NRSP10: National Database Resources for Crop Genomics, Genetics and Breeding Research

(National Research Support Project Summary)

Status: Active

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SAES-422 Reports

Annual/Termination Reports:

[01/15/2022] [01/15/2023]

Date of Annual Report: 01/15/2022

Report Information

Annual Meeting Dates: 09/30/2021 - 09/30/2021
Period the Report Covers: 10/01/2019 - 01/15/2022

Participants

Abbott, Albert (albert.abbott@uky.edu) - University of Kentucky (KY);
Ashrafi, Hamid (hamidashrafi@ncsu.edu) - North Carolina State University (NC);
Atucha, Amaya (atucha@wisc.edu) - University of Wisconson Madison (WI);
Babiker, Ebrahiem (ebrahiem.babiker@usda.gov) - USDA ARS (WV);
Bandillo, Nonoy (nonoy.bandillo@ndsu.edu), North Dakota State University (ND);
Bassil, Nahla (nahla.bassil@ars.usda.gov) - USDA ARS (OR);
Byrne, David (dbyrne@tamu.edu) - Texas A&M (TX);
Campbell, B. Todd (todd.campbell@ars.usda.gov) - USDA-ARS (SC);
Canales, Elizabeth (elizabeth.canales@msstate.edu), Mississippi State University (MS);
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);
Coe, Michael (michael@cedarlakeresearch.com) - Cedar Lake Research (OR);
Coyne, Clare (clarice.coyne@ars.usda.gov) - USDA ARS (WA);
Dardick, Chris (chris.dardick@ars.usda.gov) - USDA ARS (WV);
dePamphilis, Claude (cwd3@psu.edu) - Pennsylvania State University (PA);
Dhingra, Amit (adhingra@tamu.edu) - Texas A &M (TX);
Edger, Patrick (edgerpat@msu.edu) - Michigan State University (MI);
Elkins, Rachel (rbelkins@ucanr.edu) -
Endelman, Jeffrey (endelman@wisc.edu) - University of Wisconsin Madison (WI);
Ethalinda Cannon (ekcannon@iastate.edu) - Iowa State University (IA);
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);
Galimba, Kelsey, (kelsey.galimba@oregonstate.edu) – Oregon State University (OR);
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);
Hinze, Lori (lori.hinze@ars.usda.gov) - USDA ARS (TX);
Hokanson, Stan (hokan017@umn.edu) - University of Minnesota (MN);
Honaas, Loren (loren.honaas@usda.gov) - USDA ARS (WA);
Huala, Eva (huala@phoenixbioinformatics.org) - Pheonix Bioinformatics (CA);
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);
Kalcsits, Lee (lee.kalcsits@wsu.edu) - Washington State University (WA);
Torres, Carolina Andrea (ctorres@wsu.edu) - Washington State University (WA);
Khan, Awais (Mak427@cornell.edu) - Cornell University (NY);
Kuraparthy, Vasu (vasu_kuraparthy@ncsu.edu) - North Carolina State University (NC);
Lila, Mary (mlila@ncsu.edu) - North Carolina State University (NC);
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);
McGee, Rebecca (rebecca.mcgee@ars.usda.gov) - USDA ARS (WA);
McPhee, Kevin (kevin.mcphee@montana.edu), Montana State University (MT);
Melmaiee, Kalpalatha (kmelmaiee@desu.edu) - Delaware State University (DE)
Munoz, Patricio (p.munoz@ufl.edu) - University of Florida, (FL);
Musacchi, Stefano (stefano.musacchi@wsu.edu) - Washington State University, (WA);
Peace, Cameron (cpeace@wsu.edu) - Washington State University (WA);
Polashock, James (james.polashock@usda.gov) - USDA ARS (NJ);
Riera-Lizarazu, Oscar (o.riera-lizarazu@tamu.edu) - Texas A&M (TX)
Rife, Trevor (trife@ksu.edu) - Kansas State University (KS);
Roose, Mikeal (roose@ucr.edu) - University of California Davis (CA);
Rowland, Jeannine (Jeannine.Rowland@usda.gov) USDA ARS (DC);
Ru, Sushan (szr0099@auburn.edu) - Auburn University (AL);
Sandefur, Paul (pauls@fallcreeknursery.com) - Fall Creek Nursery (OR)
Saski, Chris (saski@clemson.edu) - Clemson University (SC);
Slovin, Januaryet (Januaryet.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);
Stover, Julia (jkstover@ucdavis.edu) - University of California Davis (CA);
Thompson, Ashley (ashley.thompson@oregonstate.edu) – Oregon State University (OR);
Tweedy, Carolina (cetweedy@ucdavis.edu) - University of California Davis (CA);
Udall, Josh (Joshua.Udall@usda.gov) - USDA ARS (TX);
Vandermark, George (george.vandermark@ars.usda.gov) - USDA ARS (WA);
Volk, Gayle (gayle.volk@ars.usda.gov) - USDA ARS (CO);
Vorsa, Nicholi (vorsa@sebs.rutgers.edu) - Rutgers University (NJ);
Waite, Jessica (Jessica.Waite@usda.gov) - USDA ARS (WA);
Wegrzyn, Jill (jill.wegrzyn@uconn.edu) - University of Connecticut (CT);
Whitaker, Vance (vwhitaker@ufl.edu) - University of Florida (FL);
Worthington, Margaret (mlworthi@uark.edu) - University of Arkansas (AK);
Xu, Kenong (kx27@cornell.edu) - Cornell University (NY);
Zalapa, Juan (Juan.Zalapa@ars.usda.gov) - University of Wisconson Madison (WI);

Brief Summary of Minutes

Discussion at meetings (in person and teleconference) and workshops held with various special interest groups during the period reported (October 1, 2019, to January 15, 2022):

In person Rosaceae Community Meetings (RosEXEC and GDR Advisory Board): January 12, 2020
Reported progress on GDR activities to RosEXEC, the advisory board for GDR and the US Rosaceae Genomics, Genetics and Breeding Coordinating Committee. Discussed new genomic, genetic, and breeding data being generated by the community that should be added to GDR, standardization of naming and processes to educate the scientific community on using standard nomenclature for map, marker, QTL and gene naming. As PAG 2021 was cancelled, and PAG 2022 was moved to online at short notice, we are organizing a Rosaceae Steering Committee Meeting for February 2022.

CottonGen Steering Committee and Users Meeting, Cotton Beltwide Conference, January 5, 2020, January 8, 2021
Oral and poster presentations followed by a CottonGen steering committee and user meeting with a focus on functionality of CottonGen and expected data from large projects. The community provided very useful feedback on CottonGen and discussions on new data forthcoming and helped us plan when and how to add these data to CottonGen.

