Transcript Introduction to NRSP databases

Introduction to NRSP databases
and other breeding databases
Topic
Why do we need integrated databases?
Data/Tools in NRSP databases
Demo of NRSP databases
Accessing genomic and genetic data
Accessing Breeding data
Introduction to other breeding databases
Future development
Integrated Databases - To Facilitate Discovery
Genomics
Basic Science
Structure and
evolution of
genome, gene
function, genetic
variability,
mechanism
underlying traits
Diversity
Genetics
Integrate
d Data &
Tools
Germplasm
Breeding
Translational
Science
QTL /marker
discovery,
genetic mapping,
Breeding values
Applied Science
Management of breeding data
Utilization of DNA information in breeding decisions
Data and Tools in NRSP databases
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Genomics Data
• Whole genome sequences and annotation
• Transcriptome
• Gene database (genes with gene symbols)
• Synteny data
• Pathway data
Genetics Data
• Markers and maps
• QTL/Molecular diversity
Breeding Data
• Genotypic data
• Phenotypic data
• Germplasm data
Tools
• Genome browser/CMap (comparative map viewer)
• Cyc (pathway viewer)
• Blast
• Breeding Decision Tools
Accessing Genomic and Genetic data
in NRSP databases
Species Pages
Sequence Search
Sequence Search Results
Search Details Page
CottonGen JBrowse
Marker Search (Citrus)
Trait Loci (QTL/MTL) Search
Database and Tools for Breeding
Data in GDR
 Data
 Private data from WA apple breeding program
 Private and Public breeding data from RosBreed
project
(apple, strawberry, peach, sweet cherry, tart cherry)
 Interface
 Data Management (Browse, Search and Download)
 Data Conversion (Generate Input files for Pedimap)
 Decision Support
Cross Assist
Data Management
 Search/Download Phenotypic Data
 Search/Download Genotypic Data
 Creating Website for Each Group
Phenotypic Data Search
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Variety Detail Page
Genotypic Data Search
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Homepage of a private breeding
program
Data Conversion
 Generate Input files for Pedimap, a tool for exploring
and visualizing the flow of phenotypes and alleles
through pedigrees
Choose Pedigree
Choose Trait and Modify Values
Generate a File and View in Pedimap
Decision Support
 Cross Assist
What is Cross Assist?
 A web interface to generate a list of parents and
the number of seedlings to get the progeny with
desired traits
 Methods
 “Phenotype” (uses only phenotypic
information of individuals in the dataset),
 “+Pedigree” (uses both phenotypic and
pedigree information)
 “+Ped+DNA” (uses phenotypic, pedigree
information and information provided by
DNA-based functional genotypes).
Step 1: Select Method
Step 2: Select target number and trait
thresholds
Step 3: Filter results by data completeness,
required number of seedlings, and parentage
Other breeding database/breeding
management system (BMS)
BMS from Integrated Breeding Platform and
CassavaBase
Nonproprietary
Both are compatible with Field Book App
Breeding data in Chado (open source database
schema)
BMS from IBP
CassavaBase
 Runs in PC
 Online Database
 Compatible with Field Book App
 Compatible with Field Book App
 Data is stored partially in Chado
 Data is stored entirely in Chado
 Breeder oriented
 Breeder oriented
 More extensive statistical tools
NRSP databases
(Tripal BMS)
Compatible with Field Book App
Data stored entirely in Chado
Online database
 Comprehensive genomic and genetic database with
a Breeding Management System
 Built in Tripal : open-source that can be adopted by
any other crop databases
Features of IBP and CassavaBase
 Data management (IBP and CassavaBase)
 Data import (From Field Book App and templates)
 Managing germplasm lists, crosses, nurseries/trials and making field
map
 Query/Browse
 Statistical tools (IBP)
 Single site/Multi site analysis (GxE) for phenotypic data
 QTL analysis
 Marker-Assisted Breeding tools
 Molecular Breeding design tools (IBP)
 OptiMAS (IBP)
 Genomic Selection (CassavaBase)
Data Management Tools in BMS (IBP)
Data Management Tools
(CassavaBase)
Create Lists
Create
Field Book File
Download File
Load to Field Book
Statistical Tools in BMS (IBP)
Single site analysis:
produces adjusted means per genotype, as well as summary statistics to
describe the data.
View box plot for a trait
and run the analysis again if
a valued need to be excluded
File of predicted
means
Choose a dataset
Future Development in NRSP
databases (Tripal BMS)
 Data Management
 Interface for data import both from templates and Field Book App
 Web interface to design/store new crosses/field maps and trials
 More query interfaces
 More data conversion tools
 Decision Tools
 Further development of the current tools
 New tools (Statistical tools, QTL discovery tool)
Acknowledgements
 Mainlab Bioinformatics Team
 Sook Jung, Taein Lee, Chun-Huai Chen, Stephen Ficklin, Jing Yu, Jodi
Humann, Ping Zheng, Anna Blenda, Sushan Ru, Yu Ma, Dorrie Main
 Project coPIs/Pis and collaborators
 tfGDR (GDR and Citrus); Cacao Genome Database; Pine Genome
Sequencing Project; Genome Database for Vaccinium; Cool Season
Food Legume Database; CottonGen; RosBreed
 Kate Evans (Breeders Toolbox for GDR), Cameron Peace (Cross Assist)
 Rosaceae, Citrus, Cacao, Blueberry, Legume, Cotton research
communities and Bioinformatics Communities
 USDA NIFA SCRI, USDA DOE, NSF Plant Genome Program, USDAARS, SAAEDS, Mars Inc, Washington Tree Fruit Research
Commission, Cotton Incorporated, USA Dry Pea and Lentil
Commission, Northern Pulse Growers, Citrus Research Commission
 US Land Grant University researchers and extension agents
The Team