Integrated Breeding Platform
Breeding Management System
(BMS)
IBP Management Team
March 2014
Rationale for the IBP
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Large private seed companies have successfully
implemented extensive suites of integrated informatics
tools to turbocharge their breeding programs
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Implementation of this integrated informatics in public
programs lags behind, especially in developing countries
l Some tools have been developed at various CG centers, but
implementation has been uneven and they are not integrated into a comprehensive system
l Most NARS programs still rely on rudimentary tools, from pen
and paper to Excel spreadsheets
l Small SMEs in developing countries typically do not have the
Breeding Management System
(BMS) – Product Concept
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Simple and easy-to-use application containing all
informatics tools needed by a breeder
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Seamless flow of data between applications
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Accumulation, sharing and re-use of breeding data
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Targets routine breeding activities and will not replace
research tools
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Will allow integration of users own tools into the system
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Implementable as a standalone system
t Access central and local DB, as well as the BMS on a local PC
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Will also be implementable as a cloud-based system via
iPlant cyber-infrastructure
t For computationally intensive analyses or large data storage
Breeding Management System
BMS Project Planning
Crop Databases
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Bean
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Cassava
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Chickpea
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Rice
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Sorghum
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Wheat
Databases used by a program :
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Cowpea
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Groundnut
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Maize
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Program Database
BMS Project Planning
Crop Databases
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Genealogy Management System (GMS)
l Germplasm nomenclature, chronology, IP and passport data
l Pedigrees and breeding history
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Phenotyping Data Management System (DMS)
l Germplasm characterization and evaluation data
l Annotated with Crop Research and Crop Trait Ontologies
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Genotypic Data Management System (GDMS)
l Medium density fingerprinting data
l Genotyping data for MAS and MABC
l Genotyping data for Marker-trait association analysis
Breeding Management System
Once the strategy and parental material have
been identified, the breeder wants to:
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make crosses,
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develop populations,
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track pedigrees,
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track inventory,
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characterize lines
Germplasm Management
List Manager Functionality
The List Manager is at the center of all activities in the Breeding
Management System:
l First screen you arrive at after opening your Breeding Program
l New left navigation menu provides direct access to all tools
l Easily build and work with the lists that are used in each stage of
the breeding cycle
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Key List Manager Features:
l Ability to browse and modify existing lists
l Ability to search for lists and germplasm entries
l Ability to create a new list dynamically by pulling from existing
lists or germplasm search results
l Expanded ability to modify list contents
l Ability to export lists for use outside of the Breeding Management
Breeding Management System
Field Testing
Once populations are developed, the breeder
wants to:
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select traits,
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make lists of germplasm,
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generate designs,
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produce fieldbooks,
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collect data,
Germplasm Evaluation
Nursery and Trial Management
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Breeding Manager configured for different crops
l Crossing manager, nursery manager, pedigree recording
l Focuses on population development and line selection
l Nursery advance and seed inventory tracking
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IB Fieldbook
l Focuses on field trial management for germplasm evaluation
l Trait selection, field design, labels and sample tracking
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Android-based hand-held device
l Optimized for use with Samsung Galaxy tablet for field data
collection
l Other Android devices can be used if preferred
Germplasm Evaluation
Trait Dictionaries
Measurement Variate
Trait property
Reporting units or scale
Molecular Analysis
Genotyping Data Management
To use molecular technologies, the breeder
wants to:
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select population,
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select markers,
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genotype population,
Breeding Management System
Statistical Analysis
Breeding View
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Breeding View provides easy access to the high
throughput analyses routinely required by breeders
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The same interface can be used to access procedures in
Genstat or R-scripts and allows analyses to be configured
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Single site analysis is available for complete and
incomplete block designs as well as row-column designs
and spatial analysis. New designs are being added at
each update,
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Analyses can be run in batches over environments and
traits,
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Two-stage multi-site analysis is available for GxE and
stability analysis with or without grouping of
environments,
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Single pass meta analysis of unbalanced site by season
data is being incorporated.
Breeding View - QTL analysis
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Single trait linkage analysis (QTL)
l Quality control phenotypes (summary statistics)
l Quality control marker data
l QTL detection – genome wide scan using single and composite IM
l Output includes profile plots and tables
l Results available for automatic viewing in Flapjack
l HTML report of QTL results
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Multiple trait sequential analysis
l QTL results for each trait combined
Decision support for
Marker implementation
l OptiMAS
Developed at INRA, Le Moulon
Implementation of markers in a MARS breeding scheme Identify and track
favorable alleles through cycles of recombination and selection
l Molecular Breeding
Decision Tool (MBDT)
Developed by team at ICRISAT
Implementation of
Future Directions
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Continuous improvement of UI based on user
feedback
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Additional analysis methods for expanded
experimental designs and genetic analysis
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Seed inventory management system
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LAN based deployment available in June 2014,
cloud based deployment available in 2015
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Data will be stored in a single shareable database
with user access roles
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