How to use GDR, the Genome Database for Rosaceae

Sook Jung, Stephen Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Jing Yu, Sushan Ru, Kate Evans, Cameron Peace, Albert Abbott, Lukas Mueller, Mercy Olmstead, Dorrie Main

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Outline

Introduction • Goals of GDR • Available data and tools • How to access GDR Demo with exercises 1. Find SSR markers for varietal discrimination of pear.

2. Obtain sequences around QTLs for chilling requirement in Prunus 3. Searching for tart cherry varieties with certain traits 4. Generates a list of parents and the number of seedlings to get the progeny with desired traits Future Directions

Introduction – Goals of GDR

Content management system Biological schema • • • Develop a genomic, genetic and breeding database for Rosaceae Crop Improvement Develop tools for breeders • Data Management • Data Translation • Decision Support Develop/use ontologies in collaboration with the consortia to facilitate data sharing • Drupal modules for construction of biological web sites Develop bioinformatics community resources to facilitate sharing of tools • Further develop search/data • • interface in Tripal Breeders toolbox in Tripal Tripal interface for field data collecting App

Current Data and Functionality

• • • • • • • • • • • • Data for Almond, Apple, Apricot, Blackberry, Cherry, Peach, Pear, Raspberry, Rose, Strawberry Annotated peach, strawberry, 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) 9K apple, 9K peach and 6K cherry illumina array SNPs 123 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

How to Access GDR

Exercise 1: Find SSR markers for varietal discrimination of pear.

Exercise 2: Obtain sequences around QTLs for chilling requirement in Prunus

Exercise 3: Searching for tart cherry varieties with certain traits

SSC TA Weight ≥16.0 ≥1.2 ≥6.0

Excersize 4: Generates a list of parents and the number of seedlings to get the progeny with desired traits

Future Directions

• • • • • Add more large-scale data (genomic, transcriptomes, phenotypic, genotypic) Add more curated QTL and trait data, annotated by standardized community agreed ontologies Further incorporate and develop online tools to aid Marker-Assisted Breeding such as field apps, expanded public and private breeders toolbox. Make the current and future Tripal modules publicly available Further refinement/developement of the Tripal modules o QTL, germplasm and diversity module o Breeders toolbox o Web services

• GDR team members

Acknowledgements

Dorrie Main Taein Lee Stephen Ficklin Jing Yu ChunHuai Cheng Ping Zheng Anna Blenda Sushan Ru • 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, USDA-ARS, Washington Tree Fruit Research Commission, WSU, Clemson University, University of Florida, Boyce Thompson Institute