New Data and Functionality of GDR, the Genome Database for Rosaceae Sook Jung, Taein Lee, Stephen Ficklin, Chun-Huai Cheng, Ping Zheng, Anna Blenda, Sushan Ru, Kate Evans, Cameron Peace, Nnadozie Oraguzie, Albert Abbott, Desmond Layne, Mercy Olmstead, Frederick Gmitter, Chunxian Chen, Lukas Mueller, Dorrie Main

Introduction Genomic, Genetic and Breeding database for Rosaceae community (11 years!) Built using open source tools for an efficient and flexible database construction Content Management System Chado Generic Database schema Drupal modules as web front-end for Chado Stephen Ficklin, GMOD workshop, Wed 11:50 AM

New Data and Functionality Genetics Breeding GermplasmDiversity Genomics Integrated Data & Tools Genomics EST Unigene NCBI data WGS and annotation (More annotation and Search tools) Synteny data Pathway data RosaR80 data Genetics Markers and maps QTL/Molecular diversity Breeding Genotypic data Phenotypic data Germplasm data (Enhanced interface) V5

Species page

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Search for genes (from WGS or NCBI) and unigene 8

Gene Search Results 9

Pathway Tools (PeachCyc, FragariaCyc and AppleCyc)

Pathway Tools cont. Comparison between MetaCyc and KEGG

Search for syntenic regions using Gbrowse_Syn

Phenotyping Data Search 13

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Variety Detail Page

Genotypic data search 16

Generate Input files for Pedimap, a breeding software

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

Current Objectives 1.Integrate more genetic data (marker, QTL, maps) and a ssociation with Trait Ontology (developing Rosaceae Trait Ontology) 2.Continue to integrate NCBI sequences 3.Develop new and improved search sites and data pages in Tripal 4.Growers Gateway where growers can view and compare cultivar performance data.

Acknowledgements GDR team members Taein Lee Stephen Ficklin ChunHuai Cheng Ping Zheng Anna Blenda Sushan Ru Dorrie Main Jing Yu 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