Brief Summary of Minutes of Annual Meeting

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)

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.

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.