NRSP_OLD_10: Database Resources for Crop Genomics, Genetics and Breeding Research

(National Research Support Project Summary)

Status: Inactive/Terminating

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SAES-422 Reports

Annual/Termination Reports:

[03/26/2018] [05/16/2018] [05/17/2018] [06/08/2019]

Date of Annual Report: 03/26/2018

Report Information

Annual Meeting Dates: 07/30/2015 - 07/30/2015
Period the Report Covers: 10/01/2014 - 09/30/2015

Participants

Abbott, Albert (albert.abbott@uky.edu) - University of Kentucky;
Bassil, Nahla (nahla.bassil@ars.usda.gov) - USDA ARS (OR);
Campbell, B. Todd (todd.campbell@ars.usda.gov) - USDA-ARS (SC);
Chee, Peng (pwchee@uga.edu) - University of Georgia;
Chen, Chunxian (Chunxian.Chen@ars.usda.gov) - USDA-ARS (WV);
Cheng, Max (zcheng@utk.edu) - University of Tennessee;
Coe, Michael (michael@cedarlakeresearch.com) - Cedar Lake Research;
Coyne, Clarice (clarice.coyne@ars.usda.gov) - USDA-ARS (WA);
Dardick, Chris (chris.dardick@ars.usda.gov) - USDA ARS (WV);
David Stelly (stelly@tamu.edu) - Texas A&M University;
Dever Jane (jdever@ag.tamu.edu)- Texas A&M AgriLife Research;
Evans, Kate (kate_evans@wsu.edu) - Washington State University;
Fazio, Gennaro (gennaro.fazio@ars.usda.gov) - USDA ARS (NY);
Fernandez, Gina (gefernan@ncsu.edu) - North Carolina State University;
Gasic, Ksenija (kgasic@clemson.edu) - Clemson University;
Gmitter jr., Fred (fgmitter@ufl.edu) - University of Florida;
Hague, Steve (shague@tamu.edu) - Texas A&M University;
Hokanson, Stan (hokan017@umn.edu) - University of Minnesota;
Iezzoni, Amy (iezzoni@msu.edu) - Michigan State University;
Janet Slovin (janet.slovin@ars.usda.gov) - USDA ARS (MD);
Jenkins, Johnie (johnie.Jenkins@ars.usda.gov) - USDA-ARS (MS);
Jones, Don (djones@cottoninc.com) - Cotton Incorporated;
Jung, Sook (sook.jung@wsu.edu) - Washington State University;
Layne, Desmond (desmond.layne@wsu.edu) Washington State University;
Lee, Taein (taein_lee@wsu.edu) - Washington State University;
Luby, Jim (lubyx001@umn.edu) - University of Minnesota;
Mahoney, Lise (lise.mahoney@unh.edu) - University of New Hampshire;
Main, Dorrie (dorrie@wsu.edu) - Washington State University;
McCarty, Jack (jack.McCarty@ars.usda.gov) - USDA-ARS (MS);
McFerson, Jim (mcfersona@treefruitresearch.com) Washington Tree Fruit Research Commission) State University;
McGee, Rebecca (rebecca.mcgee@ars.usda.gov) - USDA-ARS (WA);
Michael Wisniewski (Michael.Wisniewski@ars.usda.gov) - USDA ARS (WV);
Myers, Jim (james.myers@oregonstate.edu) - Oregon State University;
Norelli, Jay (jay.norelli@ars.usda.gov) - USDA ARS (WV);
Olmstead, Jim (jwolmstead@ufl.edu) - University of Florida;
Olmstead, Mercy (mercy1@ufl.edu) - University of Florida;
Oraguzie, Nnandozien(noraguzie@wsu.edu) - Washington State University;
Patterson, Andy (paterson@uga.edu) - University of Georgia;
Peace, Cameron (cpeace@wsu.edu) - Washington State University;
Percy, Richard (richard.percy@ars.usda.gov) - USDA-ARS (TX);
Rife, Trevor (trife@ksu.edu) - Kansas State University;
Saski, Chris (saski@clemson.edu) - Clemson University;
Scheffler, Jodi (jodi.scheffler@ars.usda.gov) - USDA-ARS (MS);
Staton, Margaret (mstaton1@utk.edu) - University of Tennessee;
Swanson, J-D (jd.swanson@salve.edu) - University of Rhode Island;
Volke, Gayle (gayle.volke@ars.usda.gov) - USDA-ARS (CO);
Wegrzyn, Jill (jill.wegrzyn@uconn.edu) - University of Connecticut;
Xu, Kenong (kx27@cornell.edu) - Cornell University;
Yu, John (john.yu@ars.usda.gov) - USDA-ARS (TX)

Brief Summary of Minutes

In person or teleconference discussed meetings held during the year with various special interest groups:

Cotton Database Community Meeting: Cotton Beltwide Conference, San Antonio, Jan 5, 2015 Discussed CottonGen and goals of NRSP and identified some new functionality the community would like, managing large data sets and development of the Breeding management Information System

NRSP10 Open Meeting: Plant and Animal Genome Conference, San Diego, CA, Jan 11, 2015

Discussed goals of NRSP with a focus on integrated breeding tools needed by the community, and ability to analyze and manage genomic, genetics and breeding datasets.

International Cotton Genomics Initiative Officers Meeting, San Diego, CA, Jan 11, 2015

Discussed role of CottonGen in coordinating cotton community communication through the ICGI portal hosted on CottonGen, including hosting biannual office elections and future ICGI conference organization.

Rosaceae Community Meetings (RosEXEC and GDR Advisory Board): January 11th, 2015; April 21, 2105; July 23, 2015 Discussed new funding obtained for GDR through NRSP10, USDA NIFA SCRI and industry, goals for the next 5 years of GDR and how the reporting structure to the Rosaceae Community would be coordinated through quarterly meetings with the US Rosaceae Executive Committee (RosEXEC), including the yearly in-person meeting at PAG. Discussion about additional functionality needed such as a new MapViewer developed in Tripal to replace the GMOD CMap and Reference transcriptome generation to distill the billions of reads from published RNASeq data for Rosaceous species into useable data for the community through GDR.

NRSP10: Breeders Needs Assessment Focus Group Meeting: July 26, 2015, Pullman

Outlined plans for Breeding Information Management System functionality and use of the Field Bool App to collect phenotype data in the field (provide breeders with a Samsung tablet with Field Book installed to test). Received feedback on the plans and modified design accordingly.

Accomplishments

Core Tripal Progress: In year 1 of this project the major achievement in core Tripal development was the release of Tripal v2.0-rc1 in Sept 2014 followed by v2.0 on June 1, 2015. Improvements in v2.0 included: (1) Improved ease of finding extension modules by addition of an interface in Tripal to directly query the tripal.info site and find available modules; (2) improved performance by fixing the memory leaks in the loaders; (3) updated  the GFF loader to support automatic creation of protein sequences for genes (4) created an initial implementation of web services based on Chado structure then decided to change direction to make Tripal database backend independent (released in year 2 of the project) and therefore widen access to use Tripal for databases who use a different database schema and help resolve possible performance issues using Chado with very large datasets; (5) fixed bugs as they were found; (6) Improved administrative pages within Tripal; (7) regularly updated the Tripal website (http://tripal.info); (8) Held the first Tripal Workshop at the 2015 International Plant and Animal Genome Conference; (9) Held monthly Tripal developer meetings; (10) provided programming support and code to other Tripal groups. Breeding Tools Progress: In year 1 of this project the major achievement in breeding tools progress was identifying NRSP10 breeders database needs. A NRSP Breeders Database Needs Assessment Workshop was held in July where a focus group of breeders (invitation only) representing the major NRSP crops, and industry representatives were presented with ideas for development of a more comprehensive breeding information management system called TripalBIMS. Building on the GDR and RosBREED project breeding tools, TripalBIMS will integrate all aspects of breeding program management, public and private data integration, with analysis capabilities from a single portal, to aid in breeding program decision-making. For more efficient collection of phenotype data the Field Book App is being evaluated by several NRSP10 crop breeders who have been provided with a Samsung tablet with Field Book installed for evaluation purposes. The feedback so far indicates Field Book is an excellent resource but will need some modifications (working with the developer from Jesse Poland’s lab on these). Information gathered from this workshop, plus discussion held at the annual RosBREED participants meeting held in March 2015 are being used to develop TripalBIMS. GenSAS Progress: In Year 1 of this project our major achievement regarding GenSAS: the Genome Sequence Annotation Server, was the release of GenSAS v3.0 in December 2014.   GenSAS v3.0 has several major improvements over the previous v2.0 release; (1) interface redesign combining the project creation options and results browsing from v2.0 into one webpage. The new interface has a flow chart of the annotation process in the webpage header as well as a right-side menu for quick access to the job queue, JBrowse and project sharing. Users interact with GenSAS through a series of tabs that open in the center part of the screen. The redesign has improved the user experience by not only making it more intuitive, but also includes integrated instructions on how to use GenSAS; (2) Integration of JBrowse and Apollo for viewing results and manual curation of the annotation. By using an already developed genome browser and annotation editor, users can easily view and curate the data. Apollo also is configured for community annotation and works well with the collaborative annotation tools that were already a part of GenSAS; (3) Addition of Evidence Modeler as a tool in GenSAS v3.0 to allow for generation of a gene model consensus from multiple gene predictor tool outputs; (4) Addition of a GenSAS Administration page under the Drupal Administration Menu so administrators on the GenSAS website can monitor job activity, configure GenSAS settings, and add/remove/configure tools that are available for use in GenSAS; (5) Presentation of GenSAS at the 2015 Plant and Animal Genome Conference, 2015 American Society of Horticultural Science Annual Meeting, and the 2015 WSU Academic Showcase and created a 15 minute video tutorial for GenSAS. We also answered questions and fixed program issues for about 15 users through the year; (6) By August 31, 2015 we had 110 GenSAS v3.0 user accounts created. In March 2015, we also started measuring GenSAS site visits using Google Analytics. In the 6th month period to August 31, 2015, GenSAS was accessed by 595 visitors from 61 countries with 1,132 sessions and 3,969 pages viewed.   Almost half of the site visitors (47.7%) were returning users (47.7%). NRSP10 Databases Progress: In year 1 our major achievements regarding the 5 NRSP10 databases were improving the data and functionality of the databases on the live sites with further improvements being tested on the development server. (1) Cool Season Food Legume Database (CSFL, https://www.coolseasonfoodlegume.org): In year 1, CSFL was fully converted to Tripal v2.0 on the development server and made current with genome, gene, trait, map, marker, germplasm, phenotype, genotype and publications data for pea, lentil, chickpea and fava bean. A new analysis pipeline was developed to combine all publicly available published RNASeq datasets (different platforms) with EST data into reference transcriptomes which were then functionally characterized and mapped. As part of the conversion to Tripal v2.0 a cleaner, more user-friendly interface has been developed which makes it easier to get to the data and tools. CSFL currently contains: 1 genome; 233,191 genes; 3,777 markers; 38 genetic maps; 215,713 transcripts; 2,255 Trait Loci; and 4,225 publications. (2) Genome Database for Rosaceae (GDR, https://www.rosaceae.org): In year 1, new functionality and data  in GDR included: 5 annotated genome sequences; SNP array data for apple, strawberry and rose and a new interface developed to access the SNP data; establishment of a gene database and a Tripal extension module developed to enable the genes to be searched by gene symbol, function, species, and genome location; establishment of a community agreed standard nomenclatures for gene designation in the Rosaceae and a template and a gene submission page; and map, marker and QTL data added. Several new interfaces were added to improve querying capability. GDR currently contains: 10 genomes; 233,191 genes; 2,193,827 markers; 123 genetic maps; 518,586 transcripts; 912 Trait Loci; 13,500 germplasm; and 6,319 publications. (3) CottonGen: In year 1, the conversion of CottonGen (www.cottongen.org) to Tripal v2.0 was initiated on the development server, with design and implementation of a new theme providing a cleaner, more user-friendly interface which makes it easier to access data and tools. On the live site major new data and functionality in CottonGen included: two cotton genome sequences and gene models with additional annotation performed though our annotation workflow. The annotated sequences are searchable by species, name, function, location, and mapped marker, viewable through GBrowse and JBrowse and made available to BLAST; 6000 SNP marker primers; and hosted ICGI elections. CottonGen currently contains: 5 genomes; 323,180 genes; 276,221 markers; 50 genetic maps; 442,954 transcripts; 988 trait loci; 106,664 genotypes; 130,756 phenotypes; 14,077 germplasm; and 15,494 publications.   (4) Citrus Genome Database (CGD, https://www.citrusgenomedb.org): In year 1 of this project, map, marker and QTL data have been collected and curated for addition to the database. GCD currently contains: 3 genomes; 2,192 genes; 3,427 markers; 51 genetic maps; 386,445 transcripts; 86 trait loci and 2,955 publications. (5) Genome Database for Vaccinium (https://www.vaccinium.org, GDV): In year 1 of this project, sequence, map, marker and QTL data have been collected. GDV currently contains: 261,775 transcripts and 402 publications. Our plans for next year of NRSP10 are to continue to add new genomics, genetics and breeding data as they become available for each of the databases; migrate remaining databases to Tripal2; release GenSAS v4.0; release Tripal v3.0, release Mainlab Tripal extension modules; finish converting CottonGen, CSFL, GDR CGD, GDV to Tripal 2 with new theme implementation on live site; complete development of new Tripal RefTrans analysis workflow and extension module; complete development of new TripalMap extension module; continue to be very proactive in presenting NRSP10 activities/products at conferences, workshops and meetings and obtaining feedback from our community of users.  (5) Genome Database for Vaccinium (https://www.vaccinium.org, GDV): In year 1 of this project, sequence, map, marker and QTL data have been collected. GDV currently contains: 261,775 transcripts and 402 publications.  (6) Able to leverage significant funding ($4,226,596) from USDA and NSF towards these efforts as a result of support for NRSP10: This funding supports data curation efforts and additional infrastructure development for the Tripal database platform across the NRSP10 databases This funding is important as it highlights that both USDA and NSF support development of Tripal as the standard platform for integrated genomics, genetics and breeding databasest. It further validates the importance of NRSP10 to not only provide resources for underserved crops but extend this resource-efficient, open-source database platform to other crops/animal genomics, genetics and breeding efforts. <ol> <ol> <li>$2,741,575: Genome Database for Rosaceae: Empowering Specialty Crop Research through Big-Data Driven Discovery and Application in Breeding. USDA NIFA SCRI Program, Sep 1, 2014 – Aug 31, 2019 Dorrie Main, Sook Jung, Cameron Peace, Kate Evans, Lisa DeVetter, Nnadozie Oraguzie - Washington State University Ksenija Gasic: Clemson University Mercy Olmstead: University of Florida</li> <li>$1,485,021: Tripal Gateway, a Platform for Next-generation Data Analysis and Sharing. NSF DIBBS Program, Jan 1, 2015-Dec 31, 2017 Stephen Ficklin, Dorrie Main, Sook Jung - Washington State University Jill Wegrzyn: University of Connecticut Margaret Staton: University of Tennessee,  Alex Feltus: Clemson University</li> </ol> </ol> Our plans for next year of NRSP10 are to continue to add new genomics, genetics and breeding data as they become available for each of the databases; migrate remaining databases to Tripal2; release GenSAS v4.0; release Tripal v3.0, release Mainlab Tripal extension modules; finish converting CottonGen, CSFL, GDR CGD, GDV to Tripal 2 with new theme implementation on live site; complete development of new Tripal RefTrans analysis workflow and extension module; complete development of new TripalMap extension module; continue to be very proactive in presenting NRSP10 activities/products at conferences, workshops and meetings and obtaining feedback from our community of users.