Vaccinium CAP Project Meetings held on the first Tuesday of every month since October 2019 - current (alternate between Executive Committee and Project Team). Discussions include the project deliverables which include adding project specific and community published data to GDV, usability of tools and new tools needed to display new data types (e.g., pan genome) and GDV training webinars, presentations, newsletters, and brochures.

Tripal Hackathon/Codefest and User Meeting: San Diego, CA, January 11 -12, 2020, January 11-15, 2021, January 26-28, 2022
The 2020 Annual Tripal Codefest (Hackathon) was held in San Diego prior to the Plant and Animal genome conference, January 2020.
It was a two-day event and was merged with the GMOD Hackathon. There were 26 participants. The benefits of a merged Hackathon were greater synergy between GMOD projects, specifically Tripal, JBrowse, Apollo and Galaxy. Major accomplishments included: (1) Updates and a new release of the Tripal Galaxy module by the Ficklin group, (2) Several community-contributed code updates to the Tripal v4, (3) Continuous Integration (functional testing) of Chado was setup, including creation of a Docker image and contribution to the GMOD chado repository.

The 2021 Annual Tripal Codefest was held virtually. There were 25 participants. Accomplishments included:

Advances made to: The Breeders API, core Tripal 4 (9 push requests completed), Tripal Galaxy release and a new gene page design.

The 2022 codefest is scheduled for January 26-28, 2022. It will be held virtually and currently has 19 registrants.

Tripal Developers and Users Meetings: Monthly online meetings held on the third Friday of every month (January to May and August to Dec, October 2019 – December 2022) and in person at PAG.
Incudes discussions on Tripal core updates, problem solving, new extension module development, governance andsustainability. Meetings typically have 15 – 20 participants.

AgBioData Consortium of Agricultural Databases: Monthly Meetings held on the first Wednesday of every month (virtual) and in person at PAG (2020)
The AgBioData consortium of agricultural databases held monthly meetings to discuss standards and best practices for the acquisition, display, and retrieval of genomic, genetic, and breeding data. The meetings typically have 20-30 participants.

Tripal Workshop, Plant and Animal Genome Conference: San Diego, CA, January 12, 2020 and January 9, 2022
Series of presentations on Tripal advances and discussion of general future needs for core Tripal and extension modules in development or needed. The 2020 workshop had over 50 attendees and the virtual 2022 workshop had 17 attendees.
Talks included:
(1) Two New Tripal Extension Modules: File Management for FAIR Data and Biological Networks (Ficklin)

(2) Extending Tripal: A Couple of New Modules (Guignon)

(3) New Features in Tripal BIMS, Breeding Information Management System (Jung)
(4) Using the Tripal Pub Curator Module to Manage Data Curation from Publications (Humann)

(5) Discussion on Tripal (Moderated by Wegrzyn)

2021 Workshop Talks:
(1) Tripal, an Open-Source Toolkit for Construction of Online, Searchable, Extendable and FAIR Biological Databases (Ficklin)
(2) Tripal Creates Online Biological, Community Based Web Portals for Research and Analysis (Ramnath)

(3) Tapping into the Tripal Galaxy: Association Mapping Studies on Forest Trees with CartograTree (Herndon)
(4) Tripal MegaSearch: An Interactive and Customizable Tool for Query and Download of Big Data from Tripal Databases (Jung)

(5) Discussion on Tripal (Moderated by Staton)

GDV Training Webinars - August 19, 2021
Provided training on topics (1) Introduction and Overview (2) Genetics Data and Tools (3) Genomics Data and Tools of GDV and (4)

Breeding Data and Tools. The trainings were followed by questions and answers and discussion on future big data and tools needed to maximize re-usability and utility to the community.

GDR Presentation and GDR Training Workshop at the 10th International Rosaceae Genomics Conference, Virtual, Dec 14-17, 2020
Presented “GDR: New Data, New Functionality, and New Opportunities” and held a two-hour GDR Training Workshop. Training included: (1) Overview of GDR, (2) How to use MegaSearch, (3) How to use MapViewer, (4) How to use Synteny Viewer, (5) How to use PathwayCyc, and (6) How to use BIMS (Breeding Information Management System). It was followed by a user meeting where we discussed new data, new tools, and willingness to provide financial support for the database.

GDV Presentations at the XII International Vaccinium Symposium, Virtual, - August 30 - September 1, 2021 (Virtual).
Presented (1) Using the GDV Breeding Information Management System and (2) Using the GDV Breeding Information Management System. 2021. Presentations were followed with a question-and-answer session and discussion about community needs for the data and tools in GDV.

Pear Researcher Meeting – March 9-10, 2021
Meeting to discuss challenges and opportunities in pear research. Presented resources for pear research and crop improvement in the GDR and discussed needs with the pear researchers participating in the two-day meeting.

November-December 2020/2021
Had discussions with citrus, Rosaceae, Vaccinium, and pulse crop breeders on needs for breeding management tools (BIMS), enhanced functionality of our databases and training and outreach efforts to include in a USDA SCRI grant proposal – proposal submitted but not funded. Resubmission in 2022 pending.

