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

Genetics Breeding Germplasm Diversity Genomics Integrate d 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 data Utilization of DNA information in breeding decisions Integrated Databases - To Facilitate Discovery

Data and Tools in NRSP databases 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

 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 Database and Tools for Breeding Data in GDR

 Search/Download Phenotypic Data  Search/Download Genotypic Data  Creating Website for Each Group Data Management

18 Phenotypic Data Search

19

Variety Detail Page

21 Genotypic Data Search

Homepage of a private breeding program

 Generate Input files for Pedimap, a tool for exploring and visualizing the flow of phenotypes and alleles through pedigrees Data Conversion

Choose Pedigree

Choose Trait and Modify Values

Generate a File and View in Pedimap

 Cross Assist Decision Support

 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). What is Cross Assist?

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  Runs in PC  Compatible with Field Book App  Data is stored partially in Chado  Breeder oriented  More extensive statistical tools CassavaBase  Online Database  Compatible with Field Book App  Data is stored entirely in Chado  Breeder oriented

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

Single site analysis: produces adjusted means per genotype, as well as summary statistics to describe the data. Choose a dataset View box plot for a trait and run the analysis again if a valued need to be excluded Statistical Tools in BMS (IBP) File of predicted means

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, USDA- ARS, 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