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The Molecular Breeding Platform

Molecular Breeding Platform Services and Communities of Practice M Carmen de Vicente Capacity building and Enabling delivery Leader Hyderabad, India February 2010. The Molecular Breeding Platform. A project to develop and deploy

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The Molecular Breeding Platform

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  1. Molecular Breeding Platform Services and Communities of PracticeM Carmen de VicenteCapacity building and Enabling delivery LeaderHyderabad, IndiaFebruary 2010

  2. The Molecular Breeding Platform A project to develop and deploy a web-based one-stop shop functional and sustainable platform for information, analytical tools and related services to design and efficiently conduct molecular breeding

  3. The word “Platform” 1 : plan, design 2 : a declaration of the principles on which a group of persons stands; 3 a (2) : a device or structure incorporating or providing a platform; especially : such a structure on legs used for offshore drilling (as for oil) 3 b : a place or opportunity for public discussion 5 a : a vehicle used for a particular purpose or to carry a usually specified kind of equipment 5 b : operating system; also : the computer architecture and equipment using a particular operating system from Webster’s dictionary

  4. The word “Platform” • It is used in several different contexts, usually referring to some kind of standing surface used to support things, give them stability, or visibility: • … • … • Automobile platform, a set of components shared by several vehicle models • … • … from Wikipedia

  5. Why Services? The GCP commitment to maximize impact with its research and products (product delivery strategy) • Research must be relevant for the needs of resource poor farmers • Modus operandi must increase the chances that our products will reach the end-users The GCP ……. subscribes to a philosophy of creating useful products for real users ….. GCP will ensure that its products contribute to and result in end-products for farmers (GCP Delivery Strategy, Nov 2005)

  6. MBP Services • Breeding Services • To facilitate and speed up implementation • Advanced breeders • Support Services • Those that include some sort of capacity, guidance and training • 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

  7. Breeding Services • Genetic Resources Supply Service (GRSS) • Marker Services • Trait and Metabolite Services

  8. Genetic Resources Supply Service (GRSS) • A platform on its own • It provides germplasm for breeders’ activities • Value added germplasm (building on past SP1 work), i.e. validated and stable genetic stocks with high data quality standards • Service integrated in the global germplasm system Activity Leader: Jean Christophe Glaszmann

  9. Marker Services • A set of options for users to access marker service laboratories in the public and private sector with clear contractual conditions • Laboratories are selected on the basis of competitive cost, fit with quality control requirements and expeditious delivery • It builds on the experience accumulated by the Genotyping Support Service Activity Leader: Humberto Gómez

  10. Trait and Metabolite Services(drought tolerance) • Some secondary traits or metabolites provide valuable information to select phenotypes for breeding • Locally, these analyses can be very expensive • Itwilloffera catalogue of recommended laboratories and other facilities available to users upon request • to analyse and quantify metabolites and • to evaluate specific traits under controlled conditions Activity Leader: Xavier Delannay

  11. Support Services • Breeding Plan Development • Information Management • Data Curation • Design and Analysis • Phenotyping sites and protocols • Genotyping Support Service (GSS) • IP and policy helpdesk

  12. Breeding Plan Development • To determine the convenience and the consequences of embarking in a given molecular breeding project, activities must be detailed over time, and the costs and benefits must be known • This service provides support for the design of breeding pathways and workflows, depending on the crop and trait(s) • 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 or an analysis of the comparison with the conventional option Activity Leader: Xavier Delannay

  13. Eg. Marker-assisted Recurrent Selection Outline • Parental choice • Population development • Genotyping • Phenotyping • QTL analysis • Recombination cycles • Diagram

  14. Information Management • Within and across experiments, data management is essential for breeders to access and manage relevant pedigree, phenotypic and genotypic data • This service assists with installing and configuring the platform information system of breeding programs as well as for global crop improvement databases • It includes visits for on-site installation and configuration, training and a virtual helpdesk • Now exploring the potential for an Information/Data Managers community of practice Activity Leader: Arllet Portugal

  15. Data Curation • It assists with all issues related to the capture and curation of data in breeding projects, and to their integration in an adequate information system • Quality control • Training of and support to data managers and breeders • Training materials • Helpdesk and web-based collaboration and communication site with users Activity Leader: Arllet Portugal