Accomplishments

Objective 1: Expand the online community databases for Rosaceae, citrus, cotton, cool season food legumes and Vaccinium crops. Progress from 10/01/19 to 02/15/22: We have continued to add genomic, genetic, and breeding data to our five databases and add/modify tools for increased functionality. For GDR, for example, this included the addition of 120 million genotypes, 52 genomes, 46 genetic maps, 800 K markers, 27K markers, 400 QTL, haplotypes, and conducting 1052 synteny and gene function analyses of the 85 published Rosaceae genomes.  All the other databases had similar types of data added and analyses conducted.  All our databases have work completed pages detailing data and tools added by date. Usage of the databases continues to grow. Usage between 10/01/19 to 02/15/22 was as follows: GDR – 78,719 users from 180 countries, with 2,723,689 pages viewed over 217,737 visits (22% U.S.); CottonGen – 54,879 users from 181 countries, 739,061 pages viewed over 112,781 visits (27%) U.S.); Pulse Crop Database – 17,877 users from 143 countries, 113,874 pages viewed over 23,984 visits (41% U.S.); Citrus Genome Database – 24,127 users from 167 countries, 286,005 pages viewed over 41,821 visits; and GDV – 12,350 users from 109 countries, 186,170 pages viewed over 21,990 vests (34% U.S.). For the first 5 years of the NRSP10 project (10/01/14-9/30/19), 3,679,433 pages of these databases were accessed by users. In just the first 2.25 years of the NRSP10 renewal, 4,054,495 pages have been accessed by our community of users and the databases have been cited in 768 peer-reviewed publications (see the general/citations page in each database for links to publications citing the databases). Objective 2: Develop a Tripal module for visualization of epigenetics data. Progress from 10/01/19 to 02/15/22: Module programming is slated to start in January 2023. Discussions have been started with the Tripal community on functionality and design so this visualization tool will meet our combined needs. Objective 3: Enhance TripalMap to integrate genomic and genetic data. Progress from 10/01/19 to 02/15/22: TripalMap, our genetic map comparison, and visualization viewer, now includes a genome comparison view with genome correspondence matrix and organism filtering for genomes (TripalMap v2.0). Chromosomes and linkage groups are linked by shared markers, allowing users to explore the genomic features around QTL, even when only the genetic position is available. The genes in chromosome view in TripalMap hyperlink to our genome viewer JBrowse. This has been implemented in the cotton, Rosaceae, and Vaccinium databases. The module has been tested by another database and will be fully released to the Tripal community by September 2023. Objective 4: Enhance TripalBIMS to (a) support phenomics data, (b) add GWAS analysis, and (c) global performance prediction capability. Progress from 10/01/19 to 02/15/22:  We continued development of the Tripal Breeding Information Management System (BIMS), a program embedded in each of our five databases. New functionality includes (1) BIMS compliant with BrAPI. This enables breeders to send data directly from any BrAPI compliant resource, such as the Field Book App, to BIMS, (2) Importing of public data from the community database into their private BIMS program, (3) Searching crosses, (4) Downloading stock site information (5) Changing the owner of the Breeding Program (e.g. when Breeders retire or leave a program), (5) Upload haplotype data (6) Configuration page allows users to choose regular and custom properties to be used as phenotype search categories (7) Searching by phenotype and downloading genotype data (8) Loading and searching genotyping data (9) Created BreedWithBIMS.org website so all the training manuals/webinars/presentations/publications for the BIMS programs are accessible from a central location for anyone using BIMS through the NRSP10 databases (or others), (10) BIMS manual updated, (11) Webinar trainings held for five breeding programs (Rose at Texas A&M, strawberry/raspberry at Agriculture Canada, strawberry at U of New Hampshire, blueberry at U of Florida, soybean at U of Minnesota), and VacCAP breeders; (12) BIMS presented at 11 conferences (13), BIMS 1.0.0 released to the Tripal community (https://gitlab.com/mainlabwsu/bims), (14) BIMS published in peer-reviewed journal, (15) Genotype, phenotype and location data for global performance predictions were gathered for peach, (15) BIMS templates and loaders updated to cover various source-dependent metadata, (16) Updated BIMS data loading system to shorten the loading time of big genotype data using a server-side object, (17) Developed a prototype Global prediction tool where users can load genotypic data of their germplasm of interest, choose an environmental condition and trait name to view predicted trait values.  Objective 5:  (a) Identify Sustainability Models and (b) provide additional tools and resources as required by the community. Progress from 10/01/19 to 02/15/22:  (a) Phoenix Bioinformatics has developed a database user survey to gauge the willingness of users/institutions/ to financially support their community database which is currently undergoing  IRB compliance checking at WSU before being sent to the Rosaceae, Cotton and Vaccinium research community. They have contacted key industry representatives to discuss possible sustainability models and their willingness to provide financial support toward sustainability. One non-federal funding organization has indicated its willingness to allow principal investigators to request funds in their research proposals to support their crop database. USDA ARS has submitted a funding request for $500,000 per year to be appropriated to support CottonGen. New federal grant proposals included funds to support data collection and curation of genomic, genetic, and breeding data for the citrus, cotton and vaccinium databases. Cotton Incorporated/USDA-ARS and the Cotton Industry have provided $360,000 to support 3 years of CottonGen Data Curation and some (2019-2022). A $5.4 M SCRI proposal to support the NRSP10 tree fruit, berry, nut, and pulse crops databases, is pending and an NSF proposal is in preparation for Tripal Database development. (b) At the request of the American Pomological Society and the ASHS we have developed an online tree fruit and nut register of cultivars database (https://www.fruitandnutlist.org/) which collates and standardizes information from the last 50 tree fruit and nut registers into searchable data for use by breeders and growers. At the request of the US Plant Breeding Coordinating Committee (PBCC SCC-80) we have developed web pages (https://www.nrsp10.org/PBCC_about_us) within the NRSP10 website for PBCC information management and resource dissemination to the plant breeding community. At the request of the National Association of Plant Breeding leadership team, we are designing and developing a new website for the NAPB using Drupal 9 (easier to manage and update that previous web site). Once this is complete the PBCC site will be added and NAPB site and provided to the NAPB web hosting contractors. Collection of data and access to information about US Plant Breeding Programs continues to be updated using tools available on the NRSP10 site (https://www.nrsp10.org/us-breeding-program). Core Tripal Database Platform.  NRSP10 continues to develop Core Tripal and provide support for communities using or interested in adopting this database platform. Between 10/01/19 to 02/15/22, core Tripal efforts focused on Tripal v4 Core Development and Tripal v3 Core Maintenance. Community Engagement includes monthly user group, Slack. Slack is used for real-time conversations amongst the Project Management Committee, Tripal Advisory Council, and users in general. Additionally, the Chado group uses the Tripal slack for conversations as well.  Releases include: Tripal v3.5 – Released 02/08/21. This release contains bug fixes to several fields, the bulk loader and a security fix that affected users who could edit Tripal content; Tripal v3.6 - Released 04/23/21. This release contains several bug fixes and an improved transcript field that supports creation of customizable gene pages; and Tripal v3.7 - Released 08/02/21. AgBioData, Consortium of Agricultural Databases: On September 1, 2021, NSF funded ($600,000) a three-year Research Coordination Network project “RCN: Reimagining a Sustainable Data Network to Accelerate Agricultural Research and Discovery”. The project team of NRSP10 helped lead this proposal and the AgBioData website (https://www.agbiodata.org) is developed and hosted through the NRSP10 project. The AgBioData Research Coordination Network (RCN) will accelerate research in agricultural science by increasing the accessibility and reuse of large- scale biological data. The AgBioData RCN will focus on increasing the value of Big Scientific Data through the FAIR (findable, accessible, interoperable, and reusable) model. Annual meetings will bring together multi-disciplinary scientists from all the major U.S. agricultural genomic, genetic, and breeding (GGB) databases and allied resources, accelerating synergistic efforts to make the huge amount of data curated by AgBioData databases FAIR. This will facilitate shortened data processing/curation times, simplified data management, and more standardized data handling between databases, making it easier for researchers to find and use data. The larger network of all data stakeholders will work together to identify and prioritize the most pressing data and metadata standardization needs and to develop and implement processes to solve them. Working groups will be created to focus on key community data issues, including unified nomenclature, metadata standards, data federation, and recommendations for emerging data types. The network will directly support data-generating scientists by developing clearly defined FAIR data management guides with a framework on how to maximize data visibility and data reuse for common types of biological data and a foundational FAIR data management educational curriculum appropriate for academic courses or short training modules. Lastly, a sustainability review and report will provide a roadmap for the future of GGB databases. The AgBioData Consortium is a model for how database managers, researchers, educators, and publishers can work together to be more resource-efficient and how, as central resources for the communities they serve, they can use a collective voice to benefit all scientists, both domestically and abroad.

