Ten years of GDR Current Resources and Functionality S Jung, T Lee, S Ficklin, CH Cheng, P Zheng, A...

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

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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

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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 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

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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 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