1. the Genome Database for Rosaceae: New Data and Functionality
GDR,
the Genome Database for Rosaceae: New Data and Functionality
Sook Jung, Taein Lee, Chun-Huai Cheng, Stephen Ficklin, Anna Blenda, Ksenija Gasic, Jing Yu, Kristin Scott, Michael Byrd, Sushan Ru, Kate Evans, Cameron Peace, Lisa DeVetter, Nnadozie Oraguzie, Albert Abbott, Mercy Olmstead, Dorrie Main

2. Outline Introduction Goals of GDR Available data and tools
Effort toward data standardization (gene symbol, QTL metadata and trait ontology)
Demo with exercises
Find sequences for DHN genes
Find apple and strawberry genomic regions that are in conserved syntenic regions with peach regions that contain QTL for SSC
Find apple varieties with an allele that are likely to be resistant to scab
Future Directions 2

3. Introduction – Goals of GDR
Develop bioinformatics community resources to facilitate sharing of tools
Further develop search/data interface in Tripal
BIMS in Tripal (compatible with the field data collecting App)
Biological schema
Content management system
Drupal modules for construction of biological web sites
Develop a genomic, genetic and breeding database and online analysis tools for Rosaceae Crop Improvement
Develop/use ontologies in collaboration with the consortia to facilitate data sharing

4. Current Data and Functionality
Data for Almond, Apple, Apricot, Blackberry, Cherry, Peach, Pear, Raspberry, Rose, Strawberry
Annotated peach, cultivated strawberry, diploid strawberries, pear and apple genome sequences
Apple-peach-strawberry synteny available through GBrowse_Syn
Curated Rosaceae gene database
Annotated genera and family unigenes (v5)
Pathway data (PeachCyc, FragariaCyc and AppleCyc)
Data from SNP arrays of IRSC (9K apple, 9K peach and 6K cherry), 90K cultivated strawberry, 20K apple 68K Rose
160 Genetic maps
Gene, EST, marker, trait, QTL, polymorphism, publications search modules
Genotypic, phenotypic and breeding data for search and download
Decision tools for breeders
BLAST, GenSAS, CAP3, SSR, Sequence Retrieval online tools

5. Effort towards data standardization
Standard gene nomenclature in the Rosaceae
QTL metadata
Rosaceae Trait ontology

6. Standard Gene nomenclature
Developed by Rosaceae Gene Name Standardization Subcommittee
Published in Tree Genetics & Genomes in 2015
GDR pages for guidelines, gene class symbol browse page and gene data template

7. Standard Gene nomenclature (gene naming guideline page)

8. Standard Gene nomenclature (gene class symbol page)

9. QTL metadata standardization
Standardized data templates available for Rosaceae (GDR), cool season food legumes (CSFL) and cotton (CottonGen)
Working with greater crop community (MOWG (metadata ontology working group) of AgBioData

10. Data Templates

11. Rosaceae Trait Ontology
Development of Rosaceae Trait Ontology to describe trait in QTL data
Based on existing Trait ontology and more terms are added as necessary
QTL and Mendelian Trait Loci are associated with Rosaceae Trait Ontology

12. Demo with exercises Find sequences for DHN genes
Find apple and strawberry genomic regions that are in conserved syntenic regions with peach regions that contain QTL for SSC
Find apple varieties with an allele that are likely to be resistant to scab

13. Exercise 1: Find sequences for DHN genes

14. Exercise 1 (cont.)
Go to gene search page

15. Exercise 1 (cont.)
Download data in Excel or in Fasta format

16. Exercise 1 (cont.)
or find sequences for DHN anchored to peach genome

17. Exercise 2: Find apple and strawberry genomic regions that are in conserved syntenic regions with peach regions that contain QTL for SSC

18. Exercise 2 (cont.)
Search for QTL for SSC

19. Exercise 2 (cont.)
Download the results

20. Exercise 2 (cont.)
Choose markers associated with QTL

21. Exercise 2 (cont.)
Search for marker data

22. Exercise 2 (cont.)
View marker data

23. Exercise 2 (cont.)
View alignment

24. Exercise 2 (cont.)
Go to Gbrowse_syn to see if the genomic regions are conserved in other Rosaceae genome

25. Exercise 2 (cont.)
Explore the conserved syntenic regions

26. Exercise 4: Find apple varieties with an allele that are likely to be resistant to scab (Md-Exp7 allele 214)

27. Exercise 4 (cont.)
Go to search by marker/allele page and search for varieties with allele 214 for the marker Md-EXP7

28. Exercise 4 (cont.)
Download search results

29. Exercise 4 (cont.)
Choose download options

30. Future Directions
Add more large-scale data (genomic, transcriptomes, phenotypic, genotypic)
Add more curated QTL and trait data, annotated by standardized community agreed ontologies
Implement Tripal BIMS (Breeding Information Management System) in GDR and further develop
Further refinement/developement of the Tripal modules
QTL, germplasm and diversity module
Breeders toolbox
Web services

31. Acknowledgements GDR team members
ChunHuai Cheng
Anna Blenda
Sushan Ru
Taein Lee
Stephen Ficklin
Ping Zheng
Dorrie Main
Jing Yu
Project coPIs- Dorrie Main (PI), Lisa DeVetter, Kate Evans, Sook Jung, Cameron Peace, Ksenija Gasic, Mercy Olmstead
Rosaceae and Bioinformatics Community 
USDA NIFA SCRI, USDA NIFA NRSP, NSF Plant Genome Program, USDA-ARS, Washington Tree Fruit Research Commission, WSU, Clemson University, University of Florida. 31