Molecular Breeding Platform Molecular Breeding Platform Services Services

and and Communities of PracticeCommunities of Practice

M Carmen de VicenteM Carmen de VicenteCapacity building and Enabling delivery LeaderCapacity building and Enabling delivery Leader

Hyderabad, IndiaHyderabad, IndiaFebruary 2010February 2010

The Molecular Breeding PlatformThe Molecular Breeding Platform

A project to develop and deploy A project to develop and deploy a web-based one-stop shop functional and sustainable a web-based one-stop shop functional and sustainable platform platform

for informationfor information, , analytical tools analytical tools and and related services related services

to design and efficiently conduct molecular breedingto design and efficiently conduct molecular breeding

1 : 1 : plan, designplan, design

2 : 2 : a declaration of the principles a declaration of the principles on which a group of persons stands;on which a group of persons stands;3 a 3 a

(2) : a device or structure incorporating or providing a platform; especially : such (2) : a device or structure incorporating or providing a platform; especially : such a a structure on legs structure on legs used for offshore drilling (as for oil)used for offshore drilling (as for oil)

3 b : 3 b : a place or opportunity for public discussiona place or opportunity for public discussion

5 a : a vehicle used for a particular purpose or to 5 a : a vehicle used for a particular purpose or to carry a usually carry a usually specified kind of equipment specified kind of equipment

5 b : 5 b : operating systemoperating system; also : the computer architecture and equipment ; also : the computer architecture and equipment using a particular operating systemusing a particular operating system

from Webster’s dictionaryfrom Webster’s dictionary

The word The word “Platform”“Platform”

The word The word “Platform”“Platform”

It is used in several different contexts, usually referring to It is used in several different contexts, usually referring to some some kind of standing kind of standing surface surface used to used to support support things, give them things, give them stability, or visibilitystability, or visibility::

…… …… Automobile Automobile platform, platform, a set of components shared a set of components shared by several by several

vehicle modelsvehicle models …… ……

from Wikipediafrom Wikipedia

Why Why ServicesServices??

The GCP The GCP ……. ……. subscribes to a philosophy of subscribes to a philosophy of creating useful products creating useful products for real for real usersusers

…….. GCP.. GCP will ensure will ensure that its products contribute to and result in end-products for that its products contribute to and result in end-products for farmers farmers (GCP Delivery Strategy, Nov 2005)(GCP Delivery Strategy, Nov 2005)

MBP ServicesMBP Services

To increase the chances that research and its products outlive the Program

• NARS and their researchers must participate actively • NARS need to have the appropriate capacity to participate

To increase the chances that research and its products outlive the Program

• NARS and their researchers must participate actively • NARS need to have the appropriate capacity to participate

Breeding Breeding Services Services To facilitate and speed up implementation Advanced breeders

Support Support ServicesServices Those that include some sort of capacity, guidance and training

Breeding Breeding ServicesServices

Genetic Resources Supply Service (GRSS)Genetic Resources Supply Service (GRSS) Marker ServicesMarker Services Trait and Metabolite ServicesTrait and Metabolite Services

Genetic Resources Supply Service (GRSS)Genetic Resources Supply Service (GRSS)

A platform on its ownA platform on its own It provides germplasm for breeders’ activitiesIt provides germplasm for breeders’ activities

Value added germplasm (building on past SP1 work), i.e. Value added germplasm (building on past SP1 work), i.e. vvalidated and stable genetic stocks with high data quality alidated and stable genetic stocks with high data quality standards standards

Service integrated in the global germplasm systemService integrated in the global germplasm system

Activity Leader: Jean Christophe GlaszmannActivity Leader: Jean Christophe Glaszmann

Marker ServicesMarker Services A set of options for users to access marker service laboratories in A set of options for users to access marker service laboratories in

the public and private sector with clear contractual conditions the public and private sector with clear contractual conditions

Laboratories are selected on the basis of competitive cost, fit with Laboratories are selected on the basis of competitive cost, fit with quality control requirements and expeditious delivery quality control requirements and expeditious delivery

It builds on the experience accumulated by the Genotyping Support It builds on the experience accumulated by the Genotyping Support ServiceService

