Building Database Resources For Translational Research in Rosaceae Sook Jung, Taein Lee, Stephen...
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Transcript of Building Database Resources For Translational Research in Rosaceae Sook Jung, Taein Lee, Stephen...
Building Database Resources For Translational Research in
Rosaceae
Sook Jung, Taein Lee, Stephen Ficklin, Chun-Huai Cheng, Anna Blenda, Sushan Ru, Ping Zheng, Kate Evans, Cameron Peace, Nnadozie
Oraguzie, Albert Abbott, Desmond Layne, Mercy Olmstead, Frederick Gmitter, Chunxian Chen, Lukas Mueller, Dorrie Main
TopicsIntroduction
• Software• Data
Demo of GDR• Species Page• Search Sites for Genomic/Genetic Data• Breeding data and tools
Current Focus
Generic Database schema
Chado
Content Management System
Drupal modules as web front-end for Chado
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Development of open source tools for an Efficient and Flexible Database Construction
Genetics
Breeding
Germplasm Diversity
Genomics
Integrated Data & Tools
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
Management of breeding dataUtilization of DNA information in breeding decisions
Integrated Data Facilitates Discovery
Species page
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Search for genes (from WGS or NCBI) and unigene
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Gene Search Results
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Search and Explore
Marker Detail Page
Search for syntenic regions using Gbrowse_Syn
Search For Trait Loci (QTL/MTL)
Breeding Data: Phenotypic Data
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Genotypic data search
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Variety Detail Page
CrossAssist: Generates a list of parents and the number of seedlings to get the progeny with desired traits
Current Objectives
1. Continue to integrate new genetic data (marker, QTL, maps) and genomic data.
2. Facilitate community gene editing effort.3. Develop online site where breeders can
upload/edit their own data.4. Develop breeders toolbox in Tripal.5. Further develop tools to facilitate marker-
assisted breeding.
Acknowledgements
• GDR team members:• Sook Jung, Taein Lee, Stephen Ficklin, Chun-Huai Cheng, Ping
Zheng, Anna Blenda and Sushan Ru
Taein Lee Stephen Ficklin Chun-Huai Cheng Ping Zheng Anna Blenda Sushan RuSook Jung
• 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