Transcript GDR computer demo

GDR,
the Genome Database for Rosaceae:
New Data and Functionality
Sook Jung, Taein Lee, Chun-Huai Cheng, Stephen Ficklin, Anna Blenda, Ksenija
Gasic, Jing Yu, Kristin Scott, Michael Byrd, Sushan Ru, Kate Evans, Cameron
Peace, Lisa DeVetter, Nnadozie Oraguzie, Albert Abbott, Mercy Olmstead,
Dorrie Main
Outline
• Introduction
• Goals of GDR
• Available data and tools
• Effort toward data standardization (gene symbol, QTL
metadata and trait ontology)
• Demo with exercises
1. Find sequences for DHN genes
2. Find apple and strawberry genomic regions that are in
conserved syntenic regions with peach regions that
contain QTL for SSC
3. Find apple varieties with an allele that are likely to be
resistant to scab
• Future Directions
Introduction – Goals of GDR
Content management system
Biological schema
Drupal modules for construction of
biological web sites
• Develop a genomic, genetic and breeding
database and online analysis tools for
Rosaceae Crop Improvement
• Develop/use ontologies in collaboration
with the consortia to facilitate data sharing
• Develop bioinformatics community
resources to facilitate sharing of
tools
• Further develop search/data
interface in Tripal
• BIMS in Tripal (compatible
with the field data collecting
App)
Current Data and Functionality
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Data for Almond, Apple, Apricot, Blackberry, Cherry, Peach, Pear,
Raspberry, Rose, Strawberry
Annotated peach, cultivated strawberry, diploid strawberries, pear and
apple genome sequences
Apple-peach-strawberry synteny available through GBrowse_Syn
Curated Rosaceae gene database
Annotated genera and family unigenes (v5)
Pathway data (PeachCyc, FragariaCyc and AppleCyc)
Data from SNP arrays of IRSC (9K apple, 9K peach and 6K cherry), 90K
cultivated strawberry, 20K apple 68K Rose
160 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
Effort towards data standardization
1. Standard gene nomenclature in the Rosaceae
2. QTL metadata
3. Rosaceae Trait ontology
Standard Gene nomenclature
1. Developed by Rosaceae Gene Name
Standardization Subcommittee
2. Published in Tree Genetics & Genomes in 2015
3. GDR pages for guidelines, gene class symbol
browse page and gene data template
Standard Gene nomenclature
(gene naming guideline page)
Standard Gene nomenclature
(gene class symbol page)
QTL metadata standardization
1. Standardized data templates available for
Rosaceae (GDR), cool season food legumes (CSFL)
and cotton (CottonGen)
2. Working with greater crop community (MOWG
(metadata ontology working group) of AgBioData
Data Templates
Rosaceae Trait Ontology
1. Development of Rosaceae Trait Ontology to
describe trait in QTL data
2. Based on existing Trait ontology and more terms
are added as necessary
3. QTL and Mendelian Trait Loci are associated with
Rosaceae Trait Ontology
Demo with exercises
1. Find sequences for DHN genes
2. Find apple and strawberry genomic regions that
are in conserved syntenic regions with peach
regions that contain QTL for SSC
3. Find apple varieties with an allele that are likely to
be resistant to scab
Exercise 1: Find sequences for DHN genes
Exercise 1 (cont.)
Go to gene search page
Exercise 1 (cont.)
Download data in Excel or in Fasta format
Exercise 1 (cont.)
or find sequences for DHN anchored to peach genome
Exercise 2: Find apple and strawberry genomic regions
that are in conserved syntenic regions with peach
regions that contain QTL for SSC
Exercise 2 (cont.)
Search for QTL for SSC
Exercise 2 (cont.)
Download the results
Exercise 2 (cont.)
Choose markers associated with QTL
Exercise 2 (cont.)
Search for marker data
Exercise 2 (cont.)
View marker data
Exercise 2 (cont.)
View alignment
Exercise 2 (cont.)
Go to Gbrowse_syn to see if the genomic regions are
conserved in other Rosaceae genome
Exercise 2 (cont.)
Explore the conserved syntenic regions
Exercise 4: Find apple varieties with an allele that are
likely to be resistant to scab (Md-Exp7 allele 214)
Exercise 4 (cont.)
Go to search by marker/allele page and search for
varieties with allele 214 for the marker Md-EXP7
Exercise 4 (cont.)
Download search results
Exercise 4 (cont.)
Choose download options
Future Directions
 Add more large-scale data (genomic, transcriptomes, phenotypic,
genotypic)
 Add more curated QTL and trait data, annotated by standardized
community agreed ontologies
 Implement Tripal BIMS (Breeding Information Management System) in GDR
and further develop
 Further refinement/developement of the Tripal modules
 QTL, germplasm and diversity module
 Breeders toolbox
 Web services
Acknowledgements
 GDR team members
Dorrie Main Taein Lee Stephen Ficklin Jing Yu ChunHuai Cheng Ping Zheng Anna Blenda Sushan Ru
• Project coPIs- Dorrie Main (PI), Lisa DeVetter, Kate Evans, Sook Jung,
Cameron Peace, Ksenija Gasic, Mercy Olmstead
• Rosaceae and Bioinformatics Community 
• USDA NIFA SCRI, USDA NIFA NRSP, NSF Plant Genome Program, USDAARS, Washington Tree Fruit Research Commission, WSU, Clemson
University, University of Florida.