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

Outline• Introduction

• Goals of GDR• Available data and tools• How to access GDR

• Demo with exercises1. Find SSR markers for varietal discrimination of pear.2. Obtain sequences around QTLs for chilling

requirement in Prunus3. Searching for tart cherry varieties with certain traits4. Generates a list of parents and the number of

seedlings to get the progeny with desired traits• Future Directions

Introduction – Goals of GDR

• 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

• 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

Biological schemaContent management system

Drupal modules for construction of biological web sites

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 traitsSSC 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 moduleo Breeders toolboxo Web services

Acknowledgements

• GDR team members

Taein Lee Stephen Ficklin ChunHuai ChengPing Zheng Anna Blenda Sushan RuDorrie 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, USDA-ARS, Washington Tree Fruit Research Commission, WSU, Clemson University, University of Florida, Boyce Thompson Institute