Publications

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 16:155.   Bett, K., Ramsay, L., Chan, C., Sharpe, A.G., Cook, D.R., Penmetsa, R.V., Chang, P., Coyne, C.J., McGee, R., Main, D., Vandenberg, A. (2015) Len Gen: The International Lentil Genome Sequencing Project. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   DeVetter, L., Main, D., Jung, S., Cheng, C-H., Lee, T., Blenda, A., Yu, S., Zheng, P., Yu, J., Ficklin, S.P., Evans, K.M., Peace, C., Oraguzie, N., Gasic, K., Olmstead, M. (2015) Resources available for Rubus research through the Genome Database for Rosaceae. Abstracts of the XIth International Rubus and Ribes Symposium; Jun 21-24, 2015; Asheville, NC.   Ficklin, S.P., Lee, T., Humann, J.L., Cheng, C.H., Wegrzyn, J., Neale, D., Main, D. (2015) GenSAS: A web-Based Platform for Automated and Manual Curation of Genomic Sequence. Abstracts of the International Plant and Animal Conference XXIII; January 10-14, 2015; San Diego   Ficklin, S.P., Sanderson, L-A., Cheng, C-H., Jung, S., Bett, K., Main, D. (2015) Tripal Overview and Future Developments. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Grau, E., Wytko, C., Soto, B., Jung, S., Wang, K., Watts, N., Staton, M., Main, D., Wegrzyn, J., Feltus, F., Ficklin, S.P. (2015) Abstracts of the Galaxy Community Conference; July 6-8, 2015; Norwich, UK.   Humann, J., Jung, S., Zheng, P., Cheng, C-H., Lee, T., Frank, M., McGaughey, D., Scott, K., Yu, J., Ficklin, S.P., Sanad, M.N.M.E., Hough, H., Coyne, C., McGee, R., Main, D. (2015) Cool Season Food Legume Genome Database: An up to date resource enabling genetics, genomics and breeding research in chickpea, faba bean, lentil and pea. Abstracts of the North American Pulse Improvement 2015 Biannual Meeting; November 4-6, 2015; Niagara Falls, Canada   Humann, J.L., Ficklin, S.P., Lee, T., Cheng, C-H., Jung, S., Wegrzyn, J.L., Neale, D., Main, D. (2015) GenSAS: An Easy-to-Use, Web-Based Solution for Specialty Crop Genome Annotation. Abstracts of the American Society for Horticultural Science Conference; August 4-7, 2015; New Orleans   Iezzoni, A., Peace, C., Bassil, N., Coe, M., Finn, C., Gasic, K., Luby, J.J., Main, D., McFerson, J., Norelli, J.L., Olmstead, M., Whitaker, V.M., Yue, C. (2015) RosBREED: Combining Disease Resistance with Horticultural Quality in New Rosaceae Cultivars. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Iezzoni, I., Peace, C.P., Bassil, N., Coe, M., Finn, C.E., Gasic, K., Hokanson, S.C., Luby, J.J., Main, D., McFerson, J.R., Norelli, J., Olmstead, M., Whitaker, V.M., Yue, C. (2015) rosBREED2: More Traits, Additional Crops, Expanded Germplasm, New Science. Abstracts of the American Society for Horticultural Science Conference; August 4-7, 2015; New Orleans   Jung, S., Ficklin, S.P., Lee, T., Cheng, C-H., Blenda, A., Yu, J., Zheng, P., Ru, S., Peace, C., Evans, K.M., Oraguzie, N., DeVetter, L., Abbott, A.G., Gasic, K., Olmstead, M., Main, D. (2015) How to Use GDR, the Genome Database for Rosaceae. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Jung, S., Piaskowski, J., Ficklin, S.P., Cheng, C-H., Zheng, P., Olmstead, M., Abbott, A.G., Cedex, d'O., Chen, C., Mueller, L., Gmitter, F.G. jr, Main, D. (2015) Citrus Genome DB Updates. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Jung, S., Yu, J., Lee, T., Cheng, C-H., Ficklin, S.P., Main, D. (2015) CottonGen: Converting Legacy Sites to Tripal. Abstracts of International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Main, D., Ficklin, S.P., Lee, T., Humann, J.L., Cheng, C-H., Wegrzyn, J., Neale, D. (2015) GenSAS. Abstracts of the International Plant and Animal Conference XXIII; January 10-14, 2015; San Diego   Main, D., Jung, S. (2015) Introducing NRSP10L Database Infrastructure for Specialty Crops. Abstracts of the American Society for Horticultural Science Conference; August 4-7, 2015; New Orleans   Main, D., Jung, S., Ficklin, S.P., Cheng, C-H., Lee, T., Zheng, P., Humann, J.L., Yu, J., Blenda, A., Scott, K., Byrd, M., Hough, H., 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.   Main, D., Jung, S., Lee, T., Ficklin, S.P., Cheng, C.H., Blenda, A., Yu, J., Zheng, P., Humann, J., Peace, C., Evans, K., Oraguzie, N., Olmstead, M., Gasic, K. (2015) GDR: A Resource for Rosaceae Breeding. Abstracts of the National Association of Plant Breeders Annual Meeting, July 27-30, 2015; Pullman, WA   Main, D., Jung, S., Lee, T., Ficklin, S.P., Cheng, C-H., 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 Meeting; Jan 27, 2015; Wenatchee.   Main, D., Jung, S., Lee, T., Ficklin, S.P., Cheng, C-H., 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 the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Paul, R., Kuruganti, S., Stevens, K., Gonzalez-Ibeas, D., Martinez-Garcia, P.J., Liechty, J., Vasquez-Gross, H., Grau, E., Loopstra, C., Zimin, A., Holtz-Morris, A., Koriabine, M., Yorke, J.A., Crepeau, M., Puiu, D., Salzberg, S.L., deJong, P.J., Mockaitis, K., Main, D., Langley, C.H., Neale, D., Wegrzyn, J. (2015) Genome Annotation and Repeat Sequence Characterization in Sugar Pine (Pinus lambertiana). Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   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 11:8.   Sanderson, L-A., Ficklin, S.P., Main, D., Bett, K. (2015) Extending Tripal for Specialized Display and Management of Diversity and Breeding data. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Sidhu, G., Mohan, A., Zheng, P., Dhaliwal, A.K., Main, D., Gill, K.S. (2015). Sequencing-Based High Throughput Mutation Detection in Bread Wheat. BMC Genomics 16(1):962.   Verde, I., Shu, S., Jenkins, J., Zuccolo, A., Dettori, M.T., Dardick, C., Rossini, L., Grimwood, J., Pirona, R., Goodstein, D.M., 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, A.G., Morgante, M., Rokhsar, D.S., Schmutz, J. (2015) The Peach v2.0 Release: An Improved Genome Sequence for Bridging the Gap Between Genomics and Breeding in Prunus. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Wegrzyn, J., Stevens, K., Paul, R., Gonzalez-Ibeas, D., Martinez-Garcia, P.J., Liechty, J., Vasquez-Gross, H., Kuruganti, S., Grau, E., Loopstra, C., Zimin, A., Yorke, J.A., Crepeau, M., Puiu, D., Holt, C., Yandell, M., Salzberg, S.L., deJong, P.J., Main, D., Langley, C.H., Neale, D. (2015) Sugar Pine Annotation. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Xu, J., Yu, J., Kohel, R., Percy, R., Beavis, W., Main, D., Yu, J. (2015). Distribution and evolution of cotton fiber development genes in the fibreless G. raimondii genome. Genomics 106:61-69.   Yu, J., Jung, S., Cheng, C-H., Ficklin, S.P., Lee, T., Zheng, P., Jones, D.C., Percy, R.G., Main, D. (2015) CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego   Yu, L-X., Zhang, T., Zheng, P., Li, Y., Main, D., Greene, S.L. (2015). Identification of Loci Associated with Drought Resistance Traits in Heterozygous Autotetraploid Alfalfa (Medicago sativa L.) Using Genome-Wide Association Studies with Genotyping by Sequencing. PloS One 10(9):e0138931   Yu, M., Holdsworth, W., Cheng, P., Grusack, M.A., Mazourek, M., Coyne, C.J., Main, D., McGee, R.J. (2015) Genome-wide SNP identification, linkage map construction and QTL mapping for mineral nutrients in pea. Abstracts of the North American Pulse Improvement 2015 Biannual Meeting; November 4-6, 2015; Niagara Falls, Canada

Impact Statements

Able to leverage significant funding ($4,226,596) from USDA and NSF towards these efforts as a result of support for NRSP10.

