1. Ten years of GDR Current Resources and Functionality S Jung, T Lee, S Ficklin, CH Cheng, P Zheng, A Blenda, S Ru, K Evans, C Peace, N Oraguzie, AG Abbott, D Layne, M Olmstead, FG Gmitter Jr., C Chen, L Mueller and D Main

2. Where is Dorrie?

3. Topics Introduction Funding Milestones Demo of GDR New search sites for WGS data Synteny data Pathway data (peach, fragaria and apple CyC) Breeding data and tools Current Focus

4. Funding GDR NSF: $795,822 over five years (2003-2008) USDA SCRI (expand to Citrus): $1,999,950 (2009-2014) Additional funded projects of Main Lab Cacao Genome Database (USDA-ARS, $366,000 2008-2012) An Online Toolbox for TreeFruit Breeding (WTFRC, $160,000, 2009-2013) Pine Genome Sequencing Project (USDA, $831,000 for GenSAS and ontology development, 2011-2015) CottonGen (Cotton Incorporated and USDA-ARS, $870,000, 2011-2016) RosBreed (USDA-SCRI, $1.1M, 2009-2013)

5. Generic Database schema Chado Content Management System Drupal modules as web front-end for Chado 5 Development of open source tools for an Efficient and Flexible Database Construction

6. Development of a New module of Chado for storing large scale data

7. Development of a Tool for Efficient Database Construction

8. GDR Milestones Genetics Breeding GermplasmDiversity Genomics Integrated Data & Tools Genomics EST unigenes WGS and annotation (More annotation and Search tools) Synteny data Pathway data Genetics Markers and maps QTL/Molecular diversity Breeding Genotypic data Phenotypic data Germplasm data

9. Genetics Breeding Germplasm Diversity Genomics Integrated Data & Tools Integrated Data Facilitates Discovery Basic Science Structure and evolution of genome, gene function, genetic variability, mechanism underlying traits Translational Science QTL /marker discovery, genetic mapping, Breeding values Applied Science Utilization of DNA information in breeding decisions

10. Who is using GDR? In the last year 14,000 unique visitors 91 countries, 173,000 pages 40,000 visits 67% returning users 33% new users

11. Species page

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15. Species Page 15

17. Search Site for predicted genes 17

18. Gene Search Results 18

19. Pathway Tools (PeachCyc, FragariaCyc and AppleCye)

20. Pathway Tools cont. Comparison between MetaCyc and KEGG http://biocyc.org/metacyc/MetaCycUserGuideNew.shtml

21. Search and Explore

22. Marker Detail Page

23. Search for syntenic regions using Gbrowse_Syn

25. Data –Private data from WA apple breeding program –Public breeding data from RosBreed project (apple, strawberry, peach, sweet cherry, tart cherry) Searching Breeding Data

26. Phenotyping Data Search 26

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28. Variety Detail Page

29. Genotypic data search 29

30. Generate Input files for Pedimap, a breeding software

31. RosBreed Tools for Marker-Assisted Breeding

32. CrossAssist: Generates a list of parents and the number of seedlings to get the progeny with desired traits

33. Current Objectives 1.Integrate more genetic data (marker, QTL, maps) - Curation of literature and author-submitted data - Association with Trait Ontology (developing Rosaceae Trait Ontology)  New curator, Anna Blenda 2.Integrate NCBI sequences –Anchor and/or associate with predicted genes from WGS, morphological markers, molecular markers, germplam, library and literature  NCBI parser and table uploader to chado is ready

34. Current Objectives Cont. 3.Develop new and improved search sites and data pages  Tripal 4.Growers Gateway where growers can view and compare cultivar performance data. Underlying these objectives is the migration of current genetic data into Chado where breeding and whole genome data reside  Beta version to be available early next year

35. Collaboration and Data Submission Collaboration with FruitBreedomics –Copy of GDR has been provided –Co-development of Tripal modules for breeding data –Regular meetings being held We want your data –Data templates

36. Acknowledgements GDR team members: Taein Lee, Stephen Ficklin, Chun-Huai Cheng, Ping Zheng, Anna Blenda, Sushan Ru, Sook Jung and Dorrie Main Taein LeeStephen Ficklin Chun-Huai ChengPing Zheng Anna BlendaSushan Ru

37. Acknowledgements Project coPIs- Dorrie Main (PI), Bert Abbott, Cameron Peace, Kate Evans, Des Layne, Nnadozie Oraguzie, Mercy Olmstead, Fred Gmitter Jr., the RosBREED teams Rosaceae and Bioinformatics Community USDA NIFA SCRI, NSF Plant Genome Program, MARS, USDA- ARS, Washington Tree Fruit Research Commission, WSU, Clemson University, University of Florida, Boyce Thompson Institute