Publications

Yu, J., Jung, S., Cheng, C.H., Lee, T., Zheng, P., Buble, K., Crabb, J., Humann, J., Hough, H., Jones, D. and Campbell, J.T., 2021. CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. Plants, 10(12), p.2805. <a href="https://doi.org/10.3390/plants10122805">https://doi.org/10.3390/plants10122805</a> Staton, M., Cannon, E., Sanderson, L.A., Wegrzyn, J., Anderson, T., Buehler, S., Cobo-Simón, I., Faaberg, K., Grau, E., Guignon, V. and Gunoskey, J., 2021. Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. Briefings in bioinformatics, 22(6), p.bbab238. <a href="https://doi.org/10.1093/bib/bbab238">https://doi.org/10.1093/bib/bbab238</a> Jung, S., Lee, T., Gasic, K., Campbell, B.T., Yu, J., Humann, J., Ru, S., Edge-Garza, D., Hough, H. and Main, D., 2021. The Breeding Information Management System (BIMS): an online resource for crop breeding. Database, baab054, 2021. <a href="https://doi.org/10.1093/database/baab054">https://doi.org/10.1093/database/baab054</a> Jung, S., Cheng, C.H., Buble, K., Lee, T., Humann, J., Yu, J., Crabb, J., Hough, H. and Main, D., 2021. Tripal MegaSearch: a tool for interactive and customizable query and download of big data. Database, baab023, 2021. <a href="https://doi.org/10.1093/database/baab023">https://doi.org/10.1093/database/baab023</a> Edge-Garza, D.A., Villamil-Castro, M., Main, D. and Hardner, C., 2021. Correction of database SNP accession numbers misassigned to SNPs of the 8K IRSC apple SNP array. Tree Genetics & Genomes, 17(2), pp.1-4. <a href="https://doi.org/10.1007/s11295-021-01500-3">https://doi.org/10.1007/s11295-021-01500-3</a> Ru, S., Hardner, C., Evans, K., Main, D., Carter, P.A., Harshman, J., Sandefur, P., Edge-Garza, D. and Peace, C., 2021. Empirical evaluation of multi-trait DNA testing in an apple seedling population. Tree Genetics & Genomes, 17(1), pp.1-10. <a href="https://doi.org/10.1007/s11295-021-01494-y">https://doi.org/10.1007/s11295-021-01494-y</a> Hardner, C., Kumar, S., Main, D. and Peace, C., 2021. Global Genomic Prediction in Horticultural Crops: Promises, Progress, Challenges and Outlook. Frontiers of Agricultural Science and Engineering, 2021, 8(2): 353–355. <a href="https://doi.org/10.15302/J-FASE-2021387">https://doi.org/10.15302/J-FASE-2021387</a> Callahan, A.M., Zhebentyayeva, T.N., Humann, J.L., Saski, C.A., Galimba, K.D., Georgi, L.L., Scorza, R., Main, D. and Dardick, C.D., 2021. Defining the ‘HoneySweet’insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica). Horticulture research, 8(1), pp.1-13. <a href="https://doi.org/10.1038/s41438-020-00438-2">https://doi.org/10.1038/s41438-020-00438-2</a> Rajendran, K., Coyne, C.J., Zheng, P., Saha, G., Main, D., Amin, N., Ma, Y., Kisha, T., Bett, K.E., McGee, R.J. and Kumar, S., 2021. Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection. Plant Genetic Resources, 19(4), pp.279-288. <a href="https://doi.org/10.1017/S147926212100006X">https://doi.org/10.1017/S147926212100006X</a> Ramsay, L., Koh, C.S., Kagale, S., Gao, D., Kaur, S., Haile, T., Gela, T.S., Chen, L.A., Cao, Z., Konkin, D.J. and Toegelová, H., 2021. Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species. bioRxiv. <a href="https://doi.org/10.1101/2021.07.23.453237">https://doi.org/10.1101/2021.07.23.453237</a> Iezzoni, A.F., McFerson, J., Luby, J., Gasic, K., Whitaker, V., Bassil, N., Yue, C., Gallardo, K., McCracken, V., Coe, M. and Hardner, C., 2020. RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops. Horticulture research, 7(1), pp.1-23. <a href="https://doi.org/10.1038/s41438-020-00398-7">https://doi.org/10.1038/s41438-020-00398-7</a> Zurn, J.D., Driskill, M., Jung, S., Main, D., Yin, M.H., Clark, M.C., Cheng, L., Ashrafi, H., Aryal, R., Clark, J.R. and Worthington, M., 2020. A Rosaceae family-level approach to identify loci influencing soluble solids content in blackberry for DNA-informed breeding. G3: Genes, Genomes, Genetics, 10(10), pp.3729-3740. <a href="https://doi.org/10.1534/g3.120.401449">https://doi.org/10.1534/g3.120.401449</a> Hellwig, T., Flor, A., Saranga, Y., Coyne, C.J., Main, D., Sherman, A., Ophir, R. and Abbo, S., 2020. Environmental and genetic determinants of amphicarpy in Pisum fulvum, a wild relative of domesticated pea. Plant Science, 298, p.110566. <a href="https://doi.org/10.1016/j.plantsci.2020.110566">https://doi.org/10.1016/j.plantsci.2020.110566</a> Coe, M.T., Evans, K.M., Gasic, K. and Main, D., 2020. Plant breeding capacity in US public institutions. Crop Science, 60(5), pp.2373-2385. <a href="https://doi.org/10.1002/csc2.20227">https://doi.org/10.1002/csc2.20227</a> Vanderzande, S., Zheng, P., Cai, L., Barac, G., Gasic, K., Main, D., Iezzoni, A. and Peace, C., 2020. The cherry 6+ 9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies. Scientific reports, 10(1), pp.1-14. <a href="https://doi.org/10.1038/s41598-020-64438-x">https://doi.org/10.1038/s41598-020-64438-x</a> Liu, Z., Ma, H., Jung, S., Main, D. and Guo, L., 2020. Developmental mechanisms of fleshy fruit diversity in Rosaceae. Annual Review of Plant Biology, 71, pp.547-573. <a href="https://doi.org/10.1146/annurev-arplant-111119-021700">https://doi.org/10.1146/annurev-arplant-111119-021700</a> Whitaker, V.M., Knapp, S.J., Hardigan, M.A., Edger, P.P., Slovin, J.P., Bassil, N.V., Hytönen, T., Mackenzie, K.K., Lee, S., Jung, S. and Main, D., 2020. A roadmap for research in octoploid strawberry. Horticulture research, 7(1), pp.1-17. <a href="https://doi.org/10.1038/s41438-020-0252-1">https://doi.org/10.1038/s41438-020-0252-1</a> Ma, Y., Marzougui, A., Coyne, C.J., Sankaran, S., Main, D., Porter, L.D., Mugabe, D., Smitchger, J.A., Zhang, C., Amin, M. and Rasheed, N., 2020. Dissecting the genetic architecture of Aphanomyces root rot resistance in lentil by QTL mapping and genome-wide association study. International journal of molecular sciences, 21(6), p.2129. <a href="https://doi.org/10.3390/ijms21062129">https://doi.org/10.3390/ijms21062129</a> Spoor, S., Wytko, C., Soto, B., Chen, M., Almsaeed, A., Condon, B., Herndon, N., Hough, H., Jung, S., Staton, M. and Wegrzyn, J., 2020. Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. Database, baaa032, 2020. <a href="https://doi.org/10.1093/database/baaa032">https://doi.org/10.1093/database/baaa032</a> Crocker, E., Condon, B., Almsaeed, A., Jarret, B., Nelson, C.D., Abbott, A.G., Main, D. and Staton, M., 2020. TreeSnap: A citizen science app connecting tree enthusiasts and forest scientists. Plants, People, Planet, 2(1), pp.47-52. <a href="https://doi.org/10.1002/ppp3.41">https://doi.org/10.1002/ppp3.41</a> Kreplak, J., Madoui, M.A., Cápal, P., Novák, P., Labadie, K., Aubert, G., Bayer, P.E., Gali, K.K., Syme, R.A., Main, D. and Klein, A., 2019. A reference genome for pea provides insight into legume genome evolution. Nature Genetics, 51(9), pp.1411-1422. <a href="https://doi.org/10.1038/s41588-019-0480-1">https://doi.org/10.1038/s41588-019-0480-1</a> Guignon, V., Cannon, E.K., Main, D., Poelchau, M., Ruiz, M., Sanderson, L.A., Staton, M., Wegrzyn, J. and Ficklin, S., 2020. Joining the Tripal community to efficiently expose your research. SFBI. <a href="https://jobim2020.sciencesconf.org/resource/page/id/23">https://jobim2020.sciencesconf.org/resource/page/id/23</a> Humann, J.L., Lee, T., Ficklin, S.P., Cheng, C.H., Hough, H., Jung, S., Wegrzyn, J., Neale, D. and Main, D., 2020, September. Structural and Functional Genome Annotation Using Web-Based Gensas v6. 0. In HORTSCIENCE (Vol. 55, No. 9, pp. S18-S18). 113 S WEST ST, STE 200, ALEXANDRIA, VA 22314-2851 USA: AMER SOC HORTICULTURAL SCIENCE. Staton, M.E., Almsaeed, A., Condon, B., Chen, M., Wegrzyn, Jill L.; Main, Doreen; Ficklin, Stephen P.; Abbott, Albert G.; Nelson, C. Dana; Carlson, John E. 2020. Searching, downloading, and analyzing tree genetic and genomic data with the hardwood genomics website. In: Nelson, C. Dana; Koch, Jennifer L.; Sniezko, Richard A., eds. Proceedings of the Sixth International Workshop on the Genetics of Host-Parasite Interactions in Forestry—Tree Resistance to Insects and Diseases: Putting Promise into Practice. Gen. Tech. Rep. SRS–252. Asheville, NC: U.S. Department of Agriculture Forest Service, Southern Research Station Jung, S., Lee, T., Cheng, C.H., Gasic, K., Humann, J.L., Yu, J., Hough, H., B.T. Campbell, Main, D. 2022. New Features on the Tripal BIMS, Breeding Information Management System. Proceedings of the Plant and Animal Genome XXIX Conference, January 8-12, 2022 (virtual). Ficklin, S.P., Wytko, C., Soto, B., Main, D., Feltus, F.A. 2022. Two New Tripal Extension Modules: File Management for FAIR Data and Biological Networks. Proceedings of the Plant and Animal Genome XXIX Conference, January 8-12, 2022 (virtual). Honaas, L.A., Zhang, H., Wafula, E.K., Eilers, J., Harkess, A., Timilsena, P., dePamphiis, C.W. Waite, J., Jung, S., Main, D. 2022. Towards a Catalog of Pome Tree Architecture Genes: The Draft ‘d’Anjou’ Genome (Pyrus communis L.). Proceedings of the Plant and Animal Genome XXIX Conference, January 8-12, 2022 (virtual). Humann, J.L., Cheng, C-H., Crabb, J., Jung, S., Yu, J., Main, D. 2022. Using the Tripal Pub Curator Module to Manage Data Curation from Publications. Proceedings of the Plant and Animal Genome XXIX Conference, January 8-12, 2022 (virtual). Ru, S., Hardner, C., Evans, K., Main, D., Carter, P.A., Harshman, J., Sandefur, P., Edge-Garza, D. and Peace, C. 2022. Empirical Evaluation of Multi-Trait DNA Testing in an Apple Seedling Population. Proceedings of the Plant and Animal Genome XXIX Conference, January 8-12, 2022 (virtual). Yu, J., Jung, S., Cheng, C.H., Lee, T., Humann, J. Zheng, P., Crabb, J., Hough, H., Campbell, B.T., Udall, J., Jones, D., Main, D. 2021. CottonGen: A Central Data Repository and Analysis Resource for the Cotton Community. Proceedings of the National Cotton Council Beltwide Cotton Conference, January 5-7, 2021 (virtual). Ramnath, R., Sanderson, L-A., Buehler, S., Burns, J., Buble, K., Senalik, D., Richter, P., Caron, C., Almsaeed, A., Condon, B., Staton, M., Main, D., Bett, K., Wegrzyn J.L., and Ficklin, S.P. 2021. Tripal Creates Online Biological, Community Based Web Portals for Research and Analysis. Proceedings of the 2021 Bioinformatics Open-Source Conference, July 29-30, 2021 (virtual). Updates to the Breeding Information Management System (BIMS). 2021. Jung, S., Lee, T., Cheng, C.H., Gasic, K., Humann, J.L., Yu, J., Hough, H., Main, D. Proceedings of the American Society of Horticultural Science Annual Meeting, August 5-9, 2021, Denver, CO, USA. Gasic, K., Jung, S., Lee, T., Cheng, C.H., Humann, J.L., Yu, J., Hough, H., Main, D. Specialty Crop Breeding Data Management. Proceedings of the National Association of Plant Breeders Annual Meeting Conference, August 15-19, 2021 (Virtual). Main, D., Humann, J.L., Cheng, C-H., Lee, T., Zheng, P., Crabb, J., Hough, H., Jung, S., Iorizzo, M. 2021. GDV Webinar - Introduction and Overview. August 19, 2021. Humann, J.L., Cheng, C-H., Lee, T., Zheng, P., Crabb, J., Hough, H., Jung, S., Iorizzo, M., Main, D. 2021. GDV Webinar - Genetics Data and Tools. August 19, 2021. Jung, S., Humann, J.L., Lee, T., Hough, H., Gasic, K., Campbell, B.T., Main, D. 2021. GDV Webinar - Breeding Data and Tools. August 19, 2021 Humann, J.L., Cheng, C-H., Lee, T., Zheng, P., Crabb, J., Hough, H., Jung, S., Iorizzo, M., Main, D. 2021. GDV Webinar - Genomics Data and Tools. August 19, 2021. Humann, J.L., Cheng, C-H., Lee, T., Zheng, P., Crabb, J., Hough, H., Jung, S., Iorizzo, M., Main, D. 2021. GDV Workshop - Using the GDV Breeding Information Management System. 2021. Proceedings of the XII International Vaccinium Symposium - August. 30- September 1, 2021 (Virtual). Main, D., Jung, S., Lee, T., Humann, J.L., Cheng, C-H., Zheng, P., Crabb, J., Hough, H., Jung, S., Iorizzo, M., 2021. GDV Workshop - Using GDV for Genetics, Genomics, and Breeding Research. 