Activity Leader: Humberto GómezActivity Leader: Humberto Gómez

Trait and Metabolite ServicesTrait and Metabolite Services((drought tolerancedrought tolerance))

Some secondary traits or metabolites provide valuable information to Some secondary traits or metabolites provide valuable information to select phenotypes for breedingselect phenotypes for breeding Locally, these analyses can be very expensive Locally, these analyses can be very expensive

It will offer It will offer a catalogue of recommended laboratories and other a catalogue of recommended laboratories and other facilities available to users upon request facilities available to users upon request 1)1) to analyse and quantify metabolites and to analyse and quantify metabolites and 2)2) to evaluate specific traits under controlled conditionsto evaluate specific traits under controlled conditions

Activity Leader: Xavier DelannayActivity Leader: Xavier Delannay

Support Support ServicesServices

Breeding Plan DevelopmentBreeding Plan Development Information ManagementInformation Management Data CurationData Curation Design and AnalysisDesign and Analysis Phenotyping sites and protocolsPhenotyping sites and protocols Genotyping Support Service (GSS)Genotyping Support Service (GSS) IP and policy helpdeskIP and policy helpdesk

Breeding Plan DevelopmentBreeding Plan Development

To determine the convenience and the consequences of embarking in To determine the convenience and the consequences of embarking in a given molecular breeding project, a given molecular breeding project, activities must be detailed over activities must be detailed over timetime, and , and the costs and benefits must be knownthe costs and benefits must be known

This service provides support for the This service provides support for the design of breeding pathways design of breeding pathways and workflowsand workflows, depending on the crop and trait(s) , depending on the crop and trait(s) Already available: Already available:

Marker-assisted Recurrent Selection (MARS) Marker-assisted Backcrossing (MABC) Marker-assisted Selection (MAS)

Soon, it will also provide a costs estimation of the selected approach Soon, it will also provide a costs estimation of the selected approach or an analysis of the comparison with the conventional option or an analysis of the comparison with the conventional option

Activity Leader: Xavier DelannayActivity Leader: Xavier Delannay

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OutlineOutline Parental choiceParental choice Population developmentPopulation development GenotypingGenotyping PhenotypingPhenotyping QTL analysisQTL analysis Recombination cyclesRecombination cycles DiagramDiagram

Information ManagementInformation Management

Within and across experiments, data management is essential for Within and across experiments, data management is essential for breeders to access and manage relevant pedigree, phenotypic and breeders to access and manage relevant pedigree, phenotypic and genotypic datagenotypic data

This service assists This service assists with installing and configuring the platform with installing and configuring the platform information systeminformation system of breeding programs as well as for global crop of breeding programs as well as for global crop improvement databases improvement databases

It includes It includes visits for on-site installation and configurationvisits for on-site installation and configuration, , training training and and a virtual helpdeska virtual helpdesk

Now exploring the potential for an Information/Data Managers Now exploring the potential for an Information/Data Managers community of practice community of practice

Activity Leader: Arllet PortugalActivity Leader: Arllet Portugal

Data CurationData Curation

It assists with all issues related to the capture and curation It assists with all issues related to the capture and curation of data in breeding projects, and to their integration in an of data in breeding projects, and to their integration in an adequate information system adequate information system Quality controlQuality control

Training of and support to data managers and breedersTraining of and support to data managers and breeders Training materials Training materials Helpdesk and web-based collaboration and Helpdesk and web-based collaboration and

communication site with userscommunication site with users

Activity Leader: Arllet PortugalActivity Leader: Arllet Portugal

Design and AnalysisDesign and Analysis

1) It includes 1) It includes trainingtraining in data generation, handling, processing and in data generation, handling, processing and interpretation, as well as experimental design from field planting to interpretation, as well as experimental design from field planting to molecular breeding schemes molecular breeding schemes

It provides assistance with It provides assistance with the ‘translation’ of the genotypic and the ‘translation’ of the genotypic and phenotypic data to the breeding context phenotypic data to the breeding context and it ensures that the and it ensures that the methodology developed for design and analysis of breeding trials is methodology developed for design and analysis of breeding trials is rapidly available to the usersrapidly available to the users

2) A 2) A Statistical HelpdeskStatistical Helpdesk that gives one-to-one support for statistical that gives one-to-one support for statistical questionsquestions

