstead MA, Main D (2016) Evaluation of Field Book: An Open-source Android App for Collecting Phenotypic Data in a Peach Breeding Program. Abstracts of the 8th International Rosaceae Genomics Conference; June 21-24, 2016; Angers, France.
  • Type: Other Status: Published Year Published: 2016 Citation: Main D (2016) Progress in the Genome Database for Rosaceae: Empowering Specialty Crop Research through Big-Data Driven Discovery and Application in Breeding and NRSP 10 Database Resources for Crop Genomics, Genetics and Breeding Research. Presentation to the Specialty Crop Committee Annual Meeting; August 2, 2016, Portland, USA
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Gasic K, Rife T, Poland JA, Jung S, Evans KM, Oraguzie N, DeVetter LW, Peace C, Olmstead MA, Main D (2016) Evaluation of Field Book: An Open-source Android App for Collecting Phenotypic Data in a Peach Breeding Program. Abstracts of the American Society for Horticultural Science Conference; August 7-11, 2016; Atlanta, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Main D, Jung S, Cheng CH, Lee T, Ficklin SP, Gasic K, Yu J, Humann JL, Zheng P, Scott K, Evans KM, Peace C, DeVetter L, Oraguzie N, Olmstead M (2016) Genome Database for Rosaceae: A Resource for Genomics, Genetics and Breeding Research. Abstracts of the American Society for Horticultural Science Conference; August 7-11, 2016; Atlanta, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Olmstead M, Iezzoni AF, Peace CP, Bassil N, Coe M, Finn CE, Gasic K, Luby JJ, Main D, McFerson JR, Norelli JL, Whitaker VM, Yue C, Sebolt A (2016) Successful Networking to Create International Collaborations in the Rosaceae Community. Abstracts of the American Society for Horticultural Science Conference; August 7-11, 2016; Atlanta, USA, USA.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Main D, Jung S, Cheng CH, Lee T, Ficklin SP, Lee T, Humann JL, Yu J, Zheng P, Peace C, Evans KM, Gasic K, Olmstead M, DeVetter LW, Kahn M, Mcferson JR, Abbott A, Bassil N (2016) Resources available for Fragaria research through the Genome Database for Rosaceae. Abstracts of the 8th International Strawberry Symposium; August 13-17, 2016; Quebec, Canada.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Ru S, Hardner C, Carter P, Harshman J, Sandefur P, Edge-Garza D, Evans K, Main D, Peace C (2016) Efficiency of marker-assisted seedling selection empirically evaluated in an apple seedling population. Abstracts of the 5th International Conference on Quantitative Genetics; June 1217, 2016; Madison, USA.
  • Type: Other Status: Published Year Published: 2016 Citation: GDR brochure for scientific audience
  • Type: Other Status: Published Year Published: 2015 Citation: GDR newsletter for GDR users (October 2015)
  • Type: Other Status: Published Year Published: 2016 Citation: GDR newsletter for GDR users (April 2016)


Progress 09/01/14 to 08/31/15

Outputs
Target Audience:The target audience is predominantly scientists, bioinformaticists, database developers/curators, and growers. Scientists have been engaged through peer-reviewed publications, presentations at scientific conferences and meetings, biannual newsletters to the GDR mailing list, emails about the website, and quarterly meetings of the community Rosaceae Genomics, Genetics and Breeding Executive Committee (RosEXEC) who serve as the GDR steering committee. Bioinformaticists and database developers have been engaged through participation in monthly Tripal meetings, monthly AgBioData meetings, release of new versions of Tripal,peer-reviewed publications, and presentations at conferences and meetings. Growers are being engaged through presentations at commodity group meetings.In year 1 of the SCRI project, GDR was accessed by 18,089 users from 145 countries, with196,562 pages viewed. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Training opportunities for undergraduate,graduate and postdoctoral researchers included attendance and presentation at several conferences and meetings. How have the results been disseminated to communities of interest?Components of the GDR project were presented at 8 meetings (local, national and international). Monthly Tripal database developer meetings were held, support was provided to groups implementing Tripal databases and the Tripal website (tripal.info) was kept current. The team participated in: monthly AgBioData meetings; the AgBioData workshop at the Plant and Animal Genome (PAG) Conference; monthly meta data ontology working group meetings; the plant database booth at PAG; provided training of GDR at PAG and the annual RosBREED participants meeting;and organized a breeders database needs assessment workshop coinciding withthe National Association of Plant Breeders annual meeting. Abiannual GDR newsletter was sent to the GDR mailing list and posted on the GDR website and quarterly reports were submitted to theGDR steering group who are elected members of the Rosaceae Genomics, Genetics and Breeding community (RosEXEC) ahead of quarterly conference calls. What do you plan to do during the next reporting period to accomplish the goals?Continue to add new genomics, genetics and breeding data as it become available; Migrate GDR to Tripal2 and implement more mobile friendly and user- friendly new theme; add reference transcriptomes for Rosaceae genera using the new Tripal RefTrans workflow and extension module we have developed;continue development of a Tripal comprehensive breeding information management system (BIMS); promote use of the FieldBook App for more efficient collection of phenotype data by Rosaceae breeding programs; present GDR at relevant conferences and meetings; continue actively participating in GGB database efforts at the national and international level.