2021. Proceedings of the XII International Vaccinium Symposium - August 30 - September 1, 2021 (Virtual). Humann J, Crabb J, Cheng C-H, Lee T, Zheng P, Buble K, Jung S, Yu J, Hough H. Coyne C, McGee R, Main D. 2021. The Pulse Crop Database: A Resource for Pulse Crop Research and Improvement. Proceedings of the 2021 Biennial NAPIA and BIC Bean Meeting, November 4-6, 2021 (Virtual). 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., Main, D. 2020. How can CottonGen Help in Crop Improvement.  Proceedings of the National Cotton Council Beltwide Cotton Conference, January 9-11, 2020, Austin, Texas, USA. Yu, J., Jung, S., Cheng, C.H., Lee, T., Humann, J. Zheng, P., Crabb, J., Hough, H., Campbell, B.T., Udall, J., Jones, D., Main, D. 2020. CottonGen, a Central Platform to Facilitate Knowledge Discovery in Cotton Research. Proceedings of the National Cotton Council Beltwide Cotton Conference, January 9-11, 2020, Austin, Texas, USA.  Jung, S., Lee, T., Cheng, C.H., Zheng, P., Buble, K., Humann, J.L., Yu, J., Hough, H., Crabb, J. and Main, D. 2020. Resources for Strawberry Genomics, Genetics and Breeding Research in GDR, Genome Database for Rosaceae. Proceedings of the Plant and Animal Genome XXVIII Conference, January 11-15, 2020. Staton, M.E., West, J., Richards, C., Sisler, P., Senu, R., Phillips, C., Huff, M., Almsaeed, A., Wegrzyn, J.L., Main, D. and Ficklin, S.P., 2020. RNAseq Data in Tripal-Two Steps Forward, One Step Back. Proceedings of the Plant and Animal Genome XXVIII Conference, January 11-15, 2020. Herndon, N., Santos, R., Ramnath, R., Richter, P., Buehler, S.T., Grau, E., Wegrzyn, J.L., Main, D., Ficklin, S.P. and Staton, M., 2020. Tapping into the Tripal Galaxy: Association Mapping Studies on Forest Trees with CartograTree. Proceedings of the Plant and Animal Genome XXVIII Conference, January 11-15, 2020. Ficklin, S.P., Sanderson, L.A., Condon, B., Spoor, S., Cheng, C.H., Almsaeed, A., Chen, M., Bretaudeau, A., Rasche, H., Main, D. and Wegrzyn, J.L. 2020. Tripal, an Open-Source Toolkit for Construction of Online, Searchable, Extendable and FAIR Biological Databases. Proceedings of the Plant and Animal Genome XXVIII Conference, January 11-15, 2020. Jung, S., Cheng, C.H., Humann, J.L., Yu, J., Lee, T., Hough, H. and Main, D. 2020. Tripal MegaSearch: An Interactive and Customizable Tool for Query and Download of Big Data from Tripal Databases. Proceedings of the Plant and Animal Genome XXVIII Conference, January 11-15, 2020. Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Crabb, J., Yu, J., Humann, J.L., Hough, H., Main D. 2020. Breeding Information Management System (BIMS) for Fruit Breeding. Proceedings of the American Society of Horticultural Science Annual Meeting, August 10-13, 2020 (virtual). Humann, J.L., Lee, T., Cheng, C-H., Ficklin, S.P. Wegrzyn, J.L., Neale, S., Main, D. 2020. Structural and Functional Genome Annotation Using Web-Based Gensas v6.0. Proceedings of the American Society of Horticultural Science Annual Meeting, August 10-13, 2020 (virtual). Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Crabb, J., Yu, J., Humann, J.L., Hough, H., Main D. 2020. GDR: New Data, New Functionality, and New Opportunities. Proceedings of the 10th International Rosaceae Genomics Conference, Dec 9-11, 16-18, 2020 (Virtual) Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Crabb, J., Yu, J., Humann, J.L., Hough, H., Main D. 2020. GDR Workshop - How to use BIMS (Breeding Information Management System). Proceedings of the 10th International Rosaceae Genomics Conference, Dec 9-11, 16-18, 2020 (Virtual) Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Crabb, J., Yu, J., Humann, J.L., Hough, H., Main D. 2020. GDR Workshop - How to use MegaSearch. Proceedings of the 10th International Rosaceae Genomics Conference, Dec 9-11, 16-18, 2020 (Virtual) Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Crabb, J., Yu, J., Humann, J.L., Hough, H., Main D. 2020. GDR Workshop - How to use MapViewer. Proceedings of the 10th International Rosaceae Genomics Conference, Dec 9-11, 16-18, 2020 (Virtual) Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Crabb, J., Yu, J., Humann, J.L., Hough, H., Main D. 2020. GDR Workshop - How to use Synteny Viewer. Proceedings of the 10th International Rosaceae Genomics Conference, Dec 9-11, 16-18, 2020 (Virtual) Jung, S., Lee, T., Cheng, C-H., Buble, K., Zheng, P., Crabb, J., Yu, J., Humann, J.L., Hough, H., Main D. 2020. GDR Workshop - How to use PathwayCyc. Proceedings of the 10th International Rosaceae Genomics Conference, Dec 9-11, 16-18, 2020 (Virtual) Coyne, C.J., Mugabe, D., Zheng, P., Smitchger, J., Ma, Y., Main, D. and McGee, R.J. (2019). Pea Seed Protein Concentration: GWAS Approach Utilizing Pea Core Plus Collection. Proceedings of the ASA, CSSA and SSSA International Annual Meetings, November 10-13, 2019; San Antonio, TX, USA. Humann J, Crabb J, Cheng C-H, Lee T, Zheng P, Buble K, Jung S, Yu J, Frank M, McGaughey D, Scott K, Sanad M, Hough H. Coyne C, McGee R, Main D .2019. The Pulse Crop Database:  Expanding the Cool Season Food Legume Database into a Resource for Pulse Crop Research and Improvement.  Proceedings of the 2019 NAPIA Biennial Meeting: November 2019, Fargo, ND, USA Humann J, Crabb J, Cheng C-H, Lee T, Zheng P, Buble K, Jung S, Yu J, Frank M, McGaughey, D., Scott K, Sanad M, Hough H. Coyne C, McGee R, Main D. 2019. The Pulse Crop Database:  Expanding the Cool Season Food Legume Database into a Resource for Pulse Crop Research and Improvement.  Proceedings of the 2019 Biennial Bean Improvement Cooperative Meeting: November 2019, Fargo, ND, USA. Main, D., Jung, S. Lee, T., Cheng, C-H., Humann, J.L., Yu, J., Zheng, P., Buble, K., Hough, H., Devetter, L., Peace, C., McFerson, J., Iorrizo, M.  (2019). Database Resources for Small Fruit Research and Breeding. Abstracts of WA Small Fruit Conference, December 4-6, 2019, Lynden, WA, USA

