The Integrated Breeding
Platform:
Progress and Perspectives
Graham McLaren
IBP Annual Meeting
1st-3rd June 2011
Wageningen, Netherlands
Vision
The IBP will provide a one-stop-shop
where breeders can access:
 high-throughput breeding services,
 logistics and data management tools,
 an intuitive analysis pipeline,
 breeding decision support tools,
 support to use these facilities and
 breeding communities of practice
in order to deploy molecular breeding
technology for sustainability and
development.
What the IBP will offer
Access to Breeding Services:
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well characterised and useful genetic resources
quality, economic high throughput genotyping
sophisticated phenotype and metabolite analyses
Support services for:
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planning and comparing breeding strategies
data management and curation and quality control
analysis and decision support
use of markers and molecular breeding techniques
phenotyping sites and protocols
use and protection of intellectual property
Access to Informatics Tools and Resources:
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for breeding logistics and data management
analysis and decision support for molecular breeding
accumulated public crop information of certified quality
Capacity and Community Development:
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support for communities of practice by crop or discipline
facilitation of germplasm exchange
Breeding Services
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Strategies to implement Integrated Breeding
(IB) in developing countries
Identification and engagement of genotyping
service laboratories to support IB
Conversion of marker technologies for
breeders to flexible SNP platforms
Facilitate access to high quality and timely
genotyping services through the service
laboratories
Support Services - data
management and curation:
1. Training in Informatics and Data Management
• Sorghum CI Data Management Workshop,
2010 May 11-13, Eldoret, Kenya
• Informatics Workshop for IBP Data Managers,
2010 May 31- June 4, Zaragosa, Spain
• Cassava CI Data Management Workshop,
2010 July 19 – 21, Accra, Ghana
• Tropical Legumes 1 Data Management Workshop,
2010 August 25-27, Madrid, Spain
• Wheat CI-India Data Management Workshop,
2010 September 13-16,New Delhi, India
• Wheat CI-China Data Management Workshop,
2010 October 25-28, Beijing, China
• West Africa Use Cases Data Management Worskhop,
2011 February 7-11, IITA, Nigeria
Support Services - data
management and curation:
2. Data Management Resources Developed
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Trait Ontologies, Trait Dictionaries and Trial Templates have
been developed for:
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Maize - http://ibp.generationcp.org/confluence/display/MBP /Maize
Wheat - http://ibp.generationcp.org/confluence/display/MBP/Wheat
Rice - http://ibp.generationcp.org/confluence/display/MBP/Rice
Sorghum - http://ibp.generationcp.org/confluence/display/MBP/Improved+Sorghum
Cassava- http://ibp.generationcp.org/confluence/pages/viewpage.action?pageId=20449469
Cowpea - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Cowpeas)
Chickpea - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Chickpeas)
Common Bean - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Beans)
Groundnut - http://ibp.generationcp.org/confluence/display/MBP/Tropical Legume (Groundnuts)
Support Services - data
management and curation:
3. Electronic Fieldbooks and Hand-held Devices
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Chickpea – Pooran Gaur (Honeywell)
Groundnuts – Vincent Vadez (Honeywell)
Cowpea – Jeff Ehlers (HP iPAQ)
Cowpea - Ousmane Boukar (Honeywell)
Bean – Matthew Blair (Honeywell)
Cassava – Jorge Franco (HP iPAQ)
Cassava – Emmanuel Okogbenin (HP iPAQ)
Rice – Ibnou Deang (HP iPAQ)
Rice - Tianqing Zheng (HP iPAQ)
Wheat - Ang Li (HP iPAQ)
Wheat – TR Sharma (HP iPAQ)
Sorghum – Niaba Teme (HP iPAQ)
Sorghum – Ibrahima Sissoko (HP iPAQ)
Support Services - data
management and curation:
4. Comments about the use of hand-held devises
• It was easy, simple and straight forward. However, the
difficulty faced by some is in synchronizing the handheld
with the PC because of configuration option
• The screen and keyboard are small and the battery life
is short
• It increases efficiency and minimize data error because
it saves time entering the data and they are already
recorded in a format in which it can be used
• There is an issue about collection of data for multiple
samples
• It is being suggested to look into other mobile device like
tablet PC
Support Services - data
management and curation:
5. Publication of Crop Information
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A generic Web query interface for Crop Information
has been under continued development and is
deployed for:
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Central Crop Information Databases have been
implemented for:
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Rice – http://rice.generationcp.org/germplasm-dev/
Wheat - http://iwis.cimmyt.org/
Maize - http://imis.cimmyt.org/
Cowpeas - http://ibp.generationcp.org/ivis/
Cassava, Cowpea, Common Bean
Web access will be extended and consolidated in
the IB Portal
Support Services - analysis and
decision support:
1. Training courses in Analysis and Decision Support
Data Analysis Workshop, 7-11 June 2010,Zaragoza, Spain
Simulation Workshop Jan 21-23 2011, CIMMYT Mexico
Informatics Tools and Services
1. Maintenance and support for existing
informatics tools
Bug fixes and New Features
2. Development of a Configurable Workflow System
to support Integrated Breeding
The IBP Configurable Workflow System
Breeding Activities
Project
Planning
Germplasm
Management
Germplasm
Evaluation
Molecular
Analysis
Data
Analysis
Open Project
Specify objectives
Identify team
Data resources
Define strategy
Parental selection
Crossing
Population
development
Experimental Design
Fieldbook production
Data collection
Data loading
