GDRWhat’s New and What’s Next

Dorrie Main, Sook Jung, Stephen Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Jing Yu, Ping Zheng, Sushan Ru, Julia Piaskowski, Cameron Peace, Kate Evans, Mercy Olmstead,

Ksenjia Gasic, Lisa Wasko DeVetter, Nnadozie Oraguzie, Albert Abbott

Fruit and Nuts WorkshopPAG XXIII, San Diego CA. Jan 10, 2015.

Genetics

Breeding

Germplasm Diversity

Genomics

Integrated Data & Tools

Basic Science• Structure and

evolution of genomes

• Gene function• Genetic variability• Mechanism

underlying traits

Translational Science• Trait discovery• Marker development• Genetic mapping• Breeding values

Applied ScienceUtilization of DNA information in breeding decisions

Integrated Data Facilitates Discovery

Vision for GDR

• To provide high-quality online community database resources to enable Rosaceae research in genomics, genetics and breeding• Easy to use• Current• Scalable and fast• Easy to manage and update• Resource efficient • Utilize a common, interoperable platform• Interoperable with other useful databases• Self-sustaining in the medium term

Rosaceae Researcher without an up to date,

comprehensive database

Button-clicking energized RR using an up to datedatabase to help make research-decisions

Building an Efficient Database

Generic Database schema

Chado

Content Management System

Drupal modules as web front-end for Chado

GDR in Tripal

Please cite usJung et al. 2014

GDR Usage in 2014

• 42,707 visits• 16,992 users • 152 countries• 192,330

pages viewedGoogle Analytics

www.rosaceae.org

Current Data and Functionality• Data for all major crops - almond, apple, apricot, blackberry, cherry,

peach, pear, raspberry, rose, strawberry• Annotated peach, strawberry, pear and apple genome sequences such

as gene models, mapped transcripts, putative gene function assignments – GO, KEGG)

• Apple-peach-strawberry synteny available through GBrowse_Syn• Curated Rosaceae gene database• Annotated genera and family unigenes (v5)• Pathway data (PeachCyc, FragariaCyc and AppleCyc)• 9K apple, 9K peach and 6K cherry illumina array SNPs• 123 Genetic maps • Gene, EST, marker, trait, QTL, polymorphism, publications search

modules• Genotypic, phenotypic and breeding data for search and download• Decision tools for breeders• BLAST, GenSAS, CAP3, SSR, Sequence Retrieval online tools

Major Data Sets in GDR

Accessing GDR

Community Databases and Big Data

Recent advances in sequencing, genotyping, and phenotyping technologies have led to a paradigm shift in crop science research – driven by “Big Data” Individual scientists now routinely

• Sequence and genotype genomes from populations, families, individuals of interest

• Pursue large-scale gene expression studies

• Create highly saturated genetic maps

• Identify genome wide loci influencing traits of interest• Conduct large-scale standardized phenotyping.

GDR Funding

• 2003-2014: Funded by NSF PGRP, USDA NIFA SCRI, WTFRC, Washington State University, & Clemson University

• 2014 – 2019: • USDA SCRI (GDR, $2.7m) • USDA NIFA NRSP10 (Crop Database Resources, $2m)• NSF DIBBs (Tripal, $1.48 m)• USDA SCRI: RosBREED 2 ($10 M – GDR $250K)

• NSF PGRP (Tree Crop Databases, $4.7m) - pending

GDR Governance

• More formalized structure has been implemented to ensure the community needs are met

• The U.S. Rosaceae Genomic, Genetics and Breeding Executive Committee (RosEXEC) will be the official Advisory Board to GDR

• Quarterly reports will be submitted and quarterly GoToMeetings held to receive input and feedback

What’s Coming – More specifically

• Add more large-scale data (genomic, transcriptomes, phenotypic, genotypic)• >1000 apple accessions - GBS data• >200 apricot genomes• Large scale phenotypic and genotypic data from

RosBREED 2 and FruitBreedOmics• RNASeq data from multiple projects• Raspberry and rose reference genomes

What’s Coming – GenSAS v3.0

What’s Coming – More specifically• Add more curated QTL and trait data, annotated by

standardized community agreed ontologies

• Further incorporate and develop online tools to aid Marker-Assisted Breeding such as field apps, expanded public and private breeders toolbox.

• Make the current and future Tripal modules publicly available

• Further refinement/development of the Tripal modules– QTL, germplasm and diversity module– Breeders Toolbox– Web services

GDR Specific Activities at PAG

• Talk: Fruit and Nut Workshop Saturday at 8.00 - 8.15 am

• Poster P0888 Monday at 10 - 11.30 am

• Computer Demo Monday at 2.30 - 2.45 pm

• Hands on Help Plant Database Booth: Sunday at 7.20 - 7.40 am,

Monday at 10.20 - 10.40 am and 3.30 - 3.40 pm

• RosEXEC Meeting on Sunday: 8.00 – 10.00 am

Other GDR Related Activities at PAGGenSAS

• Pine Workshop TalkSaturday at 10.30 – 11.00 am

• Computer Demo Saturday at 2.30 - 2.45 pm

• Poster P1153Monday at 3.00 - 4.30 pm

Tripal Workshop (Saturday 4.00 – 5.40 pm)• Funded Tripal Development 4.10 – 4.30 pm• Converting GDR/CottonGen to Tripal 4.30 pm)

The Team9

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Acknowledgements

• Project coPIs/Pis– GDR, Cacao Genome Database; Citrus Genome Database;

Pine Genome Sequencing Project; CottonGen, Genome Database for Vaccinium; Cool Season Food Legume Database;

• Rosaceae, Citrus, Cacao, Blueberry, Pea, Chickpea, Lentil, Cotton and Bioinformatics Community

• Funding Sources:USDA NIFA, NSF Plant Genome Program, USDA-ARS, Washington Tree Fruit Research Commission, Mars Inc, USA Dry Pea and Lentil Commission, Cotton Industry, Citrus Industry, Northern Pulse Growers Washington State University, Clemson University, and University of Florida

Thanks for yourattention and support