Brief Summary of Minutes of Annual Meeting

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.

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.

1. $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
2. $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

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.

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