Impact Statements

Increased sustainability of NRSP10 databases through leverage of federal/industry funding of $8,800,379 (2014-2023), of which $1,590,476 is from the current reporting period (Oct 1, 2019 – Jan 15, 2022) for Tripal and our Rosaceae, cotton, vaccinium, citrus and pulse crop databases. Federal proposals are pending that would provide a further $6 million dollars of support through 2026.

Date of Annual Report: 01/15/2023

Report Information

Annual Meeting Dates: 12/20/2022 - 12/20/2022
Period the Report Covers: 10/01/2021 - 09/30/2022

Participants

Fernandez, Gina (gefernan@ncsu.edu) - North Carolina State University (NC);
Gasic, Ksenija (kgasic@clemson.edu) - Clemson University (SC);
Hulbert, Scot (scot_hulbert@wsu.edu) – Washington State University (WA);
Iorizzo, Massimo (miorizz@ncsu.edu) - North Carolina State University (NC);
Jung, Sook (sook.jung@wsu.edu) - Washington State University (WA);
Knapp, Steven (sjknapp@ucdavis.edu)
Main, Doreen (dorrie@wsu.edu) - Washington State University (WA);
Peace, Cameron (cpeace@wsu.edu) - Washington State University (WA);

Brief Summary of Minutes

In the annual meeting we discussed progress of the project by objective and outstanding work to be completed by the end of the project in 2024. We spent a considerable amount of time discussing sustainability options for the 5 databases and its other resources that comprise NRSP10. An action plan was developed because of these discussions and plans are being made to have a second meeting of participants in May 2023. We also met several times during year 3 with project participants, database steering committee members, and over 160 community researchers to present and discuss the work of NRSP10 and provide training on use of NRSP10.

