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The Integrated Breeding Platform: Progress and Perspectives. Graham McLaren IBP Annual Meeting 1 st -3 rd 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, - PowerPoint PPT Presentation
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The Integrated Breeding Platform:Progress and Perspectives
Graham McLaren
IBP Annual Meeting1st-3rd June 2011Wageningen, Netherlands
VisionThe IBP will provide a one-stop-shop The IBP will provide a one-stop-shop where breeders can access: where breeders can access:
high-throughput breeding services, high-throughput breeding services, logistics and data management tools, logistics and data management tools, an intuitive analysis pipeline, an intuitive analysis pipeline, breeding decision support tools, breeding decision support tools, support to use these facilities andsupport to use these facilities and breeding communities of practicebreeding communities of practice
in order to deploy molecular breeding in order to deploy molecular breeding technology for sustainability and technology for sustainability and development.development.
What the IBP will offerAccess to Breeding Services:
• well characterised and useful genetic resources • quality, economic high throughput genotyping• sophisticated phenotype and metabolite analyses
Support services for:• 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:• for breeding logistics and data management• analysis and decision support for molecular breeding• accumulated public crop information of certified quality
Capacity and Community Development:• support for communities of practice by crop or discipline• facilitation of germplasm exchange
Breeding Services
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 Management1. 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:
Trait Ontologies, Trait Dictionaries and Trial Templates have been developed for: 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)
2. Data Management Resources Developed2. Data Management Resources Developed
Support Services - data management and curation:3. Electronic Fieldbooks and Hand-held Devices3. Electronic Fieldbooks and Hand-held Devices
• 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:
• 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
4. Comments about the use of hand-held devises4. Comments about the use of hand-held devises
Support Services - data management and curation:5. Publication of Crop Information5. Publication of Crop Information
A generic Web query interface for Crop Information has been under continued development and is deployed for: Rice – http://rice.generationcp.org/germplasm-dev/ Wheat - http://iwis.cimmyt.org/ Maize - http://imis.cimmyt.org/ Cowpeas - http://ibp.generationcp.org/ivis/
Central Crop Information Databases have been implemented for: 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 Support1. Training courses in Analysis and Decision Support
Data Analysis Workshop, 7-11 June 2010,Zaragoza, SpainSimulation Workshop Jan 21-23 2011, CIMMYT Mexico
Informatics Tools and Services1.1. Maintenance and support for existing Maintenance and support for existing informatics toolsinformatics tools
Bug fixes and New Features
The IBP Configurable Workflow System
Breeding Activities
Parental selectionCrossingPopulation development
GermplasmManagement
Open ProjectSpecify objectivesIdentify teamData resourcesDefine strategy
Project Planning
Experimental DesignFieldbook productionData collectionData loading
GermplasmEvaluation
Marker selectionFingerprintingGenotypingData loading
MolecularAnalysis
Quality AssuranceTrait analysisGenetic AnalysisQTL AnalysisIndex Analysis
DataAnalysis
Selected linesRecombinesRecombination plans
BreedingDecisions
MB design tool,Cross predictionand Strategic simulation
Breeding ProjectPlanning
Breeding nurseryand pedigreerecordmanagement
Breeding Management
System
Trial field bookand environment characterizationsystem
Field Trial Management
System
Genotypic DataManagement
System
Statistical analysisapplications andselection indices
AnalyticalPipeline
MABCMASMARSGWS
Decision Support System
Breeding Applications
Lab book,quality assuranceand diversityanalysis
2. Development of a Configurable Workflow System 2. Development of a Configurable Workflow System to support Integrated Breedingto support Integrated Breeding
The MARS Breeding Workflow
Functionalities and timeline for the Stand-alone Configurable Workflow System
Application 1: Application 1: Configuration and Configuration and Customization - Customization - The IB WorkbenchThe IB Workbench
Application 2: Application 2: Field Trial Management Field Trial Management SystemSystem
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
I
12345
6a 6b
Basic mock-up (MU) Stages 2&3 iteration (3–4weeks)
Functional MU: α & β prototypes
Stand-alone version (Java, C ++, etc)
Coordination parametersfor the user interface
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
Integrated version in iPLant Cyber-infrastructure
User interactions
Integrated Breeding Field Book
http://wiki.cimmyt.org/confluence/display/MBP/Objective%202.3%20IBFB
1. Functionalities design – Dec 2010Reviewed in CIMMYT Jan 2011and at San Diego Jan 2011
2. Informatics Architecture – Dec 2010Reviewed at San Diego Jan 2011
3. Technical Design – Jan 2011
4. User Interface Mockup – Jan 2011Reviewed by breeders at CIMMYT
5. Alpha Prototype – Feb 2011Reviewed by data managers at IITA WS- FebDistributed to IBP Use Cases – MarTested by Data Managers at ICRISAT WS - MarTested by breeders at TL1 - Apr
6. Stand-alone Beta Version – May 2011To be tested by breeders at IBP WS - May
Application 4: Genotyping Data Management System Team established between ICRISAT and IRRI
led by Trushar Shah 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 PipelineStatistical MethodologyStatistical Methodology Experimental design
Generate basic designs with R connected to the Fieldbook
Phenotype analysis Genetic variance analysis, single site and multi-site
analysis available in GenStat and R QTL analysis
QTL and QTLxE analysis tools with tutorials available in Genstat and R
Selection Indices Phenotype Selection Indices available in R scripts
Application 5: Decision Support Tools
MB Design Tool (MBDT) MBDT available for planning MB experiment with
data inputs from local files. MAS decision tool
Marker aided selection processing facilities based on major known genes added to MBDT
MARS decision tool OptiMAS – a tool for tracking and assembling
favorable alleles at QTL through bi- and multi-allelic breeding populations.
Application 6: Simulation Tools
Stand-alone versions of simulation programs available for use with manuals and training material for: inbred line development (QULine) hybrid development and (QUHybred) MARS schemes (QUMARS)
CommunicationCommunication Communication strategy drafted, incorporating Communication strategy drafted, incorporating
feedback from launch meeting + input from feedback from launch meeting + input from Communications and Marketing Advisor on Communications and Marketing Advisor on SiMAC (Nancy White)SiMAC (Nancy White)
Branding the project: name and logoBranding the project: name and logo Name change from Molecular Breeding Platform to Integrated Name change from Molecular Breeding Platform to Integrated
Breeding Platform, following recommendations from Breeding Platform, following recommendations from participants at launch meeting in Feb 2010participants at launch meeting in Feb 2010
Name choice a consultative process between GCP MT, UC Name choice a consultative process between GCP MT, UC and SiMAC, with MT presenting 3 choices to UC and SiMACand SiMAC, with MT presenting 3 choices to UC and SiMAC
Logo colours and art direction representative of water, Logo colours and art direction representative of water, farming, people, productivity and integrationfarming, people, productivity and integration
Public awareness (PA)Public awareness (PA) 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 forwardGoing forward 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 Fledgling IB Portal Training courses in marker technology, data
management, statistical analysis, simulation, phenotyping and farm management
Communities of practice established: Rice biotechnology (since 2005) Cassava research and breeding (since) Breeding Informatics (since 2010) Chickpea Integrated Breeding (since 2011) Cowpea Integrated Breeding (since 2011)