Activity Leader: Fred van EeuwijkActivity Leader: Fred van Eeuwijk

Design and AnalysisDesign and Analysis3) 3) CoursesCourses::

Time: Twice a year (April/ May, October/ November) Time: Twice a year (April/ May, October/ November) Venue: Wageningen (the Netherlands) Venue: Wageningen (the Netherlands) Content: Content: a one week course in basic statisticsa one week course in basic statistics a one week course in advanced statistics & statistical geneticsa one week course in advanced statistics & statistical geneticsCourse participants can follow one or both courses, and can stay up Course participants can follow one or both courses, and can stay up to two more weeks to work on specific problems under supervision of to two more weeks to work on specific problems under supervision of WUR-Biometris staff WUR-Biometris staff

Plus, WUR-Biometris will teach one week course on demandPlus, WUR-Biometris will teach one week course on demand

Phenotyping sites and protocolsPhenotyping sites and protocols

It gives access to information on phenotyping sites to ensure that It gives access to information on phenotyping sites to ensure that selection is carried out under appropriate stress conditions, and that selection is carried out under appropriate stress conditions, and that germplasm adaptation is well characterised germplasm adaptation is well characterised Ongoing investment plans to establish and enhance selected Ongoing investment plans to establish and enhance selected

phenotyping facilities and expertisephenotyping facilities and expertise

It makes available the technical advice of crop-specific experts -- It makes available the technical advice of crop-specific experts -- accuracy and relevance of the trait(s) to be measured, stress accuracy and relevance of the trait(s) to be measured, stress intensity needed and appropriate protocols intensity needed and appropriate protocols

Activity Leader: Xavier DelannayActivity Leader: Xavier Delannay

Genotyping Support Service (GSS)Genotyping Support Service (GSS)

Ongoing since 2006, this service provides financial and technical Ongoing since 2006, this service provides financial and technical support for breeders in developing countries to access cost-efficient support for breeders in developing countries to access cost-efficient genotyping services worldwide, and supports training activities in genotyping services worldwide, and supports training activities in experimental design and data analysis for diversity analyses and experimental design and data analysis for diversity analyses and molecular breeding projects (MAS, and others)molecular breeding projects (MAS, and others)

To date, about To date, about 36 services have been provided, genotyping 8000+ 36 services have been provided, genotyping 8000+ samples of 12 crops to teams working in 14 countriessamples of 12 crops to teams working in 14 countries. . Markers used: a majority of SSR, but also DArT and now SNP. Markers used: a majority of SSR, but also DArT and now SNP. Many services have dealt with germplasm characterization, a Many services have dealt with germplasm characterization, a

few with marker-assisted breeding.few with marker-assisted breeding.

Activity Leader: Humberto GómezActivity Leader: Humberto Gómez

IP and policy helpdeskIP and policy helpdesk

Support on intellectual property rights and freedom to operate for Support on intellectual property rights and freedom to operate for biotechnology research and germplasm use biotechnology research and germplasm use In particular, emerging issues to address needs of MBP users, In particular, emerging issues to address needs of MBP users,

e.g. germplasm exchange e.g. germplasm exchange It will link with the existing GCP IP Help Desk It will link with the existing GCP IP Help Desk

A repository of resources A repository of resources Help Line Help Line

Activity Leader: Platform ManagerActivity Leader: Platform Manager

1)1) Genetic Resource Support ServiceGenetic Resource Support Service2)2) Marker ServicesMarker Services3)3) Phenotyping ServicesPhenotyping Services4)4) Information ManagementInformation Management5)5) Design and AnalysisDesign and Analysis

“…“….Critical for the adoption of modern breeding technologies .Critical for the adoption of modern breeding technologies in developing countries will be supporting in developing countries will be supporting communities of communities of practice practice on molecular breeding on molecular breeding for the most important food for the most important food security crops, security crops, developing local infrastructure to improve developing local infrastructure to improve plant phenotypingplant phenotyping, and , and appropriate and targeted capacity appropriate and targeted capacity building”building”

Communities of PracticeCommunities of Practice

• ““Groups of people who share a concern or a passion for something Groups of people who share a concern or a passion for something they do and learn how to do it better as they they do and learn how to do it better as they interact regularlyinteract regularly””