Marker selection
Fingerprinting
Genotyping
Data loading
Quality Assurance
Trait analysis
Genetic Analysis
QTL Analysis
Index Analysis
Breeding
Management
System
Field Trial
Management
System
Genotypic Data
Management
System
Analytical
Pipeline
Breeding nursery
and pedigree
record
management
Trial field book
and environment
characterization
system
Breeding Project
Planning
MB design tool,
Cross prediction
and Strategic
simulation
Breeding Applications
Lab book,
quality assurance
and diversity
analysis
Statistical analysis
applications and
selection indices
Breeding
Decisions
Selected lines
Recombines
Recombination
plans
Decision
Support System
MABC
MAS
MARS
GWS
The MARS Breeding Workflow
Functionalities and timeline for the
Stand-alone Configurable Workflow
System
Application 1: Configuration and
Customization - The IB Workbench
Application 2: Field Trial Management
System
The IB FieldBook wizard takes you through eight steps
required to construct a Trial Fieldbook by merging together
a Trial Template, a Germplasm List and a Field Design
Development stages of the
IB Fieldbook
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Documentation of the structure and functionality of the tool
Graphical representation of the tool workflow annotated flow diagrams
Development of corresponding algorithms to run the analysis
Basic mock-up (MU) Stages 2&3 iteration (3–4weeks)
Functional MU: α & β prototypes
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6a
Coordination parameters
for the user interface
Integrated version in iPLant
Cyber-infrastructure
User interactions
6b
Stand-alone version
(Java, C ++, etc)
Integrate
d
Breeding
Field
Book
1. Functionalities design – Dec 2010
Reviewed in CIMMYT Jan 2011
and at San Diego Jan 2011
http://wiki.cimmyt.org/confluence/display/MBP/Objective%202.3%20IBFB
2. Informatics Architecture – Dec 2010
Reviewed at San Diego Jan 2011
3. Technical Design – Jan 2011
4. User Interface Mockup – Jan 2011
Reviewed by breeders at CIMMYT
5. Alpha Prototype – Feb 2011
Reviewed by data managers at IITA WS- Feb
Distributed to IBP Use Cases – Mar
Tested by Data Managers at ICRISAT WS - Mar
Tested by breeders at TL1 - Apr
6. Stand-alone Beta Version – May 2011
To be tested by breeders at IBP WS - May
Application 4: Genotyping Data
Management System
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Team established between ICRISAT and IRRI
led by Trushar Shah
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to convert the ICRIS web-based genotyping system to
a stand-alone system
improve integration of the system with sample tracking
and genealogy management components
developing data loading algorithms
load data for different use case crops
improve and expand the user query interface
Application 4: Analytical Pipeline
Statistical Methodology
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Experimental design
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Phenotype analysis
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Genetic variance analysis, single site and multi-site
analysis available in GenStat and R
QTL analysis
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Generate basic designs with R connected to the
Fieldbook
QTL and QTLxE analysis tools with tutorials available in
Genstat and R
Selection Indices
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Phenotype Selection Indices available in R scripts
Application 5: Decision Support
Tools
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MB Design Tool (MBDT)
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MAS decision tool
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MBDT available for planning MB experiment with
data inputs from local files.
Marker aided selection processing facilities
based on major known genes added to MBDT
MARS decision tool
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OptiMAS – a tool for tracking and assembling
favorable alleles at QTL through bi- and multiallelic breeding populations.
Application 6: Simulation Tools
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Stand-alone versions of simulation
programs available for use with manuals
and training material for:
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inbred line development (QULine)
hybrid development and (QUHybred)
MARS schemes (QUMARS)
Communication
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Communication strategy drafted, incorporating
feedback from launch meeting + input from
Communications and Marketing Advisor on
SiMAC (Nancy White)
Branding the project: name and logo
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Name change from Molecular Breeding Platform to Integrated
Breeding Platform, following recommendations from
participants at launch meeting in Feb 2010
Name choice a consultative process between GCP MT, UC
and SiMAC, with MT presenting 3 choices to UC and SiMAC
Logo colours and art direction representative of water,
farming, people, productivity and integration
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Public awareness (PA)
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Press releases and feature stories written
and circulated widely
Brochure, bookmarks and posters to
present IBP to a non-technical audience
Website: alpha version
Going forward
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Phase I (early years): continue focus on
supporting the development of the platform, and
dissemination (new products, user testimonies, etc)
Phase II:
communications to
support building
membership,
usage and support
for IBP
Capacity Building and
Community Development
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Fledgling IB Portal
Training courses in marker technology, data
management, statistical analysis, simulation,
phenotyping and farm management
Communities of practice established:
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Rice biotechnology (since 2005)
Cassava research and breeding (since)
Breeding Informatics (since 2010)
Chickpea Integrated Breeding (since 2011)
Cowpea Integrated Breeding (since 2011)