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