The Integrated Breeding Platform:Progress and Perspectives

Graham McLaren

IBP Annual Meeting1st-3rd June 2011Wageningen, Netherlands

Vision

The 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

II

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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 Pipeline

Statistical 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)