Accomplishments

Objective 1: Expand the online community databases for Rosaceae, citrus, cotton, cool season food legumes and Vaccinium crops. Progress from 10/01/21 to 09/30/22 (Year 3): We have continued to add genomic, genetic, and breeding data to our five databases and added new or modified tools for increased functionality. In year 3, we added 74 genomes, 4,480,397 genes, 4,662,527 mRNAs, 27 genetic maps, 298,463 markers, 66,392 phenotypes, 534 Trait Loci, 5,997,856 genotypes and 3,729 germplasm. A total of 9 TB of data was added to NRSP10 database resources. These data were provided by participants and community partners or from publications. In addition, we perform data analysis to add functional annotation for every genome, align markers and transcripts to the genomes, perform synteny analysis and identify orthologs/paralogs, and create pathway maps for genome sequences.  Manual curation of data includes standardizing marker and QTL names between publications and continuing to update trait ontologies that we develop and maintain. All our databases have work completed pages detailing data and tools added by date. Usage of the databases continues to grow. Usage between 10/01/21 to 09/30/22 was as follows:  GDR – 37,755 users from 180 countries, with 1,235,564 pages viewed over 102,615 visits (22% U.S.);  CottonGen – 30,976 users from 175 countries, 400,492 pages viewed over 61,989 visits (23% U.S.);  Pulse Crop Database – 10,182 users from 141 countries, 68,506 pages viewed over 13,666 visits (17% U.S.);  Citrus Genome Database – 15,273 users from 165 countries, 286,005 pages viewed over 25,850 visits (18% U.S.); and  GDV – 6,038 users from 109 countries, 99,170 pages viewed over 11,085 visits (27% U.S.). For the first 5 years of the NRS10 project (10/01/14-9/30/19), 3,679,433 pages of these databases were accessed by users. In the first 3 years of the current NRSP10, 5,465,318 pages have been accessed by our community of users and the databases have been cited in 482 peer-reviewed publications. Objective 2: Develop a Tripal module for visualization of epigenetics data. Progress from 10/01/19 to 02/15/22:  This module is no longer needed as methylation data is now being visualized in the JBrowse genome browser. Objective 3: Enhance TripalMap to integrate genomic and genetic data. Progress from 10/01/21 to 02/15/22: TripalMap, our genetic map comparison, and visualization viewer, now includes a genome comparison view with genome correspondence matrix and organism filtering for genomes (TripalMap v2.0). Chromosomes and linkage groups are linked by shared markers, allowing users to explore the genomic features around QTL, even when only the genetic position is available. The genes in chromosome view in TripalMap hyperlink to our genome viewer JBrowse. This has been implemented in all the NRSP10 databases. Objective 4: Enhance TripalBIMS to (a) support phenomics data, (b) add GWAS analysis, and (c) global performance prediction capability. Progress from 10/01/21 to 09/30/22:  We continued development of the Tripal Breeding Information Management System (BIMS), a program embedded in each of our five databases and began development of a non-database associated BIMS (standalone BIMS: https://www.breedwithbims.org) to meet the request by non NRSP10 crop breeders to have access to such a resource. It also includes access to all training manuals/webinars/presentations/publications for the BIMS programs are accessible from a central location, and updated BIMS manual, so it is very comprehensive site. New functionality during year 3 includes (1) BIMS compliant with BrAPI. This enables breeders to send data directly from any BrAPI compliant resource, such as the Field Book App, to BIMS, (2) Updates to BIMS as FieldBook updated, (3) Importing of public data from the community database into their private BIMS program, (4) Developed a prototype Global prediction tool where users can load genotypic data of their germplasm of interest, choose an environmental condition and trait name to view predicted trait values, (5) BIMS training manual updated, (6) Dedicated BIMS training provided for 3 program and multiple crops. Objective 5: (a) Identify Sustainability Models and (b) provide additional tools and resources as required by the community. Progress from 10/01/21 to 09/30/22: (a) Phoenix Bioinformatics conducted a database user survey in Year 3 to gauge the willingness of users/institutions/ to financially support our GDR, CottonGen and GDV NRSP10 databases (representative models for all 5 of our databases). They contacted key industry representatives to discuss possible sustainability models and their willingness to provide financial support toward sustainability. One non-federal funding organization has indicated its willingness to allow principal investigators to request funds in their research proposals to support their crop database. USDA ARS has submitted a funding request for $500,000 per year to be appropriated to support CottonGen. A new SCRI database project (PD Main) was funded ($5.2 M, 2022-2026) to support data collection and curation of genomic, genetic, and breeding data for our Rosaceae citrus, vaccinium, and pulse crop databases, with significant resources allocated to training and outreach. Cotton Incorporated/USDA-ARS and the Cotton Industry provided $154,000 in year 3 for CottonGen Data Curation and some development work. At the request of the American Pomological Society and the ASHS we have developed an online tree fruit and nut register of cultivars database (https://www.fruitandnutlist.org/) which collates and standardizes information from the last 50 tree fruit and nut registers into searchable data for use by breeders and growers. At the request of the US Plant Breeding Coordinating Committee (PBCC SCC-80) we developed and maintain web pages (https://www.nrsp10.org/PBCC_about_us) within the NRSP10 website for PBCC information management and resource dissemination to the plant breeding community. At the request of the National Association of Plant Breeding leadership team, we have designed and developed a new website for the NAPB using Drupal 9 (easier to manage and update than the previous web site). Collection of data and access to information about US Plant Breeding Programs (https://www.nrsp10.org/us-breeding-program) continues to be updated using tools available on the NRSP10 site and a new 5-year survey is slated for spring 2023 through the NRSP10 site, with the results ready for presenting at the annual NAPB meeting in July 2023. Core Tripal Database Platform.  NRSP10 continues to develop Core Tripal and provide support for communities using or interested in adopting this database platform. Between 10/01/21 to 09/30/22 core Tripal efforts focused on Tripal v4 Core Development and Tripal v3 Core Maintenance. Community Engagement includes monthly user group meeting, Slack is used for real-time conversations amongst the Project Management Committee, Tripal Advisory Council, and users in general. Additionally, the Chado group uses the Tripal slack for conversations as well.  Releases include: Tripal v3.8 – Released 02/22/22. This release contains various bug fixes, improvements to the OBO loader and Tripal fields; Tripal v3.9 - Released 08/12/22. This release contains mostly of minor bug fixes and compatibility improvements. On 09/27/22 Tripal MegaSearch v1.4.0 was also released. Over 140 sites have installed the Tripal database platform to date. AgBioData, Consortium of Agricultural Databases: On September 1, 2021, NSF funded ($600,000) a three-year Research Coordination Network project “RCN: Reimagining a Sustainable Data Network to Accelerate Agricultural Research and Discovery”. The project team of NRSP10 helped lead this proposal and the AgBioData website (https://www.agbiodata.org) is developed and hosted through the NRSP10 project. The AgBioData Research Coordination Network (RCN) aims to accelerate research in agricultural science by increasing the accessibility and reuse of large- scale biological data. It focuses on increasing the value of Big Scientific Data through the FAIR (findable, accessible, interoperable, and reusable) model. Annual meetings bring together multi-disciplinary scientists from all the major U.S. agricultural genomic, genetic, and breeding (GGB) databases and allied resources, accelerating synergistic efforts to make the huge amount of data curated by AgBioData databases FAIR. This facilitates shortened data processing/curation times, simplified data management, and more standardized data handling between databases, making it easier for researchers to find and use data. The larger network of all data stakeholders is working together to identify and prioritize the most pressing data and metadata standardization needs and to develop and implement processes to solve them. Working groups have been created to focus on key community data issues, including unified nomenclature, metadata standards, data federation, and recommendations for emerging data types. The network directly supports data-generating scientists by developing clearly defined FAIR data management guides with a framework on how to maximize data visibility and data reuse for common types of biological data and a foundational FAIR data management educational curriculum appropriate for academic courses or short training modules. Lastly, sustainability efforts will provide a roadmap for the future of GGB databases. The AgBioData Consortium is a model for how database managers, researchers, educators, and publishers can work together to be more resource-efficient and how, as central resources for the communities they serve, they can use a collective voice to benefit all scientists, both domestically and abroad.

Publications

Impact Statements

Increased sustainability of NRSP10 databases through leverage of federal/industry funding of > $14M (2014-2026). This includes the newly funded $5.2 M USDA NIFA SCRI to PDs Main/Jung/Peace (WSU), Gasic/Rife (Clemson), Ru (Auburn), Gmitter (Florida), Bassil/McGee (USDA ARS) for our Rosaceae, vaccinium, citrus and pulse crop databases; and $~350,000 from USDA NIFA, Cotton Incorporated, Cotton Industry, and USDA ARS for CottonGen (2021-2024). Other sources of support include two SCRI’s (VacCAP, PD Iorriza, NCSU; Lentil, PD Burrows, Montana State University).