Data overload – Breeding decision-support software to the rescue !
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Transcript of Data overload – Breeding decision-support software to the rescue !
Data overload – Breeding decision-support software to
the rescue!
S. Jung, Taein Lee, Kate Evans, Cameron Peace, Gennaro Fazio, Sushan Ru, Amy F. Iezzoni,
Doreen Main
Outline of Presentation
BIMS (Breeding Information Management System) – what is it?
Why BIMS?
What data does BIMS have?
What features are in BIMS?
Testimonials
BIMS for your crop!
RosBREED
RosBREED
What is BIMS?
• BIMS Breeding Information Management System
• FunctionalityWeb portal that leverage genomics information for maximum utility within the Marker-Assisted Breeding (MAB) Pipeline, including functions to aid breeding decision-making
• Where is it?Integrated with GDR (Genome database for Rosaceae) that contains genomic, genetic and breeding data
RosBREED
Why BIMS?Genotypic data, phenotypic data – Too much to handle!
Which parents to cross? Which seedlings to select?Which QTLs to try to adapt to my breeding program?
RosBREED
With BIMS
we can help you with what trees to cross
RosBREED
What data does BIMS have?
• Breeding Data from participating RosBREED breeders (apple, strawberry, tart cherry, sweet cherry and peach)Phenotypic data, genotypic data, pedigree data, germplasm data, etc
• Integrated with other GDR genetics and genomics datamarkers, QTL, genetic map, whole genome sequences, trait ontology
RosBREED
What features are in BIMS?
• Comprehensive search site for breeding data• Modules to support MAB pipeline
Database for breeding data
• Browse by dataset• Search phenotypic data• Search genotypic data• Generate input file for software (Pedimap,
FlexQTL)
Phenotypic data search
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Variety Detail Page
Genotypic data search
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Tools – Generate Input files for Pedimap, a breeding software
RosBREED
Modules to support MAB pipeline
Trait Locus Warehouse
Selection Target Identifier
Choose market class
•Fresh market•Processing market…
See SE Valuesmock-
up only
Acidity
BF 21.3
SweetnessTrait 2Trait 1
Market Type
Select Target Identifier
Choices Made
Trait Name
Statistical Significance of QTL
LOD 7.6
Fresh Fresh
QTL name
Trait Effect Stat. signif.
Population/germplasm
Source Genomic location
Market type
Range Priority index/EWLocusV
Glu7.1 sweetness
±4⁰Brix BF 23.1 RosBREED CR Set
Tex134 2:37-43 Fresh 1.4-2.4
11 ±3
MDH3 acidity ± 0.32 mea
LOD 7.6
Con × Bolinha
Bolinha 1:21.4 Fresh 8-10 5 ±1
Search Result Print
Reset
User can rewrite these values
mock-up only
Technology Portfolio
Genome Database Resources
LG1 LG2 LG3 LG4 LG5
Graphical location of chosen QTL
Zoom in on QTL interval and discover what markers are there to be utilized for MAS
x
QTL name Trait Effect Range Genomic Location/Interval QTL origin info Genomic Resources available near QTL
SSC 4.5 SSC LG4 – 45-55 cM Apple RosBREED flexQTL SSR1, SNP12343, SCAR abcd, ….
TA 1.4 TA LG1 – 30-32 cM FiestaxDiscovery cross
SSC 4.2 SSC LG4 – 15-21 cMo
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If better marker is necessary, look up to find SSRs and SNPS around QTL and design primers using online software
mock-up only
RosBREED
Reference Germplasm Database
• A module to help a breeder to become convinced or otherwise that an unproven DNA test of interest indeed holds predictive power for germplasm of interest.
Simple Validation Functional genotype effects
Cross AssistGenerates a list of parents and the number of seedlings to
get the progeny with desired traits
RosBREED
A RosBREED Tart Cherry breeder
Amy Iezzoni says..
“I really like having my breeding data searchable from a web portal. No more pouring over spreadsheets hoping I have the latest one, looking for a particular data point! With the toolbox, I can just log in and search for the data point and have it in a matter of minutes.”
RosBREED
A RosBREED Apple breeder
Jim Luby says..
“I like the searchable database format for my potential parents and the ability to get a Pedimap-ready output without the worry about format is really efficient for visualizing phenotypes in our breeding program.”
RosBREED
A RosBREED Strawberry breeder
Jim Hancock says..
“To date, I have done all my evaluations and parent selection by shuffling through spread sheets and hand written notes. I hope to streamline my whole operation with BIMS.”
RosBREED
A RosBREED Apple breeder
Kate Evans says..
“Being able to search through multiple years of phenotypic data as well as link in genotypic data is wonderful. I can easily make selections and chose potential parents using the Toolbox format.”
RosBREED
BIMS for your crop group
• Underlying database for BIMS is constructed using Chado, an open-source, generic, modular, ontology-based database for biological data
• BIMS is developed by the collaboration between breeders, geneticists, genomicists, and bioinformaticists
Can be applicable for any other crops, not just for Rosaceae
Acknowledgement
• BIMS team• Team Leader: Gennaro Fazio• BIMS module design team: Cameron Peace, Gennaro Fazio, Sushan Ru• BIMS database designer: Sook Jung• BIMS Database developer: Taein Lee• BIMS Trainee: Sushan Ru• Genomics Team Leader/ GDR : Dorrie Main• MAP Pipeline Team Leader: Cameron Peace
• Other RosBREED Team Members• PD: Amy Iezzoni• Kate Evans (Design of breeding database)• Breeding team who provided data
This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture