Upload
dominick-hopkins
View
212
Download
0
Embed Size (px)
Citation preview
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?
TopicsIntroduction
• Funding• Milestones
Demo of GDR• 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)
Generic Database schema
Chado
Content Management System
Drupal modules as web front-end for Chado
5
Development of open source tools for an Efficient and Flexible Database Construction
Development of a New module of Chado for storing large scale data
Development of a Tool for Efficient Database Construction
GDR Milestones
Genetics
Breeding
Germplasm Diversity
Genomics
Integrated Data & Tools
• Genomics• EST unigenes • WGS and annotation(More annotation and Search tools)• Synteny data• Pathway data
• Genetics• Markers and maps• QTL/Molecular diversity
• Breeding• Genotypic data• Phenotypic data• Germplasm data
Genetics
Breeding
Germplasm Diversity
Genomics
Integrated Data & Tools
Integrated Data Facilitates Discovery
Basic Science
Structure and evolution of genome, gene function, genetic variability, mechanism underlying traits
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
• 14,000 unique visitors • 91 countries, • 173,000 pages • 40,000 visits• 67% returning users • 33% new users
Species page
12
13
14
Species Page
15
Search Site for predicted genes
17
Gene Search Results
18
Pathway Tools (PeachCyc, FragariaCyc and AppleCye)
Pathway Tools cont.
Comparison between MetaCyc and KEGGhttp://biocyc.org/metacyc/MetaCycUserGuideNew.shtml
Search and Explore
Marker Detail Page
Search for syntenic regions using Gbrowse_Syn
• Data– Private data from WA apple breeding program – Public breeding data from RosBreed project (apple, strawberry, peach, sweet cherry, tart cherry)
Searching Breeding Data
Phenotyping Data Search
26
27
Variety Detail Page
Genotypic data search
29
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 currentgenetic data into Chado where breeding and wholegenome 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, USDA-ARS, Washington Tree Fruit Research Commission, WSU, Clemson University, University of Florida, Boyce Thompson Institute