Date of Annual Report: 05/16/2018

Report Information

Annual Meeting Dates: 07/30/2016 - 07/30/2016
Period the Report Covers: 10/01/2015 - 09/30/2016

Participants

Abbott, Albert (albert.abbott@uky.edu) - University of Kentucky;
Bassil, Nahla (nahla.bassil@ars.usda.gov) - USDA ARS (OR);
Bell, Richard (richard.bell@ars.usda.gov) - USDA ARS (WV);
Bernardo, Rex (bernardo@umn.edu) - University of Minnesota;
Bielenberg, Doug (dbielen@clemson.edu) - Clemson University;
Bourland, Fred (fbourland@uaex.edu) - University of Arkansas;
Bushakra, Jill (jill.bushakra@ars.usda.gov) - USDA ARS (OR);
Byrne, David (dbyrne@tamu.edu) - Texas A&M University;
Campbell, B. Todd (todd.campbell@ars.usda.gov) - USDA-ARS (SC);
Ethalinda Cannon (ekcannon@iastate.edu) – Iowa State University (IA);
Cantrell, Roy (roy.cantrell@monsanto.com) – Monsanto;
Chee, Peng (pwchee@uga.edu) - University of Georgia;
Chen, Chunxian (Chunxian.Chen@ars.usda.gov) - USDA-ARS (WV);
Cho, Seungho (seungho.cho@monsanto.com) – Monsanto;
Clark, John (jrclark@uark.edu) - University of Arkansas;
Coe, Michael (michael@cedarlakeresearch.com) - Cedar Lake Research;
Coyne, Clare (clarice.coyne@ars.usda.gov) - USDA ARS (WA);
Curtis, Bob (rcurtis@almondboard.com) - Almond Board of California;
Dardick, Chris (chris.dardick@ars.usda.gov) - USDA ARS (WV);
David Stelly (stelly@tamu.edu) - Texas A&M University;
David Stelly (stelly@tamu.edu) - Texas A&M University;
Davis, Tom (tom.davis@unh.edu) - University of New Hampshire;
Dever Jane (jdever@ag.tamu.edu)- Texas A&M AgriLife Research;
Deveter, Lisa (lisa.devetter@wsu.edu) - Washington State University;
Dossett, Michael (michael.dossett@agr.gc.ca) - BC Blueberry Crowers;
Edger, Patrick (edgerpat@msu.edu) - Michigan State University;
Fang, David (david.fang@ars.usda.gov) - USDA ARS (LA);
Fazio, Gennaro (gennaro.fazio@ars.usda.gov) - USDA ARS (NY);
Fernandez, Gina (gefernan@ncsu.edu) - North Carolina State University;
Finn, Chad (chad.finn@ars.usda.gov) - USDA ARS (OR);
Frelichowski, James (james.frelichowski@ars.usda.gov) - USDA ARS (TX);
Gasic, Ksenija (kgasic@clemson.edu) - Clemson University;
Gmitter, Fred jr. (fgmitter@ufl.edu) - University of Florida;
Gross, Briana (blgross@d.umn.edu) - University of Minnesota Duluth;
Grusak, Michael (michael.grusak@ars.usda.gov) - USDA ARS (TX);
Hague, Steve (shague@tamu.edu) - Texas A&M University;
Hinze, Lori (lori.hinze@ars.usda.gov) - USDA ARS (TX);
Hokanson, Stan (hokan017@umn.edu) - University of Minnesota;
Iezzoni, Amy (iezzoni@msu.edu) - Michigan State University;
Jenkins, Johnie (johnie.Jenkins@ars.usda.gov) - USDA-ARS (MS);
Jones, Don (djones@cottoninc.com) - Cotton Incorporated;
Jung, Sook (sook.jung@wsu.edu) - Washington State University;
Knapp, Steve (sjknapp@ucdavis.edu) - University of California Davis;
Koebernick, Jenny (jenny.koebernick@auburn.edu) - Auburn University;
Layne, Desmond (desmond.layne@wsu.edu) Washington State University;
Luby, Jim (lubyx001@umn.edu) - University of Minnesota;
Mahoney, Lise (lise.mahoney@unh.edu) - University of New Hampshire;
Main, Dorrie (dorrie@wsu.edu) - Washington State University;
McCarty, Jack (jack.McCarty@ars.usda.gov) - USDA-ARS (MS);
McFerson, Jim (mcferson@treefruitresearch.com) Washington Tree Fruit Research Commission) State University;
McGee, Rebecca (rebecca.mcgee@ars.usda.gov) - USDA ARS (WA);
Moore, Pat (moorepp@wsu.edu) - Washington State University;
Myers, Gerald (gmyers@agcenter.lsu.edu) - Lousiana State University;
Norelli, Jay (jay.norelli@ars.usda.gov) - USDA ARS (WV);
Olmstead, Mercy (mercy1@ufl.edu) - University of Florida;
Patterson, Andrew (paterson@uga.edu) - University of Georgia;
Peace, Cameron (cpeace@wsu.edu) - Washington State University;
Poland, Jesse (jpoland@ksu.edu) - Kansas State University;
Reighard, Greg (grghrd@clemson.edu) - Clemson University;
Rife, Trevor (trife@ksu.edu) - Kansas State University;
Roose, Mikeal (mikeal.roose@ucr.edu) - University of California Davis;
Saha, Sukamar (sukamar.saha@ars.usda.gov) - USDA ARS (MS);
Saski, Chris (saski@clemson.edu) - Clemson University;
Scheffler, Jodi (jodi.scheffler@ars.usda.gov) - USDA-ARS (MS);
Scorza, Ralph (ralph.scorza@ars.usda.gov) - USDA ARS (WV);
Seabolt, Audrey (grantzau@msu.edu) - Michigan State University;
Slovin, Janet (janet.slovin@ars.usda.gov) - USDA ARS (MD);
Staton, Margaret (mstaton1@utk.edu) - University of Tennessee;
Stover, Ed (Ed.Stover@ars.usda.gov) - USDA ARS (FL);
Swanson, J-D (jd.swanson@salve.edu) - University of Rhode Island;
Udall, Josh (jaudall@byu.edu) - Brigham Young University;
Ulloa, Mauricio (mauricio.ulloa@ars.usda.gov);
Vandermark, George (george.vandermark@ars.usda.gov) - USDA ARS (WA);
Volk, Gayle (gayle.volk@ars.usda.gov) - USDA ARS;
Wegrzyn, Jill (jill.wegrzyn@uconn.edu) - University of Connecticut;
Whitaker, Vance (vwhitaker@ufl.edu) - University of Florida;
Wiesniewski, Michael (michael.wiesniewski@ars.usda.gov) - USDA ARS (WV);
Xu, Kenong (kx27@cornell.edu) - Cornell University;
Yu, John (john.yu@ars.usda.gov) - USDA ARS (TX);
Yue, Chengyang (yuechy@umn.edu) - University of Minnesota;

Brief Summary of Minutes

In person or teleconference discussed meetings held during the year with various special interest groups:

Rosaceae Community Meetings (RosEXEC and GDR Advisory Board): October 28, 2015; January 11, 2016; April 27, 2016; August 31, 2016 Reported progress on GDR activities every quarter (report provided ahead of meetings) and plans for the next quarter to RosEXEC, the advisory board for GDR and the US Rosaeace Genomics, Genetics and Breeding Coordinating Committee. Discussed new sources of data being generated by the community through large projects and how best GDR might host and integrate. Reported on publication of a standard nomenclature for gene designation in the Rosaceae and uptake of standardization in the community and how best to keep promoting this. We also discussed outreach efforts by the GDR team to encourage journals to request data be submitted to GDR by authors.

CottonGen Cotton Breeders Workshop: Cotton Beltwide Conference, New Orleans, Jan 3, 2016 Held a 2 hour workshop for cotton breeders providing use of CottonGen for breeding, including use of the FieldBook App for collecting phenotypic data in the field. Samsung tablets with the FieldBook App were distributed to those breeders who had not already received one for evaluation. We discussed breeders’ needs for data management and analysis capability in the Tripal Breeding Management Information System being developed, as well as access to data in CottonGen. We reviewed the goals of NRSP10 as they relate specifically to CottonGen and the group agreed CottonGen was on track to meet the needs for a community database.

International Cotton Genomics Initiative Officers Meeting, San Diego, CA, Jan 10, 2016 As part of the annual in-person ICGI meeting at PAG we discussed progress in CottonGen with a focus on genomic data and resources and its role in helping coordinate cotton community through the ICGI portal hosted on CottonGen, including hosting biannual office elections and future ICGI conference organization. Committee agreed CottonGen was keeping update to date with data and tools to enable cotton genomics research.

Two day Tripal Hackathon and User Meeting: San Diego, CA, Jan 7-8, 2016 Discussion with participants about plan for Tripal under NRSP10, feedback provided and larger network of Tripal developers built. Tripal Workshop, Plant and Animal Genome Conference: San Diego, CA, Jan 10, 2016 Presentations on Tripal advances and discussion of general future needs for core Tripal and extension modules in development or needed AgBioData Meeting, Plant and Animal Genome Conference, San Diego, CA, Jan 11, 2016 Met with various participants from the agricultural database community to discuss common practices amongst databases, included discussions about NRSP10 and the Tripal platform and how adoptable it was.

GDR Users Meeting at 8^th International Rosaceae Genomics Initiative, Angers, France, June 23, 2016 After the GDR presentations, met with Rosaceae community members to discuss new developments, data acquisition, community annotation using GenSAS and functionality needed in TripalBIMS plus use of the FieldBook App. The feedback received led us to implement a new advanced search in GDR and provide input to FieldBook App developers on improved functionality needed for specialty crop breeders.

NRSP10 Open Meeting at ASHS Annual Conference, Atlanta, GA, August 9, 2016 Met with specialty crop scientists and discussed reasons for switching to Field Book from both a breeding perspective but also the database perspective and role of ontologies and standardization of data for integration and querying. We also went over the progress from the past year and the goals of NRSP10 for the next year. Had detailed discussions about use of SNP arrays and tools needed for their application to facilitate breeding.

