Transcript Sep 2012

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
Where is Dorrie?
Topics
Introduction
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Funding
Milestones
Demo of GDR
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New search sites for WGS data
Synteny data
Pathway data (peach, fragaria and apple CyC)
Breeding data and tools
Current Focus
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)
Development of open source tools for an
Efficient and Flexible Database Construction
Content Management System
Drupal modules as web front-end for Chado
Chado
Generic Database schema
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Development of a New module of
Chado for storing large scale data
Development of a Tool for Efficient
Database Construction
GDR Milestones
• Genomics
Genomics
Diversity
Genetics
Integrated
Data &
Tools
• EST unigenes
• WGS and annotation
(More annotation and
Search tools)
• Synteny data
• Pathway data
• Genetics
Germplasm
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Markers and maps
QTL/Molecular diversity
• Breeding
Breeding
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Genotypic data
Phenotypic data
Germplasm data
Integrated Data Facilitates Discovery
Genomics
Basic Science
Structure and
evolution of
genome, gene
function, genetic
variability,
mechanism
underlying traits
Diversity
Genetics
Integrated
Data &
Tools
Germplasm
Breeding
Translational
Science
QTL /marker
discovery,
genetic mapping,
Breeding values
Applied Science
Utilization of DNA information in breeding decisions
Who is using GDR?
In the last year
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14,000 unique visitors
91 countries,
173,000 pages
40,000 visits
67% returning users
33% new users
Species page
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Species Page
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Search Site for predicted genes
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Gene Search Results
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Pathway Tools
(PeachCyc, FragariaCyc and AppleCye)
Pathway Tools cont.
Comparison between MetaCyc and KEGG
http://biocyc.org/metacyc/MetaCycUserGuideNew.shtml
Search and Explore
Marker Detail Page
Search for syntenic regions using Gbrowse_Syn
Searching Breeding Data
• Data
– Private data from WA apple breeding program
– Public breeding data from RosBreed project
(apple, strawberry, peach, sweet cherry, tart cherry)
Phenotyping Data Search
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Variety Detail Page
Genotypic data search
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Generate Input files for Pedimap, a
breeding software
RosBreed Tools for Marker-Assisted
Breeding
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)
- 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
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
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
Acknowledgements
• GDR team members:
• Taein Lee, Stephen Ficklin, Chun-Huai Cheng, Ping Zheng, Anna
Blenda, Sushan Ru, Sook Jung and Dorrie Main
Taein Lee
Stephen Ficklin
Chun-Huai Cheng
Ping Zheng
Anna Blenda
Sushan Ru
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, USDAARS, Washington Tree Fruit Research Commission, WSU,
Clemson University, University of Florida, Boyce Thompson
Institute