GDR, the Genome Database for Rosaceae, in Chado and Tripal Sook Jung, Stephen Ficklin, Taein Lee,...

GDR, the Genome Database for Rosaceae,

in Chado and Tripal

Sook Jung, Stephen Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Sushan Ru, Ping Zheng, Jing Yu, Aureliano Bombarely, Sushan Ru, Kate Evans, Cameron Peace, Albert Abbott, Lukas Mueller, Mercy Olmstead,

Dorrie Main

Introduction• Genomic, Genetic and Breeding database for

Rosaceae community (12 years!)

Genetics

Breeding

Germplasm Diversity

Genomics

Integrated Data & Tools

What’s New - platform

• Converted to use open source tools for an efficient and flexible database construction

• Completely in Chado!• New and improved search sites and data pages in

Tripal

Content Management System

Chado

Generic Database schema

Drupal modules as web front-end for Chado

What’s New – data and functionality• Genomics

• EST Unigenes • NCBI Data (Gene search site)• WGS and annotation(Pear WGS data!)• Synteny data• Pathway data

• Genetics• Markers and maps• QTL/Molecular diversity• New search/detail page in Tripal!

• Breeding• Genotypic data• Phenotypic data• Germplasm data

• New Tool – Sequence retrieval tool• New tutorials!

GDR Demo

• Species/Genome Pages• New Tripal pages for gene, sequence, marker,

QTL, diversity and publication data• New tool for sequence retrieval• Breeding data and tools

Species page

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Sequence search site

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Gene Search Results

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Gene search site

Search for syntenic regions using Gbrowse_Syn

Marker Search

Search pages for diversity, QTL and publication

Sequence Retrieval Tool

Access Sequence Retrieval Tool from GBrowse

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

CrossAssist: Generates a list of parents and the number of seedlings to get the progeny with desired traits

Current Objectives

1. Continue to add more genetic and genomic data

2. Facilitate community gene annotation by building online gene curation pages.

3. Develop breeders toolbox in Tripal

4. Further develop online tools to aid Marker Assisted Breeding.

Acknowledgements

• GDR team members

Taein Lee Stephen Ficklin ChunHuai ChengPing Zheng Anna Blenda Sushan RuDorrie Main Jing Yu

• 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