Accomplishments

Tripal Progress: In year 2 the major achievement in core Tripal development was the release of an alpha version of Tripal v3 in Jan 2016, set up of a demo site at http//demo.tripal.info/3.X for user exploration, and provision of a demo for stakeholders at the July Tripal users’s conference call. Web service implementation is underway in Tripal 3 which makes Tripal back-end database schema independent and helps overcome some of the limitations of having to use a chado database schema. This provides more flexibility for Tripal use and extends its utility to other genomic, genetic and breeding databases that do not want to be reliant on using Chado. In addition to work on version 3, we worked on finalizing extension modules for Tripal v2 which were developed to be easily upgraded to v3. These extension modules which will be released in November 2016 include a Chado Loader, Chado Data Display and Chado Search. These modules provide site developers with tools 1) to collect and upload data 2) to organize and display data and 3) to enable advanced search functions. Supported data types include organism, marker, QTL, Mendelian Trait Loci, germplasm, map, project, phenotype, genotype and their associated metadata. The Chado Loader module provides data collection templates and PHP loaders to enable site developers to collect and store various types of data that are required to build comprehensive genomic and genetic databases. The Chado Data Display module contains a set of Drupal/PHP templates which can be used as is or customized as desired. The Chado Search module provides comprehensive search and download functionality for sequence, gene, marker, map, QTL, phenotype, genotype and germplasm. Also included are the tools to build map data and species summary pages. The use of materialized views in the Chado Search module enables better performance as well as flexibility of data modeling in Chado, allowing existing Tripal databases with their data stored in different ways to utilize the module. These Tripal Extension modules are implemented in the Genome Database for Rosaceae (rosaceae.org), CottonGEN (cottongen.org) and Cool Season Food Legume Database (coolseasonfoodlegume.org). Other ongoing Tripal extension work includes development of a MapViewer called TripalMap, designed to replace CMap. Outreach efforts to aid community development and adoption of Tripal included: Monthly Tripal developer meetings (includes international attendees), organizing the first Tripal hackathon and the 3rd Tripal workshop at PAG 2016 , keeping the Tripal website current and providing programming support and code to other Tripal groups. At the end of year 2, Tripal was being used by over 90 databases. GenSAS Progress: GenSAS v4.0 was released in January 2016. Major improvements completed in year 2 include; the ability to use high performance computing where jobs can be submitted to a cluster rather than just a single server (enhanced speed); functional annotation capability through the addition of the BLAST, InterProScan, Pfam, SignalP, and TargetP tools to help assign a function to the proteins encoded by the predicted gene models; as well as additional tools added for structural annotation, and integration with JBrowse and WebApollo. Major work started in year 2 for a release of GenSAS v5.0 in January 2016. It includes: (1) ability to upload sequences before project creation so sequence subsets can be created from multiple-sequence fasta files. Sequence subsets can also be filtered by sequence name or minimum size (2) ability to upload RNA-seq reads use them to train gene model predictors (Augustus, during structural step) (3) addition of the tool Tophat to enable alignment specifically for the RNA-Seq reads. Alignment tools (blast, blat, PASA, tophat) are now included as a step before structural annotation (4) structural annotation (previously labelled as the "genes" step) now also has GeneMark for prokaryotic and eukaryotic gene prediction and (5) an official genes step (OGS) was added where users can either use EvidenceModeler to create a genes consensus and use it as the OGS, or can select another data track (from gene prediction program or alignment) as the OGS. Manual curation is merged with the OGS at the end of the GenSAS protocol. It was demonstrated at several conferences (see results disseminated section). In Year 2 GenSAS was accessed by 1,135 visitors from 73 countries, with 2,333 sessions and 7,850 pages viewed. Breeding Tools Progress: We received encouraging feedback from our 20 stakeholder breeders who had been testing or deploying the FieldBook App for collection of phenotypic data in their breeding programs. As a result, we decided to more formally collaborate with the FieldBook PI, Jesse Poland at Kansas State University, and divert funds (0.5 FTE of a developer’s salary) in years 3-5 of NRSP10 to help expedite further development relative to the expressed needs of our breeders. Following an initial needs assessment for breeding information data management tool functionality in year 1, we began BIMS design and implementation in year 2. BIMS will allow breeders to store, manage and analyze all their breeding data within a secure portal that connects their private data with all the data and tools available in their community genomics, genetics and breeding databases. We focused on working with two representative breeding programs from the 25 crops covered in the NRSP10; the peach breeding program of Dr. Kensija Gasic at Clemson University and the USDA ARS cotton breeding program of Dr. Todd Campbell in South Carolina. To gain further breeder input, we demonstrated goals and design of BIMS and FieldBook at several venues in year 2 (see the results disseminated section). These included a dedicated cotton breeder’s workshop we organized at the Cotton Beltwide conference in January 2016, the International Plant and Animal Genome Conference in January 2016, the RosBREED project participants meeting in March 2016, the International Rosaceae Genomics Conference in June 2016 and the American Society for Horticultural Science annual meeting in August 2016. By the end of year 2 the design of BIMS was decided and programming initiated. NRSP10 Databases Progress: In year 2 we completed upgrade of the CottonGen and GDR databases to Tripal 2 and Durpal 7 with a more user-friendly design on the live site and have done the same for the Citrus (CGD) and Vaccinium (GDV) databases on the development site. We are in the process of updating the data in the latter two and will go live with the new design in year 3. Significant data and new functionality have been added to all five databases. The specific details are documented in the work completed page of each database. Use of the databases continued to increase compared with year 1 as more data and functionality was added. During the reporting period the databases were accessed as follows (as recorded by Google Analytics): GDR - accessed by 19,272 users from 152 countries, who viewed 232,162 pages; CottonGen - accessed by 9,422 users from 139 countries, who viewed 134,123 pages; CSFL - accessed by 2,982 users from 114 countries, who viewed 22,162 pages; CGD - accessed by 4,516 users from 123 countries, who viewed 24,064 pages; GDV- accessed by 1,349 users from 77 countries, who viewed 6,116 pages. Leveraged Federal Funding: Added new NSF funded project ($2,983,307) to increase federal funding leveraged for NRSP10 efforts to $7,209,903 (listed below). This funding supports data curation efforts and additional infrastructure development for the Tripal database platform across the NRSP10 databases and adds forest/hardwood trees databases to the Tripal community of databases. This funding is important as it highlights that USDA and NSF recognize the need to support Tripal as the standard platform for database development. It further validates the importance of NRSP10 to not only provide resources for underserved crops but extend this resource-efficient, open-source database platform to other crops/animal genomics, genetics and breeding efforts. <ul> <li>$2,983,307: Standards and CyberInfrastructure that Enable Big-Data Driven Discovery for Tree Crop Research. NSF PGRP, July 1, 2016 – June 30, 2019, to Dorrie Main, Sook Jung Stephen Ficklin - Washington State University; Jill Wegrzyn: University of Connecticut; Margaret Staton: University of Tennessee,　 Albert Abbott: University of Kentucky </li> </ul> <ul> <li>$2,741,575: Genome Database for Rosaceae: Empowering Specialty Crop Research through Big-Data Driven Discovery and Application in Breeding. USDA NIFA SCRI Program, Sep 1, 2014 – Aug 31, 2019, to Dorrie Main, Sook Jung, Cameron Peace, Kate Evans, Lisa DeVetter, Nnadozie Oraguzie - Washington State University; Ksenija Gasic: Clemson University Mercy Olmstead: University of Florida </li> </ul> <ul> <li>$1,485,021: Tripal Gateway, a Platform for Next-generation Data Analysis and Sharing. NSF DIBBS Program, Jan 1, 2015-Dec 31, 2017, to Stephen Ficklin, Dorrie Main, Sook Jung - Washington State University; Jill Wegrzyn: University of Connecticut; Margaret Staton: University of Tennessee;　 Alex Feltus: Clemson University </li> </ul> Our plans for year 3 of NRSP10 are to 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.

Publications

Jung, S., Lee, T., Yu, J., Ficklin, S.P., Main, D. (2016). Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. Database (Oxford) baw010. Ma, Y., Myers, J.R., Mazourek, M., Coyne, C.J., Main, D., Humann, J.L., McGee, R. (2016). Development of SCAR markers linked to sin-2, the stringless pod locus in pea (Pisum sativum L.). Molecular Plant Breeding 36(7):1-10. Shin, S.S., 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 94:16-26. 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 3, 16015. Sidhu, G., Mohan, A., Zheng, P., Dhaliwal, A.K., Main, D., Gill, K.S. (2015). Sequencing-Based High Throughput Mutation Detection in Bread Wheat. BMC Genomics 16(1):962. Bett K, Ramsay L, Chan C, Sharpe AG, Cook DR, Penmetsa RV, Chang P, Coyne CJ, McGee R, Main D, Edwards D, Kaur S, Vandenberg A (2016) Lentil 1.0 and Beyond. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego, USA. 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. 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. 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. 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. 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. Humann JL, Ficklin SP, Lee T, Cheng C-H, Jung S, Wegrzyn J, Neale D, Main D (2016) GenSAS v4.0: An Easy-to-Use, Web-Based Platform for Structural and Functional Genome Annotation and Curation. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA. Humann JL, Ficklin SP, Lee T, Cheng C-H, Jung S, Wegrzyn J, Neale D, Main D (2016) Gensas v5.0: An Easy-to-use, Web-based Platform for Individual or Collaborative Structural and Functional Genome Annotation and Curation. Abstracts of the American Society for Horticultural Science Conference; August 7-11, 2016; Atlanta, USA. Humann JL, Jung S, Zheng , Cheng C-H, Lee T, Frank M, McGaughey D, Scott K, Yu J, Ficklin SP, Sanad MNME, Hough H, Coyne C, McGee R, Main D (2016) Cool Season Food Legume Genome Database: An Up-to-Date Resource Enabling Genetics, Genomics and Breeding Research in Pea, Lentil, Faba Bean and Chickpea. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA. Humann JL, Jung S, Zheng P , Cheng C-H, Lee T, Frank M, McGaughey D, Scott K, Yu J, Ficklin SP, Sanad MNME, Hough H, Coyne C, McGee R, Main D (2016) Cool Season Food Legume Genome Database: An up-to-Date Resource Enabling Genetics, Genomics and Breeding Research in Pea, Lentil, Faba Bean and Chickpea. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA. Humann JL, Jung S, Zheng P , Cheng C-H, Lee T, Frank M, McGaughey D, Scott K, Yu J, Ficklin SP, Sanad MNME, Hough H, Coyne C, McGee R, Main D (2016) Cool Season Food Legume Genome Database: An up-to-Date Resource Enabling Genetics, Genomics and Breeding Research in Pea, Lentil, Faba Bean and Chickpea. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA. Humann, J, JungS, Zheng P, ChengC-H, Lee T, Frank M, McGaughey D, Scott K, Yu J, Ficklin SP, Sanad MNME,, Hough H, Coyne C, McGee R, Main D(2015) Cool Season Food Legume Genome Database: An up to date resource enabling genetics, genomics and breeding research in chickpea, faba bean, lentil and pea. Abstracts of the North American Pulse Improvement 2015 Biannual Meeting; November 4-6, 2015; Niagara Falls, Canada 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. 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 8thInternational Rosaceae Genomics Conference; June 21-24, 2016; Angers, France. 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. 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. Jung, S., Bassett, C., Bielenberg, D.C., Cheng, C-H., Dardick, C., Main, D., Meisel, L., Slovin, J., Troggio, M., Schaffer, R.J. (2015) A standard nomenclature for gene designation in the Rosaceae. Tree Genetics & Genomes 11(5): 108 Jung, S., Lee, T., Yu, J., Ficklin, S.P., Main, D. (2016). Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. Database (Oxford) baw010. Long-Xi Yu, Zheng P, Ho J, Bhamidimarri S, Main D (2016) A Whole Genome Association Study on Verticillium Wilt Resistance in Heterozygous Autotetraploid Alfalfa (Medicago sativa L.). Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA. Ma Y, Holdsworth B, Cheng P, Mazourek M, Coyne C, Main D, McGee R (2016) Genome-wide SNP identification, linkage map construction and QTL mapping for mineral nutrients. Poster presentation at WSU Academic Showcase, March 25, 2016, Pullman, WA Ma Y, Holdsworth B, Cheng P, Mazourek M, Coyne C, Main D, McGee R (2016) Genome-wide SNP identification, linkage map construction and QTL mapping for mineral nutrients. Poster presentation at WSU Molecular Plant Sciences Retreat, March 5, 2016, Pullman, WA Ma, Y., Myers, J.R., Mazourek, M., Coyne, C.J., Main, D., Humann, J.L., McGee, R. (2016). Development of SCAR markers linked to sin-2, the stringless pod locus in pea (Pisum sativum L.). Molecular Plant Breeding 36(7):1-10. 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. 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. 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. 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. 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. 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. Main D, Jung S, Kahn M, Peace C, Mcferson J (2016) Overview of NRSP and Planned Tripal development. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA. Main D, Jung S, Lee T, Cheng C-H, Yu J, Gasic K, Campbell BT, Evans KM, Peace C (2016) TripalBIMS: development of a Breeding Information Management System. Abstracts of Cotton Breeders Workshop, 2016 Cotton Beltwide Conference; January 5-7, 2016; New Orleans, USA. Main D, Rife T, Poland JA, Gasic K, Jung S, Campbell BT, Evans KM (2016) Introduction to Field Book: An Open-source Android App for Collecting Phenotypic Data in a Breeding Programs. Abstracts of Cotton Breeders Workshop, 2016 Cotton Beltwide Conference; January 5-7, 2016; New Orleans, USA. Main D, Yu J, Jung S, Cheng CH, Lee T, Zheng P, Humann JL, McGaughey D, Hough H, Ficklin SP, Campbell BT, Percy RG, Jones DC (2016) Overview of CottonGen for Breeders. Abstracts of Cotton Breeders Workshop, 2016 Cotton Beltwide Conference; January 5-7, 2016; New Orleans, USA. 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. Reid R, Brown A, Main D, Broewer C, Walstead RN, Chen Y (2016) Blueprints for Blueberry: A Genome Assembly and Annotation. Abstracts of the International Plant and Animal Genome Conference XXIV; January 9-13, 2016; San Diego, USA. 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 3, 16015. 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. Shin, S.S., 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 94:16-26. Sidhu, G., Mohan, A., Zheng, P., Dhaliwal, A.K., Main, D., Gill, K.S. (2015). Sequencing-Based High Throughput Mutation Detection in Bread Wheat. BMC Genomics 16(1):962. Yu J, Jung S, Cheng CH, Lee T, Buble K, Zheng P, Humann JL, McGaughey D, Hough H, Ficklin SP, Camobell BT, Percy RG, Jones DC, Main D (2016) Updates to CottonGen: The Community Database for Genomics, Genetics and Breeding Research in Cotton. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego, USA. Yu J, Jung S, Cheng CH, Lee T, Buble K, Zheng P, Humann JL, McGaughey D, Hough H, Ficklin SP, Camobell BT, Percy RG, Jones DC, Main D (2016) Updates to CottonGen: The Community Database for Genomics, Genetics and Breeding Research in Cotton. Abstracts of the International Plant and Animal Genome Conference XXIII; January 10-14, 2015; San Diego, USA. Yu J, Jung S, Cheng CH, Lee T, Buble K, Zheng P, Humann JL, McGaughey D, Hough H, Ficklin SP, Campbell BT, Percy RG, Jones DC , Main D (2016) CottonGen: Current Functionality and Future Direction. 2016 World Cotton Research Conference 6 and 2016 ICGI Conference; May 2-6, 2016;. Goiânia, Brazil Yu J, Jung S, Cheng CH, Lee T, Zheng P, Humann JL, McGaughey D, Hough H, Ficklin SP, Campbell BT, Percy RG, Jones DC , Main D (2016) New Breeding Data and Tools in CottonGen: The Community Resource for Cotton Genomics, Genetics and Breeding Researches. Abstracts of the Cotton Improvement Conference, 2016 Cotton Beltwide Conference; January 5-7, 2016; New Orleans, USA. Yu M, Holdsworth W, Cheng P, Grisack MA, Mazourek M, Coyne C, Main D, McGee RJ (2015) Genome-wide SNP identification, linkage map construction and QTL mapping for mineral nutrients in pea. Abstracts of the North American Pulse Improvement 2015 Biannual Meeting; November 4-6, 2015; Niagara Falls, Canada