Impacts
What was accomplished under these goals? New functionality and dataadded toGDR in Year 1 include the following: (1) Genome sequences - sequence and annotation (genes and predicted functions) of pear, peach, strawberry and apple genome sequences (Pyrus communisv1.0.a1,Prunus Persicav2.0.a.1,Fragaria vescav1.1.a2, Fragaria vesca v2.0.a1,Malus x domesticav3.0.a1) was made available to browse, search and download. Additionally, genome assemblies of Fragaria x Ananassa v1.0 and four wild species were made available to download and view in JBrowse; (2) SNP data - SNP data from the 20K Apple SNP Array, 90K cultivated strawberry SNP array, 68K Rose SNP array were added and a new interface developed to access the SNP data; (3) Genes - (a) working with the Rosaceae community we established a standard nomenclatures for gene designation in the Rosaceae (published), (b) a gene database was added by extracting gene data from NCBI nr and manually curating the data to check gene symbols and anchoring to the appropriate genome, (c) a Tripal extension module was developed to enable the genes to be searched by gene symbol, function, species, and genome location, and (d) a template and a gene submission page were created to enable scientists to submit gene/gene class data to GDR; (4) Map, Marker and QTL data - Data from 22 publications added. The Tripal QTL search module was expanded to enable searching by species, trait category, trait name, published symbol and label; (5) Phenotype and genotype data were added for the RosBREED project and three interfaces developed for searching haplotype data; (6) Reorganized the GDR species pages to enable clear, one-stop access to all the data and tools available for each genus and major species. GDR by the numbers: By the end of year 1 of this project, GDR contained the following data: 10 genomes; 233,191 genes; 2,193,827 markers; 123 genetic maps; 2,255 Trait Loci; 28,296 genotypes; 734,343 phenotypes; 13,500 germplasm; and 6,319 publications.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Jung S, Bassett C, Bielenberg DG, Dardick C, Main D, Meisel L, Slovin J, Troggio M, Schaffer RJ (2015) A standard nomenclature for gene designation in the Rosaceae. Tree Genetics and Genomes 11(108)
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Jung S, Lee T, Yu J Ficklin SP, Main D. Integration of genomic, genetic and breeding data using Chado. Database (Oxford)
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bassil N, Davis T, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin E, Rosyara U, Koehorst-van Putten H, Monford A, Amaya I, Denoyes B, Sargent D, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E (2015) Development and Preliminary Evaluation of a 90K Axiom SNP Array for the Allo-octoploid Cultivated Strawberry Fragaria x ananassa. BMC Genomics 16 (1):155.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ru S, Main D, Evans K, Peace C (2015) Current applications, challenges, and perspectives of marker-assisted seedling selection in Rosaceae tree fruit breeding. Tree Genetics and Genomes 11(1):1-12.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Main D, Jung S, Lee T, Ficklin SP, Cheng CH, Blenda A, Yu J, Zheng P, Humann J, Peace C, Evans K, Oraguzie N, Olmstead M, Gasic K (2015) GDR: Updates and Future Development. WA Apple Genomics, Genetics and Genomics Conference; Jan 27, 2015; Wenatchee.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Main D, Jung S, Lee T, Ficklin SP, Cheng CH, Blenda A, Yu J, Zheng P, Humann J, Peace C, Evans K, Oraguzie N, Olmstead M, Gasic K (2015) GDR: A Community Database for Rosaceae Genomics, Genetics and Breeding Research. Abstracts of International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Jung S, Ficklin SP, Lee T, Cheng CH, Blenda A, Yu J, Zheng P, Ru S, Peace C, Evans KM, Oraguzie N, DeVetter L, Abbott AG, Gasic K, Olmstead M, Main D (2015) How to Use GDR, the Genome Database for Rosaceae. Abstracts of International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Verde I, Shu S, Jenkins J, Zuccolo A, Dettori MT, Dardick C, Rossini L, Grimwood J, Pirona R, Goodstein DM, Dondini L, Vendramin E, Martinez-Gomez P, Silva H, Micali S, Falchi R, Scalabrin S, Bassi D, Main D, Orellana A, Vizzotto G, Tartarini S, Meisel L, Abbott AG, Morgante M, Rokhsar DS, Schmutz J (2015) The Peach v2.0 Release: An Improved Genome Sequence for Bridging the Gap Between Genomics and Breeding in Prunus. International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Iezzoni A, Peace C, Bassil N, Coe M, Finn C, Gasic K, Luby JJ, Main D, McFerson J, Norelli JL, Olmstead M, Whitaker VM, Yue C (2015) RosBREED: Combining Disease Resistance with Horticultural Quality in New Rosaceae Cultivars. Abstracts of International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: DeVetter L, Main D, Jung S, Cheng CH, Lee T, Blenda A, Yu S, Zheng P, Yu J, Ficklin SP, Evans KM, Peace C, Oraguzie N, Gasic K, Olmstead M (2015) Resources available for Rubus research through the Genome Database for Rosaceae. XIth International Rubus and Ribes Symposium; Jun 21-24, 2015; Asheville, NC.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Jung S., T. Lee, S. Ficklin, K. Evans, C. Peace, D. Main. Breeders Toolbox in GDR, Genome Database for Rosaceae. 2014. Breeders Toolbox Workshop at Noble Foundation; Nov 17-19, 2014; Noble Foundation, Ardmore, OK.