  16. Design and Analysis 1) It includes training in data generation, handling, processing and interpretation, as well as experimental design from field planting to molecular breeding schemes • It provides assistance with the ‘translation’ of the genotypic and phenotypic data to the breeding context and it ensures that the methodology developed for design and analysis of breeding trials is rapidly available to the users 2) A Statistical Helpdesk that gives one-to-one support for statistical questions Activity Leader: Fred van Eeuwijk

  17. Design and Analysis 3) Courses: Time: Twice a year (April/ May, October/ November) Venue: Wageningen (the Netherlands) Content: • a one week course in basic statistics • a one week course in advanced statistics & statistical genetics Course participants can follow one or both courses, and can stay up to two more weeks to work on specific problems under supervision of WUR-Biometris staff • Plus, WUR-Biometris will teach one week course on demand

  18. Phenotyping sites and protocols • It gives access to information on phenotyping sites to ensure that selection is carried out under appropriate stress conditions, and that germplasm adaptation is well characterised • Ongoing investment plans to establish and enhance selected phenotyping facilities and expertise • It makes available the technical advice of crop-specific experts -- accuracy and relevance of the trait(s) to be measured, stress intensity needed and appropriate protocols Activity Leader: Xavier Delannay

  19. Genotyping Support Service (GSS) • Ongoing since 2006, this service provides financial and technical support for breeders in developing countries to access cost-efficient genotyping services worldwide, and supports training activities in experimental design and data analysis for diversity analyses and molecular breeding projects (MAS, and others) • To date, about 36 services have been provided, genotyping 8000+ samples of 12 crops to teams working in 14 countries. • Markers used: a majority of SSR, but also DArT and now SNP. • Many services have dealt with germplasm characterization, a few with marker-assisted breeding. Activity Leader: Humberto Gómez

  20. IP and policy helpdesk • Support on intellectual property rights and freedom to operate for biotechnology research and germplasm use • In particular, emerging issues to address needs of MBP users, e.g. germplasm exchange • It will link with the existing GCP IP Help Desk • A repository of resources • Help Line Activity Leader: Platform Manager

  21. Parallel discussion groupsFeb 19th • Genetic Resource Support Service • Marker Services • Phenotyping Services • Information Management • Design and Analysis

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

  23. Communities of Practice • “Groups of people who share a concern or a passion for something they do and learn how to do it better as they interact regularly” • CoP members have a commitment to the common interest, engage in joint activities and discussions, help each other, and share information. They interact and learn together. They build relationships that enable them to learn from each other. Members of a CoP are practitioners. They develop a shared repertoire of resources: experiences, stories, tools and ways of addressing recurring problems • It nurtures knowledge and promotes innovation

  24. The cassava CoP: an example(courtesy of E. Okogbenin) “A partnership for molecular breeding and product delivery in Africa” • Nigeria – NRCRI • Ghana – CRI • Tanzania – ARI • Uganda – NACRRI • International and inter‐institutional framework for regional cooperation in R4D (through shared experiences) addressing specific cassava research needs (Farmer‐Preferred Cassava Varieties Resistant to Pests and Diseases)

  25. Sharing experiences, germplasm and information • Breeding and molecular breeding methodologies • Phenotyping protocols • Molecular markers • Research highlights • Data on biotic and abiotic stresses • Status on cassava production • Country research strengths • Market information • Technical backstopping from CoP members and IARC • End-user information • Links to CoP members • Etc….

  26. Breeder 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

  27. Integration of marker-assisted breeding with field research • MAS for CMD • Screening for new sources of CMD resistance • Genetic mapping for CMD3 and early bulking • Diversity Dabodabo identified as a potential new source of CMD resistance

  28. Workshops • 2009 theme: field breeding strategies, breeding schemes, QTL mapping, and introduction to SNP platforms • Uganda Training • Damian Njoku (Nigeria) • Bunmi Olasanmi (Nigeria) • Esuma Williams (Tanzania) • Bright Peprah (Ghana)

  29. Criteria for success of a CoP 1) A good coordinator and leader 2) A group of people that share an interest 3) Access to the resources necessary to learn, practice and make decisions that fully engage members’ capacity

  30. CoP small group discussionFeb 17th 1) Does the CoP approach seem adequate as a means to advance and sustain the MBP? If so, how? 2) What should the foundation of CoPs be: Crops? Regions? Other? 3) What size (number of members) of CoP has higher chances of success? 4) What should the CoP offer: Resources?, Communication channels?, Training?, Other? 5) How can CoPs be sustained in the future?

  31. END

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