Impact Statements

Attracted significant funding ($7,209,903)) from USDA and NSF to further leverage support for NRSP10 databases as described in the NRSP10 proposal

Date of Annual Report: 05/17/2018

Report Information

Annual Meeting Dates: 07/30/2017 - 07/30/2017
Period the Report Covers: 10/01/2016 - 09/30/2017

Participants

Abbott, Albert (albert.abbott@uky.edu) - University of Kentucky;
Anguiano, Mario (gabriel.anguiano@bayer.com) - Bayer Crop Science;
Ayele, Addissu (addissu.ayele@ttu.edu) - Texas Tech University;
Ayre, Brian (Brian.Ayre@unt.edu) - University of North Texas;
Bassil, Nahla (nahla.bassil@ars.usda.gov) - USDA ARS (OR);
Bernardo, Rex (bernardo@umn.edu) - University of Minnesota;
Bourland, Fred (fbourland@uaex.edu) - University of Arkansas;
Bretting, Peter (peter.bretting@ars.usda.gov) – USDA ARS;
Bushakra, Jill (jill.bushakra@ars.usda.gov) - USDA ARS (OR);
Campbell, B. Todd (todd.campbell@ars.usda.gov) - USDA-ARS (SC);
Cantrell, Roy (roy.cantrell@monsanto.com) – Monsanto;
Carter, Katie (katie.carter@oregonstate.edu) - Oregon State University;
Chavez, Dario (dchavez@uga.edu) - University of Georgia;
Chee, Peng (pwchee@uga.edu) - University of Georgia;
Chen, Chunxian (Chunxian.Chen@ars.usda.gov) - USDA-ARS (WV);
Cheng, Max (zcheng@utk.edu) - University of Tennessee;
Coe, Michael (michael@cedarlakeresearch.com) - Cedar Lake Research;
Coyne, Clare (clarice.coyne@ars.usda.gov) - USDA ARS (WA);
Curtis, Bob (rcurtis@almondboard.com) - Almond Board of California;
Dardick, Chris (chris.dardick@ars.usda.gov) - USDA ARS (WV);
Dever Jane (jdever@ag.tamu.edu)- Texas A&M AgriLife Research;
Dossett, Michael (michael.dossett@agr.gc.ca) - BC Blueberry Crowers;
Evans, Kate (kate.evans@wsu.edu) - Washington State University;
Fang, David (david.fang@ars.usda.gov) - USDA ARS (LA);
Fazio, Gennaro (gennaro.fazio@ars.usda.gov) - USDA ARS (NY);
Fernandez, Gina (gefernan@ncsu.edu) - North Carolina State University;
Ficklin, Stephen (stephen.ficklin@wsu.edu) – Washington State University
Finn, Chad (chad.finn@ars.usda.gov) - USDA ARS (OR);
Fraser, Dawn (dawn.e.fraser@monsanto.com) – Monsanto;
Frelichowski, James (james.frelichowski@ars.usda.gov) - USDA ARS (TX);
Gasic, Ksenija (kgasic@clemson.edu) - Clemson University;
Gmitter, Fred jr. (fgmitter@ufl.edu) - University of Florida;
Gross, Briana (blgross@d.umn.edu) - University of Minnesota;
Grusak, Michael (michael.grusak@ars.usda.gov) - USDA ARS (ND);
Gusemann, Jessica (jeddica.gusemann@ars.usda.gov) - USDA ARS (WV);
Hague, Steve (shague@tamu.edu) - Texas A&M University;
Hinze, Lori (lori.hinze@ars.usda.gov) - USDA ARS (TX);
Hokanson, Stan (hokan017@umn.edu) - University of Minnesota;
Honaas, Loren (loren.honass@ars.usda.gov) - USDA ARS (WA);
Iezzoni, Amy (iezzoni@msu.edu) - Michigan State University;
Jones, Don (djones@cottoninc.com) - Cotton Incorporated;
Jung, Sook (sook.jung@wsu.edu) - Washington State University;
Kahn, Michael (kan@wsu.edu) - Washington State University;
Khan, Awais (Mak427@cornell.edu) - Cornell University;
Knapp, Steve (sjknapp@ucdavis.edu) - University of California Davis;
Koebernick, Jenny (jenny.koebernick@auburn.edu) - Auburn University;
Koepke, Tyson (tyson@phytelligence.com) – Phytelligence;
Kuraparthy, Vasu (vasu_kuraparthy@ncsu.edu) - North Carolina State University;
Layne, Desmond (desmond.layne@wsu.edu) Washington State University;
Liu, Zhongchi (zliu@umd.edu) - University of Maryland;
Luby, Jim (lubyx001@umn.edu) - University of Minnesota;
Mahoney, Lise (lise.mahoney@unh.edu) - University of New Hampshire;
Main, Dorrie (dorrie@wsu.edu) - Washington State University;
McCarty, Jack (jack.McCarty@ars.usda.gov) - USDA-ARS (MS);
McFerson, Jim (jim.mcferson@wsu.edu) Washington State University;
McGee, Rebecca (rebecca.mcgee@ars.usda.gov) - USDA ARS (WA);
Moore, Pat (moorepp@wsu.edu) - Washington State University;
Myers, Gerald (gmyers@agcenter.lsu.edu) - Louisiana State University;
Mueller, Lukas (iam86@cornell.edu) – Boyce Thompson Institute
Norelli, Jay (jay.norelli@ars.usda.gov) - USDA ARS (WV);
Olmstead, Mercy (mercy1@ufl.edu) - University of Florida;
Patterson, Andrew (paterson@uga.edu) - University of Georgia;
Peace, Cameron (cpeace@wsu.edu) - Washington State University;
Poland, Jesse (jpoland@ksu.edu) - Kansas State University;
Rife, Trevor (trife@ksu.edu) - Kansas State University;
Saha, Sukamar (sukamar.saha@ars.usda.gov) - USDA ARS (MS);
Saski, Chris (saski@clemson.edu) - Clemson University;
Scheffler, Jodi (jodi.scheffler@ars.usda.gov) - USDA-ARS (MS);
Seabolt, Audrey (grantzau@msu.edu) - Michigan State University;
Slovin, Janet (janet.slovin@ars.usda.gov) - USDA ARS (MD);
Staton, Margaret (mstaton1@utk.edu) - University of Tennessee;
Stelly, David (stelly@tamu.edu) - Texas A&M University;
Stover, Ed (Ed.Stover@ars.usda.gov) - USDA ARS (FL);
Swanson, J-D (jd.swanson@salve.edu) - University of Rhode Island;
Thompson, Alison (alison.thompson@ars.usda.gov) - USDA ARS (AZ);
Thompson, Ellen ( a.ellen.thompson@gmail.com) - Pacific Berry Breeding;
Udall, Josh (jaudall@byu.edu) - Brigham Young University;
Ulloa, Mauricio (mauricio.ulloa@ars.usda.gov) - USDA ARS (CA);
Vandermark, George (george.vandermark@ars.usda.gov) - USDA ARS (WA);
Volk, Gayle (gayle.volk@ars.usda.gov) - USDA ARS;
Wegrzyn, Jill (jill.wegrzyn@uconn.edu) - University of Connecticut;
Whitaker, Vance (vwhitaker@ufl.edu) - University of Florida;
Wiesniewski, Michael (michael.wiesniewski@ars.usda.gov) - USDA ARS (WV);
Worthington, Margaret (mlworthi@uark.edu) - University of Arkansas;
Xu, Kenong (kx27@cornell.edu) - Cornell University;
Yu, John (john.yu@ars.usda.gov) - USDA ARS (TX);
Yue, Chengyang (yuechy@umn.edu) - University of Minnesota

Brief Summary of Minutes

In person or teleconference discussed meetings and workshops held during the year with various special interest groups:

Rosaceae Community Meetings (RosEXEC and GDR Advisory Board): October 31, 2016; January 15, 2017; April 26, 2017; July 27, 2017 Reported progress on GDR activities every quarter (report provided ahead of meetings) and plans for the next quarter to RosEXEC, the advisory board for GDR and the US Rosaeace Genomics, Genetics and Breeding Coordinating Committee. Discussed new data being generated by the community that should be added to GDR, how we need to start looking at possibility of providing access to high throughput phenotypic data being generated for certain Rosaceae crops (not yet available to share), how to best educate the scientific community on using standard nomenclature for map, marker, QTL and gene naming. We also discussed plans to host the first GDR workshop at the Plant and Animal Genome Conference in San Diego, who should be asked to present and how we would like to organize the discussion at the end.

CottonGen Breeders Workshop, Beltwide Conference, Dallas, TX, Jan 4, 2017 Two hour workshop providing training on how to use the FieldBook App for collecting phenotypic data, presenting development of the CottonGen Tripal Breeding Information Management System (BIMS) and other resources in CottonGen. Resulted in all the breeders attending and some allied scientists being given hand held tablets with the FieldBook App installed to test and review. Detailed discussions provided valuable feedback on priorities for BIMS functionality for cotton breeders.

Two day Tripal Hackathon and User Meeting: San Diego, CA, Jan 12-13, 2017 Reviewed code for existing core Tripal functionality and extension modules available, and discussed future plans for development of Tripal 3. Continue to develop a larger network of Tripal developers.

GDR Training Workshop, Plant and Animal Genome Conference, San Diego, CA, Jan 14, 2017 Two hour workshop with a series of presentations mainly by users of GDR resources on how they used the database - Using GDR: An Overview (Sook Jung) - Use of Strawberry Genomic Resources in GDR (Richard Harrison) - Using the New Apple Genome Assembly v4.0 Data in GDR (Riccardo Velasco) - The GDR Is a Critical Resource for Developing and Refining Trait-Predictive DNA Tests (Cameron Peace) - Using Field Book App and Bims in GDR for Peach Breeding (Ksenija Gasic) - Open Discussion on GDR (moderated by Michael Coe)

International Cotton Genomics Initiative Officers Meeting, San Diego, CA, Jan 15, 2017 As part of the annual in-person ICGI meeting at the Plant and Animal Genome Conference, we discussed progress in collecting an curating genomic data for CottonGen and discussed projects that would likely deposit data in the following year; genomic tools needed for distilling and re-using RNA Seq data deposited in the NCBI SRA so it could be used by the community, and performing and visualizing synteny data. We also discussed the role of continuing role of CottonGen to host ICGI portal as part of the database.

Tripal Workshop, Plant and Animal Genome Conference: San Diego, CA, Jan 15 2017 Series of presentations on Tripal advances and discussion of general future needs for core Tripal and extension modules in development or needed. - Tripal Introduction and Core Development Efforts (Stephen Ficklin) - Development of TripalMap (Katheryn Buble) - Extending Tripal for Community-Based Management and Distribution of Genotypic and Phenotypic Data (Lacey-Anne Sanderson) - CartograTree Workflows with Tripal API for Association Mapping in Forest Trees (Nic Herndon) - Mainlab Chado Loader, Data Display and Search for Sequence, Map, Marker, QTL, Genotype, Phenotype and Germplasm Data (Sook Jung) - Customizing Tripal Sites with Non-Tripal Components at the Legume Information System and Peanutbase (Sudhansu Dash) - The i5k Workspace@Nal (Christopher Childers) AgBioData Meeting, Plant and Animal Genome Conference, San Diego, CA, Jan 11, 2016 Meeting with various participants from the agricultural database community to progress in developing communication and collaboration among the Agricultural Biological Database community (AgBioData). Successfully requested supplementary funding to PI Main’s 2016 PGRP award to hold a 2 day workshop on this topic and write a whitepaper. Developed and hosted the AgBioData website for the consortium (https://www.agbiodata.org).