CoP members have a commitment to the common interest, engage CoP members have a commitment to the common interest, engage in joint activities and discussions, help each other, and share in joint activities and discussions, help each other, and share information. They information. They interactinteract and and learn together.learn together. They build They build relationships that enable them to learn from each other. Members of relationships that enable them to learn from each other. Members of a CoP are a CoP are practitionerspractitioners. They develop a shared repertoire of . They develop a shared repertoire of resources: experiences, stories, tools and ways of addressing resources: experiences, stories, tools and ways of addressing recurring problemsrecurring problems

It nurtures knowledge and promotes innovationIt nurtures knowledge and promotes innovation

The cassava CoP: an exampleThe cassava CoP: an example(courtesy of E. Okogbenin)(courtesy of E. Okogbenin)

““A partnership for molecular breeding and product delivery in Africa”A partnership for molecular breeding and product delivery in Africa” Nigeria – NRCRINigeria – NRCRI Ghana – CRIGhana – CRI Tanzania – ARITanzania – ARI Uganda – NACRRIUganda – NACRRI

International and inter‐institutional framework for regional International and inter‐institutional framework for regional cooperation in R4D (through cooperation in R4D (through shared shared experiences) addressing experiences) addressing specific cassava research needs (specific cassava research needs (Farmer‐Preferred Cassava Farmer‐Preferred Cassava Varieties Resistant to Pests and DiseasesVarieties Resistant to Pests and Diseases))

Sharing experiences, germplasm and informationSharing experiences, germplasm and information Breeding and molecular breeding methodologiesBreeding and molecular breeding methodologies Phenotyping protocolsPhenotyping protocols Molecular markersMolecular markers Research highlightsResearch highlights Data on biotic and abiotic stressesData on biotic and abiotic stresses Status on cassava productionStatus on cassava production Country research strengthsCountry research strengths Market informationMarket information Technical backstopping from Technical backstopping from

CoP members and IARCCoP members and IARC End-user informationEnd-user information Links to CoP membersLinks to CoP members Etc….Etc….

Breeder to breeder visitsBreeder to breeder visits

Elizabeth Parkes in Nigeria; evaluating for vigor

Tanzanian Breeder, Bernadetha Kimata discussing CBSD symptom expression in the field at NaCRRI, Namulonge, Uganda

Integration of marker-assisted breeding with field researchIntegration of marker-assisted breeding with field research

MAS for CMDMAS for CMD Screening for new sources of CMD resistanceScreening for new sources of CMD resistance Genetic mapping for CMD3 and early bulkingGenetic mapping for CMD3 and early bulking DiversityDiversity Dabodabo identified as a

potential new source of CMD resistance

WorkshopsWorkshops 2009 theme: field breeding strategies, breeding schemes, QTL 2009 theme: field breeding strategies, breeding schemes, QTL

mapping, and introduction to SNP platforms mapping, and introduction to SNP platforms UgandaUganda

TrainingTraining Damian Njoku (Nigeria)Damian Njoku (Nigeria) Bunmi Olasanmi (Nigeria)Bunmi Olasanmi (Nigeria) Esuma Williams (Tanzania)Esuma Williams (Tanzania) Bright Peprah (Ghana)Bright Peprah (Ghana)

Criteria for success of a CoPCriteria for success of a CoP

1)1) A good coordinator and leaderA good coordinator and leader2) A group of people that share an interest2) A group of people that share an interest3) 3) Access to the resources necessary to learn, practice and Access to the resources necessary to learn, practice and

make decisions that fully engage members’ capacitymake decisions that fully engage members’ capacity

1) Does the CoP approach seem adequate as a means to advance 1) Does the CoP approach seem adequate as a means to advance and sustain the MBP? If so, how?and sustain the MBP? If so, how?

2) What should the foundation of CoPs be: Crops? Regions? Other?2) What should the foundation of CoPs be: Crops? Regions? Other? 3) What size (number of members) of CoP has higher chances of 3) What size (number of members) of CoP has higher chances of

success?success? 4) What should the CoP offer: Resources?, Communication channels?, 4) What should the CoP offer: Resources?, Communication channels?,

Training?, Other? Training?, Other? 5) How can CoPs be sustained in the future?5) How can CoPs be sustained in the future?