5th International Research Conference on Huanglongbing, Orlando, FL, March 14-17, 2017 Presented update on Citrus Genome Database and had discussions with citrus scientists on needs for the database to expand and include more data and tools relevant to citrus greening

AgBioData Workshop, Salt Lake City, UT, April 18-19, 2017 The workshop brought together 42 scientists associated with more than 20 agricultural databases and supporting resources to achieve two main goals: (1) Planning for writing a white paper to define key components of genomic, genetic, and breeding (GGB) databases in agriculture; recommend best practices for these components; and identify immediate, future and unmet needs across databases; and (2) Plan a submission of a NSF Research Coordination Network grant to help us continue to coordinate and collaborate across agricultural GGB databases. A key component of these activities and discussion was sustainability of these databases and how to build resource-efficient, useful databases. Tripal databases were well represented and part of these discussions.

ASPB Conference, Honolulu, HI, June 24-28, 2017 Presented NRSP resources (databases and GenSAS) at the Plant Database Booth and at the Bioinformatics Workshop. Networked with basic scientists on utility and needs of current resources for this component of the databases. Emphasized need for the databases to be current with genomic data and mapping of genes between new assemblies or different annotations (e.g. NCBI vs Phytozome annotations with different gene names being used).

NRSP10: Bioinformatic and Database Resources for Specialty Crops Workshop at ASHS Annual Conference, Big Island, HI, Sept 21, 2017 Two hour workshop with a series of presentations on resources available from NRSP10, followed by a discussion session on progress and future plans and direction. - What Is NRSP10 and What Can It Do for Specialty Crop Research (Dorrie Main) - NRSP10 Resources for Translational Tree Fruit Research (Cameron Peace) - Using Tripal As a Project Database (Meg Staton) - NRSP10 Resources for Small Fruit Research (Nahla Bassil) - Using Gensas for Specialty Crop Community Genome Annotation (Jodi Humann) - Using Fieldbook and Other Free Apps for Specialty Crop Field and Lab Data Collection (Trevor Rife) - A Breeders Perspective on Using the Breeding Information Management System for Fruit Breeding (Ksenija Gasic) - Open Discussion on Direction of NRSP10 (moderated by Michael Kahn)

Cotton Breeders Tour, Phoenix, AZ, Sept 24-26, 2017 Presentations on CottonGen and the Breeding Information Management system by two users. Informal discussions followed on utility and timeline for additional data, functionality and community resources requested in CottonGen, such as a SNP genotyping search and visualization tools and synteny visualization tools. - A Breeders Perspective on using the Breeding Information Management System for Cotton Breeding (Todd Campbell) - CottonGen: An Overview for Breeders (Josh Udall)

Accomplishments

Tripal Progress: Major progress for Tripal in Yr3 includes releases of Core Tripal (v2.1, v3.0.rc1, v3.0.rc2); and release of several Tripal Extension modules. These included modules to load, search and display sequence, map, marker, QTL, genotype, phenotype and germplasm data and implementation of the popular search engine Elasticsearch for the chado database tables that has now enabled cross-database site querying capability; Tripal Analysis Expression modules and Tripal Galaxy and associated workflows. There are now over 31 Tripal extension modules available to use or test from the Tripal.info site, with many more under development including the Tripal MapViewer, Tripal Synteny, Tripal Galaxy etc. Outreach efforts provided for Tripal include monthly conference calls, 2 day hackathon, Tripal workshop held at Plant and Animal Genome Conference, 258 correspondences through the Tripal support mailing list, ), keeping the Tripal website (https://tripal.info) current and providing programming support and code to other Tripal groups. Tripal is now being used for more than 100 species/clade/project databases. GenSAS Progress: GenSAS v5.0 released in January 2017. Major improvements completed include (1) ability to upload sequences before project creation so sequence subsets can be created from multiple-sequence fasta files. Sequence subsets can also be filtered by sequence name or minimum size (2) ability to upload RNA-seq reads use them to train gene model predictors (Augustus, during structural step) (3) addition of the tool Tophat to enable alignment specifically for the RNA-Seq reads. Alignment tools (blast, blat, PASA, tophat) are now included as a step before structural annotation (4) structural annotation (previously labelled as the "genes" step) now also has GeneMark for prokaryotic and eukaryotic gene prediction and (5) an official genes step (OGS) was added where users can either use EvidenceModeler to create a genes consensus and use it as the OGS, or can select another data track (from gene prediction program or alignment) as the OGS. Manual curation is merged with the OGS at the end of the GenSAS protocol. GenSAS was demonstrated/presented at several conferences. In Year 3 GenSAS was accessed by 1,779 visitors from 76 countries, with 6,434 sessions and 27,566 pages viewed. Breeding Tools Progress: In year 3 of the NRSP10 we continued development of the Tripal Breeding Information Management System (BIMS) and the phenotype data collection tool FieldBook App (Poland Program). New functionality includes the ability to view and download breeding data by cross population; generate trait and field files as input files for the Field Book App; ability for users to upload exported trait and field files to the database from excel templates or the FieldBook App; improved error checking for trait evaluation data to prevent outliers and flag invalid data prior to uploading; ability to create lists and generate statistics on them; and enhanced search stock functionality. We currently have peach and cotton breeding program data loaded in BIMS with functionality under testing by the respective breeding programs. Development on Field Book has primarily focused on adding user-requested features and patching user-reported bugs. A new trait format, 'Location', was added to facilitate collection of location point data and ability to add traits as a multi-trait category. A button was added to the main screen for missing values to help breeders distinguish between missing data and missing entries. Users can now load files directly from Dropbox, eliminating a file transfer step and streamlining the data collection process. Photos now also include the name of the trait to help researchers know better what they're looking at. A dedicated Android programmer was hired in the Poland lab in January 2017 to work on rewriting parts of the apps to fix bugs, increase efficiency, and better-adhere to best programming practices. Handheld Samsung tablets with Field Book have been provided to more than 50 NRSP10 associated breeders and allied researchers to test and use. A Field Book App and BIMS webinar was held in November, 2016 and FieldBook and BIMS were presented at several conferences NRSP10 Databases: In year 3 we completed the upgrade of the Genome Database for Vaccinium, all five databases are now current in Tripal 2.1 and Drupal 7. CSFL and GDV have been converted to the next version, Tripal 3, on the development server and are being tested. Significant new data and functionality has been added to all five databases (documented in the work completed section of each database) and CGD has been expanded to include information specifically relevant to HLB research. The NRSP10 website (https://www.nrsp10.org) was updated with information so it is current and a website was developed and hosted the AgBioData website for the consortium (https://www.agbiodata.org).Usage of the five NRSP databases continues to grow and in 2017 was as follows: GDR - 21,845 users from 157 countries, 392,245 pages viewed; CottonGen - 11,328 users from 138 countries, 212,204 pages viewed; CSFL - 3,306 users from 110 countries, 34,475 pages viewed; CGD - 5,410 users from 127 countries, 76,653 pages viewed; and GDV -2,265 users from 91 countries, 21,781 pages viewed. Our plans for Year 4 of NSRP10 are as follows: (1) GenSAS: Further develop GenSAS to add more tools and error checking of assemblies, and create a GenSASLite version that directly plugs into Tripal for better community curation within Tripal databases (2) BIMS: Further develop BIMS by adding more searching and analysis capability, with more testing by additional breeding programs, and provision of training workshops.(3) Keep the NRSP10 databases current with tools and data while serving as community communication portals for their respective communities (4) Continue contributing to development of Tripal Core and Tripal Extension Module Development while providing advocacy and support for Tripal database adoption and module development by the developer community (help desk, web site, hackathon, monthly meetings) (5) Further participate in database advocacy by contributing to the publication of the Agricultural Biological Database (AgBioData) whitepaper, contributing to the NSF Data Repository Sustainability Process Guide and participating in other database outreach activities of the AgBioData Consortium (6) present the outcomes of NRSP10 through peer-reviewed publications, conferences, meetings and training activities and specifically develop outreach materials to inform industry of NRSP10 activities and their contribution to basic, translational and applied research.

Publications

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. Resources in the Genome Database for Rosaceae for Peach Research. Acta Horticulturae (in press). 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) bax092. 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.2017.1172.20. Ma, Y., Coyne, C.J., Main, D., Pavan, S., Sun, S., Zhu, Z., Zong, X., Leitao, J., McGee, R.J. (2017). Development and validation of breeder-friendly KASPar markers for er1, a powdery mildew resistance gene in pea (Pisum sativum L.). Molecular Breeding 37:151. Ma, Y., Coyne, C.J., Grusack, M., Mazourek, M., Cheng, P., Main, D., McGee, RJ. (2017) Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.) BMC Plant Biology 17(1):43  Yu, L.X., Zheng, P., Zhang, T., Rodringuez, J., Main, D. (2017) Genotyping‐by‐sequencing‐based genome‐wide association studies on Verticillium wilt resistance in autotetraploid alfalfa (Medicago sativa L.). Molecular Plant Pathology 18(2):187-194  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  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  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  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  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  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  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  Yu, J., Jung, S., Cheng, C.H., Lee, T, Zheng, P., Humann, J., McGaughey, D., Frank, M., Hough, H., Campbell, B.T., Percy, R.G., Jones, D.C., Main, D. 2017. CottonGen: An upto-date Resource for Cotton Genomics, Genetics and Breeding Research. Abstracts of the International Plant and Animal Genome Conference XXV; January 14-18, 2017; San Diego, USA  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  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  Humann, J.L., Piaskowski, J., Jung, S., Cheng, C-H., Lee, L., Frank, M., Scott K., Zheng, P., Flores, M., Saha, S., Mueller, L.A., Gmitter, F.G. jr, Abbott, A.G., and Main, D. 2017. Resources in the Citrus Genome Database that enable basic, translational, and applied research. 5th International Research Conference on Huanglongbing, Mar. 15-17, 2017, Orlando, FL. Journal of Citrus Pathology, 2017, 4(1):20.  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, South Korea  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  Jung S., Lee, T., Gasic, K., Campbell, B.T., Cheng C-H., Yu, Y., Humann, J.L., Evans, K., Peace, C., and Main, D. 2017. TripalBMS: the Breeding Management System in Tripal for efficient management of private breeding data that are integrated with public genomic and genetic data. 2017. Proceedings of the American Society of Plant Biologist Annual Meeting; June 24-28, 2017; Honolulu, HI  Main, D., Humann, J.L., Lee, T., Ficklin, S.P., Cheng, C-H., Hough, H., Jung, S., Wegrzyn, J.L., and D.B. Neale. 2017. Structural and functional annotation of model and non-model organisms with GenSAS v5.0, a web-based annotation platform. Proceedings of the American Society of Plant Biologist Annual Meeting; June 24-28, 2017; Honolulu, HI  Main, D., Jung, S., Kahn, M., Peace, C., and J. McFerson. 2017. National Research Support Project 10. American Society of Plant Biologist Annual Meeting June 24-28, 2017, Honolulu, HI  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  Gasic, K., Lee, T., Jung, S., and 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, Waikoloa, HI  Jung S., Lee, T., Cheng, C.H., Zheng, P., Humann, J.L., Yu, J., Scott, K., Frank, M., McGaughey, D., Hough, H., Gasic, K., Evans, K., Peace, C., McFerson, J., Coe, M., and Main, D,. 2017. Resources for Breeders in the Genome Database for Rosaceae. . Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI  Bassil, N., Jung, S., Cheng, C-H., Lee, T., Zheng, P., and Main, D., 2017. NRSP10 Resources for Small Fruit Research. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI  Humann, J.L., Lee, T., Ficklin, S.P., Cheng, C-H., Hough, H., Jung, S., Wegrzyn, J.L., and D.B. Neale. 2017. Using Gensas for Specialty Crop Community Genome Annotation. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI  Humann, J., Piaskowski, J., Jung, S., Cheng, C-H., Lee, L., Frank, M., Scott K., Zheng, P., Flores, M., Saha, S., Mueller, L.A., Gmitter, F.G. jr, Abbott, A.G., and Main, D. 2017. Citrus Genome Database: Resources That Enable Basic, Translational, and Applied Research. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI  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, Waikoloa, HI  Peace, C., Vanderzande, S., Iezzoni, A., Jung, S., and Main, D. 2017. NRSP10 Resources for Translational Tree Fruit Research. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI  Main, D., Jung, S., Kahn, M., Peace, C., and J. McFerson. 2017. What Is NRSP10 and What Can It Do for Specialty Crop Research. Proceedings of the ASHS Annual Conference; September 19-22, Waikoloa, HI  Campbell B.T., Lee, T., Jung, S., Yu, J., Jones, D., and Main, D. 2017. A Breeders Perspective on using the Breeding Information Management System for Cotton Breeding. Proceedings of the 2017 Cotton Breeders Tour, September 24-26, Arizona.  Udall, J., Yu, J., Jung, S., Cheng, C.H., Lee, T, Zheng, P., Humann, J., McGaughey, D., Frank, M., Hough, H., Campbell, B.T., Percy, R.G., Jones, D.C., Main, D. 2017. CottonGen: An An Overview for Breeders. Proceedings of the 2017 Cotton Breeders Tour, September 24-26, Arizona.

Impact Statements

Increased sustainability of NRSP10 databases through leverage of federal funding of $7,209,903 (2014-2019) from USDA and NSF projects for Tripal and GDR, CGD and CSFL Databases as well as industry/USDA-ARS funding for CottonGen of $780,000 (2016-2020).

Date of Annual Report: 06/08/2019

Report Information

Annual Meeting Dates: 09/30/2018 - 09/30/2018
Period the Report Covers: 10/01/2017 - 09/30/2018

Participants

Abbott, Albert (albert.abbott@uky.edu) - University of Kentucky (KY);
Ashrafi, Hamid (hamidashrafi@ncsu.edu) - North Carolina State University (NC);
Bassil, Nahla (nahla.bassil@ars.usda.gov) - USDA ARS (OR);
Bernardo, Rex (bernardo@umn.edu) - University of Minnesota (MN);
Bourland, Fred (fbourland@uaex.edu) - University of Arkansas (AK);
Bushakra, Jill (jill.bushakra@ars.usda.gov) - USDA ARS (OR);
Campbell, B. Todd (todd.campbell@ars.usda.gov) - USDA-ARS (SC);
Ethalinda Cannon (ekcannon@iastate.edu) - Iowa State University (IA);
Cantrell, Roy (roy.cantrell@monsanto.com) – Monsanto;
Chavez, Dario (dchavez@uga.edu) - University of Georgia (GA);
Chee, Peng (pwchee@uga.edu) - University of Georgia (GA);
Chen, Chunxian (Chunxian.Chen@ars.usda.gov) - USDA-ARS (WV);
Cheng, Max (zcheng@utk.edu) - University of Tennessee (TN);
Coe, Michael (michael@cedarlakeresearch.com) - Cedar Lake Research (OR);
Coyne, Clare (clarice.coyne@ars.usda.gov) - USDA ARS (WA);
Curtis, Bob (rcurtis@almondboard.com) - Almond Board of California (CA);
Dardick, Chris (chris.dardick@ars.usda.gov) - USDA ARS (WV);
Dever Jane (jdever@ag.tamu.edu)- Texas A&M AgriLife Research (TX);
Dossett, Michael (michael.dossett@agr.gc.ca) - BC Blueberry Crowers;
Evans, Kate (kate.evans@wsu.edu) - Washington State University (WA);
Fang, David (david.fang@ars.usda.gov) - USDA ARS (LA);
Fernandez, Gina (gefernan@ncsu.edu) - North Carolina State University (NC);
Ficklin, Stephen (stephen.ficklin@wsu.edu) - Washington State University (WA);
Finn, Chad (chad.finn@ars.usda.gov) - USDA ARS (OR);
Frelichowski, James (james.frelichowski@ars.usda.gov) - USDA ARS (TX);
Fresnedo Ramirez, Jonathan (fresnedoramirez.1@osu.edu) - Ohio State University (OH);
Gasic, Ksenija (kgasic@clemson.edu) - Clemson University (SC);
Gmitter, Fred jr. (fgmitter@ufl.edu) - University of Florida (FL);
Gross, Briana (blgross@d.umn.edu) - University of Minnesota Duluth (MN);
Grusak, Michael (michael.grusak@ars.usda.gov) - USDA ARS (ND);
Hague, Steve (shague@tamu.edu) - Texas A&M University (TX);
Hinze, Lori (lori.hinze@ars.usda.gov) - USDA ARS (TX);
Hokanson, Stan (hokan017@umn.edu) - University of Minnesota (MN);
Iezzoni, Amy (iezzoni@msu.edu) - Michigan State University (MI);
Iorizzo, Massimo (miorizz@ncsu.edu) - North Carolina State University (NC);
Jones, Don (djones@cottoninc.com) - Cotton Incorporated (NC);
Jung, Sook (sook.jung@wsu.edu) - Washington State University (WA);
Kahn, Michael (kan@wsu.edu) - Washington State University (WA);
Khan, Awais (Mak427@cornell.edu) - Cornell University (NY);
Knapp, Steve (sjknapp@ucdavis.edu) - University of California Davis (CA);
Koebernick, Jenny (jenny.koebernick@auburn.edu) - Auburn University (AL);
Kuraparthy, Vasu (vasu_kuraparthy@ncsu.edu) - North Carolina State University (NC);
Layne, Desmond (desmond.layne@wsu.edu) - Washington State University (WA);
Liu, Zhongchi (zliu@umd.edu) - University of Maryland (MD);
Luby, Jim (lubyx001@umn.edu) - University of Minnesota (MN);
Mahoney, Lise (lise.mahoney@unh.edu) - University of New Hampshire (NH);
Main, Dorrie (dorrie@wsu.edu) - Washington State University (WA);
McCarty, Jack (jack.McCarty@ars.usda.gov) - USDA-ARS (MS);
McFerson, Jim (jim.mcferson@wsu.edu) Washington State University (WA);
McGee, Rebecca (rebecca.mcgee@ars.usda.gov) - USDA ARS (WA);
Moore, Pat (moorepp@wsu.edu) - Washington State University (WA);
Norelli, Jay (jay.norelli@ars.usda.gov) - USDA ARS (WV);
Olmstead, Mercy (mercy1@ufl.edu) - University of Florida (FL);
Peace, Cameron (cpeace@wsu.edu) - Washington State University (WA);
Poland, Jesse (jpoland@ksu.edu) - Kansas State University (KS);
Rife, Trevor (trife@ksu.edu) - Kansas State University (KS);
Roose, Mikeal (roose@ucr.edu) - University of California Davis (CA);
Saski, Chris (saski@clemson.edu) - Clemson University (SC);
Scheffler, Jodi (jodi.scheffler@ars.usda.gov) - USDA-ARS (MS);
Seabolt, Audrey (grantzau@msu.edu) - Michigan State University (MI);
Slovin, Janet (janet.slovin@ars.usda.gov) - USDA ARS (MD);
Staton, Margaret (mstaton1@utk.edu) - University of Tennessee (TN);
Stelly, David (stelly@tamu.edu) - Texas A&M University (TX);
Stewart, Philip (philip.stewart@driscolls.com) - Driscolls (CA);
Swanson, J-D (jd.swanson@salve.edu) - University of Rhode Island (RI);
Thompson, Ellen ( a.ellen.thompson@gmail.com) - Pacific Berry Breeding;
Udall, Josh (jaudall@byu.edu) - Brigham Young University (UT);
Vandermark, George (george.vandermark@ars.usda.gov) - USDA ARS (WA);
Volk, Gayle (gayle.volk@ars.usda.gov) - USDA ARS (CO);
Wegrzyn, Jill (jill.wegrzyn@uconn.edu) - University of Connecticut (CT);
Whitaker, Vance (vwhitaker@ufl.edu) - University of Florida (FL);
Wiesniewski, Michael (michael.wiesniewski@ars.usda.gov) - USDA ARS (WV);
Worthington, Margaret (mlworthi@uark.edu) - University of Arkansas (AK);
Xu, Kenong (kx27@cornell.edu) - Cornell University (NY);
Yu, John (john.yu@ars.usda.gov) - USDA ARS (TX);
Yue, Chengyang (yuechy@umn.edu) - University of Minnesota (MN);

Brief Summary of Minutes

In person or teleconference discussed meetings and workshops held during the year with various special interest groups:

Rosaceae Community Meetings (RosEXEC and GDR Advisory Board): October 31, 2017; January 14, 2018; April 25, 2018; Aug 30, 2018
Reported progress on GDR activities every quarter and plans for the next quarter to RosEXEC, the advisory board for GDR and the US Rosaeace Genomics, Genetics and Breeding Coordinating Committee (formal report provided ahead of meetings to RosEXEC). Discussed new genomic, genetic and breeding data being generated by the community that should be added to GDR, plans to provide access to high throughput phenotypic data being generated for certain Rosaceae crops, standardization of naming and how to best educate the scientific community on using standard nomenclature for map, marker, QTL and gene naming. We also discussed outcome and feedback after holding the first GDR workshop at the Plant and Animal Genome Conference in San Diego in 2018.

CottonGen Steering Committee and Users Meeting, Cotton Beltwide Conference, Dallas, TX, Jan 4, 2018
Oral and poster presentation followed by a CottonGen steering committee and user meeting with a focus on training of use of CottonGen and BIMS and how it could be improved. The community provided very useful feedback on the improvements in the Breeding Information Management System and additional needs for it and CottonGen in general. Discussions on new data forthcoming helped us plan when and how to add these data to CottonGen.

Two day Tripal Hackathon and User Meeting: San Diego, CA, Jan 11-12, 2018
Reviewed code for existing core Tripal functionality and extension modules available, and discussed future plans for development of Tripal 4 and how to fund the project in a sustainable way. Continue to develop a larger network of Tripal developers.

Tripal Developers and Users Meetings: Nine online meetings held on the third Friday of every month (Jan to May and Aug to Dec)
Discussion on Tripal core updates, problem solving, new extension module development. Discussions initiated on governance management.

International Cotton Genomics Initiative Officers Meeting, San Diego, CA, Jan 13, 2018
As part of the annual in-person ICGI meeting at the Plant and Animal Genome Conference, we discussed progress in collecting and curating genomic and genetic data for CottonGen and discussed larger projects that would likely deposit data in the following year; and the genomic tools for transcriptome expression querying and visualization. We further discussed the continuing role of CottonGen in hosting the ICGI portal as part of the database and in hosting the ICGI biannual conference registration and documentation.

AgBioData Meeting, Plant and Animal Genome Conference, San Diego, CA, Jan 13, 2018
Meeting with participants of the 30 plus agricultural database community members to discuss further opportunities for the AgBioData community (https://www.agbiodata.org) such as submitting a networking grant to the USDA FACT CIN program. Also finalized the outline for our AgBioData peer-reviewed manuscript which was submitted and published in 2018 in Databases.

Tripal Workshop, Plant and Animal Genome Conference: San Diego, CA, Jan 14, 2018
Series of presentations on Tripal advances and discussion of general future needs for core Tripal and extension modules in development or needed.
- Cucurbit Genomics Database: Integration Genetic and Genomics Resources for Cucurbit Breeding (Yi Zheng)
- Updates on Tripal Mapviewer and the Tripal Breeding Information Management System (BIMS) (Dorrie Main)
- The Tripal Gateway Project: Supporting Exchange, Transfer and Analysis of Large-Scale Data for Online Biological Databases (Stephen Ficklin)
- Tripal Extensions Facilitate Association Mapping Studies on Forest Trees with CartograTree (Nic Herndon)
- Tripal Elasticsearch: Bringing Simple and Powerful Sitewide Search to Tripal Websites (Abdullah Almsaeed)
- National Center for Genome Analysis Support use and development of Tripal Genome Browsers on XSEDE’s Jetstream (Sheri A. Sanders)
- An Open and Community Oriented Web Portal for Subtropical Fruit Trees Genomic, Phenotype and Breeding Data Analysis (Alicia Talavera)

9th International Rosaceae Genomics Conference Conference, Nanjing, China, June 24-28, 2018
Presented update on the Genome Database for Rosaceae and Breeding Information Management System and held a user meeting with rosaceae scientists on forthcoming data, and new tools needed for the database. Discussed submission of NRSP10 renewal proposal and the GDR SRS for the USDA SCRI program.

NRSP10: Bioinformatic and Database Resources for Specialty Crops Workshop at ASHS Annual Conference, Washington, DC, August 2, 21, 2018
Two hour workshop with a series of presentations on resources available from NRSP10, followed by a discussion session on progress and future plans and direction.
- Welcome and Goals of NRSP10 Workshop (Mike Kahn)
- Tripal v3, the Collaborative Online Database Platform Supporting an International Community of Plant Genome Databases (Meg Staton)
- New Data and Functionality in NRSP10 Databases (Sook Jung)
- Integrating Free Mobile Apps into Specialty Crop Breeding and Horticultural Programs (Trevor Rife)
- Using the Tripal Breeding Information Management System to Improve Breeding Efficiency (Ksenija Gasic)
- Extending the Tripal Breeding Information System to Combine International Data for Global Performance Predictions (Cameron Peace)
- NSRP10 - the Next Five Year Plan: Furthering Integration of Big Data, Tools and Analysis Capability to Enable Specialty Crop Research Discovery and Improvement (Dorrie Main)
- Open Discussion on Direction of NRSP10 (moderated by Michael Kahn)

Accomplishments

Tripal Progress: Major progress for Tripal in Yr 4 includes release of Tripal v3.0.rc3 and the first stable release of Tripal v3 as well as release of the Tripal MapViewer extension module (for Tripal v2.1 and v3.0) and several other extension modules. Of the available modules 30 are already Tripal v3.0 compatible with the remainder being converted. In the Tripal website, the extensions modules are now classified by category into Administration, Analysis/Annotation, Data Loading/Collection, Developer Tools, Third Party Integration (BrAPI, JBrowse, Galaxy, BLAST, VCF Filter), Searching, Visualization/Display and Development. There are 12 groups active in Tripal development in five countries, over 150 downloads of the Tripal platform and over 500 help desk support questions submitted and answered over the last 4 years. We estimate that over 4000 crop and wild relative species are now served through a Tripal database. Monthly Tripal meetings are regularly attended by 20 to 30 developers and the yearly codefest (formerly hackathon) attracts a similar number of developers. A Tripal workshop is held yearly at PAG with participant numbers exceeding 60 in the last 2 years following the inaugural workshop in 2015. The Tripal website (https://tripal.info) is kept current with tutorials and documentation, and regular webinars are provided for the community. In year 4 of NRSP, the Tripal site has been accessed by 6,760 users from 163 countries (1,332 U.S.) with 10,085 visits and 23,574 page views. All code is checked and approved by the Project Management Committee (PMC) before it is released to ensure standards are maintained. For newer projects, when required, we provide images of established databases, such as CottonGen to accelerate the transition to production, or provide programmatic support to update to newer Tripal versions, e.g. PeanutBase. While all new versions of Tripal core are backward compatible, a lack of Drupal experience can make it a challenging for developers at times. Having access to an experienced support system led by initiators of Tripal, Drs. Stephen Ficklin (WSU) and Meg Staton (UTenn) has been highly effective when accompanied by training for new developers. GenSAS Progress: GenSAS v5.1 was released in January 2018. Major improvements include (1) Upgraded to Tomcat v8 and Apollo v2 and enabled GenSAS to submit jobs to computational cluster which significantly increased performance (2) Implemented restrictions to user accounts to limit the number of jobs that can be run concurrently and also added PRINSEQ to check assembly quality (3) Gene models manually edited in Apollo have functional annotation jobs run on then during publish step and integration into final annotation. GenSAS v6.0 was released September 2018. Major improvements include (4) Addition of the tools BUSCO, HISAT2, DIAMOND, pBLAT (version of BLAT that runs multi-threaded), and BRAKER2 (5) GenSAS now allows tools that can run multi-threaded to run as such on cluster, this has decreased the time it takes for jobs to complete (6) At the final publish step, summary reports about the types of repeats and annotation metrics are produced along with the final annotation files. A file with a summary of which tools were used to generate the final annotation, and the tool settings, is also produced. Users also have the option of creating a merged GFF3 file of the final annotation that is suitable for submission to GenBank. GenSAS was presented at the International Plant & Animal Genome Conference in January 2018 and as a component in general NRSP10 presentations. A book chapter called "Structural and functional annotation of eukaryotic genomes with GenSAS" was accepted for publication in a "Eurkaryotic Gene Prediction" volume of the Methods in Molecular Biology series. In Year 4, GenSAS was accessed by 1,424 visitors from 78 countries, with 2,252 sessions and 7,079 pages viewed. It was used to annotate bacteria, viruses, fungi, plants and animal species. Breeding Tools Progress: In year 4 of the NRSP10 we continued development of the Tripal Breeding Information Management System (BIMS) and the phenotype data collection tool FieldBook App (Poland Program). New functionality includes addition of: (1) ability to archive data , (2) graphical and tabular view of phenotype statistics, (3) configuration page to set column names for phenotype files, (4) new search/download, (5) ability to generate Field Book input file for progeny from a new cross, (6) ability to add more columns to the downloaded file, (6) generate list of accessions for searches, (7) Mean/max/min/std and frequency were added in the downloaded file from search, (8) Google Map embedded in BIMS to show the locations of the sites when breeding program coordinates are provided, (9) ability to change order of traits in ''Manage Breeding' section, (10) ability to compare trait statistics from different categories (year, cross, etc), (11) Frequency of each categories are now displayed for categorical traits for a given dataset, and (12) Updated User Manual and FAQ and added video tutorials. Two full day BIMS training workshops held, several webinars and BIMS presented at several conferences in year 4. In year 4, at the request of the Plant Breeding Coordinating Committee SCC-80, we also developed and hosted infrastructure on NRSP10 for a US Plant Breeding Capacity Survey. In addition to collecting the data we created a dynamically generated interactive map of the States to enable browsing and searching of the data by crop and state (see https://www.nrsp10.org/us-breeding-program). NRSP10 Databases: In year 4 we upgraded the Citrus Genome Database to Tripal v3.0. and begun converting the other 4 to Tripal 3.0. This involved converting our Mainlab search and display modules to this new version and releasing these to the Tripal community. Conversion to Tripal 3.0 means users are now able to cross query data from the TreeGenes and Hardwood Genomics databases.  Details on improvements to each database can be found in the work completed section of each database. Highlights include (1) synteny analysis performed for all sequenced genomes in each database, with results visualized in the Tripal Synteny Viewer (Fei Lab, BTI) and linked to all ortholog and functional annotation, (2) major expansion of the map, marker, QTL and genome sequence datasets (curated) in GDR and CottonGen as well as keeping the Citrus, Vaccinium and Legume databases up to date with published data, (3) GRIN data added for all the databases, (4) Several new/modified search interfaces added such as genotype and marker searching and (5) Updated RefTrans expression data analyses and Pathway analyses. Usage of the databases continues to grow. In year 4 usage was as follows: GDR - 24,331 users from 156 countries, 649,026 pages viewed; CottonGen - 12,098 users from 143 countries, 278,001 pages viewed; CSFL - 3,685 users from 108 countries, 47,203 pages viewed; CGD - 5,410 users from 127 countries, 76,653 pages viewed; and GDV - 2,664 users from 92 countries, 30,997 pages viewed. For the first four years of the NRSP10 project, over 2.5 million pages have been accessed. In Year 4, NRSP10 databases were cited in 323 peer-reviewed publications, increasing the total number to 1059 in the first 4 years of the NRSP10 award. Our plans for Year 5 of NSRP10 are as follows: (1) GenSAS: Further develop GenSAS to add more tools and error checking of assemblies, and complete creation of a GenSASLite version that directly plugs into Tripal for better community curation within Tripal databases (2) BIMS: Further develop BIMS by adding more searching and analysis capability, with more testing by additional breeding programs, and provision of training workshops.(3) Keep the NRSP10 databases current with tools and data while serving as community communication portals for their respective communities (4) Continue contributing to development of Tripal Core and Tripal Extension Module Development while providing advocacy and support for Tripal database adoption and module development by the developer community (help desk, web site, hackathon, monthly meetings) (5) Further participate in database advocacy by contributing to the AgBioData consortium outreach activities, including leading submission of federal proposals for the consortium (6) present the outcomes of NRSP10 through peer-reviewed publications, conferences, meetings and training activities and continue to develop outreach materials to inform industry of NRSP10 activities and their contribution to basic, translational and applied research.

Publications

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) 15 years of GDR: New data and functionality in the Genome Database for Rosaceae.  Nucleic Acids Research 47(D1), D1137-D1145. 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. 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. Herndon, N., Falk, T., Grau, E.S., Jung, S., Ficklin, S., Main, D., Staton, M.E., Wegrzyn, J.L. (2018) Association Mapping for Forest Trees with CartograTree. Studies on the Semantic Web, 33, Chapter 8, 137-149. IOS Press eBooks (Ed. Anne E. Thessen) Humann, J. L., Lee, T., Ficklin, S., & Main, D. Structural and Functional Annotation of Eukaryotic Genomes with GenSAS. Gene Prediction (pp. 29-51). Humana, New York, NY (in press). 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. Resources in the Genome Database for Rosaceae for Peach Research. Acta Horticulturae (in press). McFerson, J., Jung, S., Cheng, C-H., Lee, T., Zheng, P., Evans, K., Peace, C., Main, D. (2017) Tree Fruit Breeding and Big Data Get together in the Genome Database for Rosaceae. Presentation at the Washington State Tree Fruit Association Annual Meeting, Dec 5, 2017, Kennewick, WA, USA. Main, D., Yu, J., Jung, S., Cheng, C.H., Lee, T., Humann, J. Zheng, P., McGaughey, D., Frank, M., Scott, K., Hough, H., Campbell, B.T., Mohan, A., Udall, J., Percy, R.G., Jones, D. (2018). Using CottonGen for Crop Improvement.  Proceedings of the National Cotton Council Beltwide Cotton Conference, January 3-5, 2018, San Antonio, Texas, USA.  Campbell, J.D., Cannon, E., Jung, S., Main, D., Poelchau, M., Walls, R., Harper, L.C. (2018). AgBioData: Identifying and Meeting Common Goals in the Management of Agricultural Biological Data. Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.  Poelchau, M., Campbell, J.D., Cannon, E., Jung, S., Main, D., Walls, R., Harper, L.C. (2018). Challenges and Recommendations for Genomics, Genetics and Breeding Databases from the AgBioData Consortium. Proceedings of the International Plant & Animal Genome Conference XXVI, January 13-17, 2018, San Diego, CA, USA.  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, USA.  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, USA.  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, USA.  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, USA.  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, USA.  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, USA.  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, USA.  Jung, S., Lee, T., Yu, J., Humann, J.L., Hough, H., Main, D. (2018). Breeding Information Management System Training Workshop Presentations. Breeders Workshop at the RosBREED Participants Meeting, March 5, 2018, East Lansing, MI, USA. 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, USA. Main, D. (2018). CottonGen: A Database Resource for Genomics, Genetics and Breeding Research. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.  Yu, J., Lee, T., Jung, S., Campbell, B.T., Gasic, K., Humann, J., Hough, H., Jones, D., Percy, R., Main, D. (2018). CottonGen BIMS for effective and efficient management of breeding data. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.  Cheng, C.H., Yu, J., Jung, S., Zheng, P., Humann, J., Lee, T., McGaughey, D., Mohan, A., Frank, M., Hough, H., Udall, J., Jones, D., Main, D. (2018). How to Effectively Search and Download Data in CottonGen. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.  Zheng, P., Jung, S., Cheng, Cheng, C.H., Yu, J., Hough, H., Udall, J., Jones, D., Main, D. (2018). Visualization of Conserved Syntenic Blocks Among Six Cotton Genomes in CottonGen. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.  Buble, K., Yu, J., Jung, S., Humann, J., Cheng, C.H., Lee, T., Hough, H., McGaughey, D., Frank, M., Main, D. (2018). Using TripalMap for Genetics Research. Proceedings of the International Cotton Genome Initiative (ICGI) Research Conference, May 31 - June 4, 2018, Edinburgh, Scotland, United Kingdom.  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 Rosaceae Genomics Conference, June 26-30, 2018. Nanjing, China.  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.  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. &lrm;July 5th 2018, Chungbuk National University, Cheongju, South Korea.  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  NRSP10 databases and Tripal brochures at AgBioData Booth. ASPB Annual Conference; July 14-18, 2018,  Montreal, Canada Staton, M (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., USA.  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., USA.  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., USA. Gasic, K., Lee, T., Jung, S., Humann, J.L.,Yu, J., Hough, H., Campbell, B.T.,  Peace, P., Evans, K., Main D. (208). Using the Tripal Breeding Information Management System to Improve Breeding Efficiency. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C., USA.  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., USA.  Main, D., Jung, S., Humann, J.L., Peace, C., Gasic, K., Kanh, M., McFerson, J. (2018). NSRP10 - the Next Five Year Plan: Furthering Integration of Big Data, Tools and Analysis Capability to Enable Specialty Crop Research Discovery and Improvement. Proceedings of the ASHS Annual Conference; July 31-Aug 4, 2018, Washington, D.C., USA. Plant Breeding Coordinating Committee SCC-80 (2018). U.S. Public Plant Breeding Capacity. Proceedings of the National Association of Plant Breeders Annual Meeting, August 7-10, Guelph, Canada.

Impact Statements

Increased sustainability of NRSP10 databases through leverage of federal funding of $7,209,903 (2014-2019) from USDA and NSF projects for Tripal and GDR, CGD and CSFL Databases as well as industry/USDA-ARS funding for CottonGen of $780,000 (2016-2020).