An initiative of the CGIAR Generation Challenge Programme (GCP) About the Integrated Breeding Platform General overview Presenter’s name Venue/name of event Date Photo credit: Neil Palmer/CIAT

IBP General Overview IBP Vision Overall objectives Target users Development approach

Rationale for the IBP  Large private seed companies have successfully implemented extensive suites of integrated informatics tools to turbocharge their breeding programmes  Implementation of this integrated informatics in public programmes lags behind, especially in developing countries Some tools have been developed at various CG centres, but implementation has been uneven and they are not integrated into a comprehensive system Most NARS programs still rely on rudimentary tools, from pen and paper to Excel spreadsheets Small SMEs in developing countries typically do not have the resources to acquire available commercial software or to implement breeding IT systems on their own Lack of availability of molecular services and of easy-to-use informatics systems for plant breeding, and lack of human capacity. IBP General Overview

Mission  Breeding programmes in developing countries use state-of-the-art, modern breeding tools and management processes that will increase agricultural productivity and enhance the livelihoods of smallholder farmers. IBP General Overview

Objectives  Overall objective To improve the efficiency of plant breeding programmes in developing countries by enabling plant breeders to access modern breeding technologies, breeding materials and related information in a centralised, integrated and practical manner. IBP General Overview

Objectives  Short term objective To increase the effectiveness and efficiency of plant breeding programmes in small and medium-sized breeding organisations by using an integrated, high- performing breeding management system that manages both phenotypic and/or genotypic data.  Long term objective To increase the effectiveness and efficiency of up to 500 plant breeding programmes across the world within the next five years, with specific focus in smallholder farmers in the developing world. IBP General Overview

Strategy  The IBP brokers access to affordable, quality breeding services and provides a user-friendly Breeding Management System, along with adequate support and capacity building for their adoption. IBP General Overview

Targeted users  Primary target: NARS partners wanting to enhance the effectiveness of their breeding programmes by integrating molecular methods and end-to-end informatics pipelines All interested CGIAR breeding programmes and networks SMEs working in developing countries, without the in- house capacity to build a breeding workflow system  Secondary target: Basically anyone running breeding activities Both the public and the private sectors IBP General Overview

Public-Private partnerships  Leafnode (formerly Efficio) Development of the middleware architecture and API Development and maintenance of all the code Data management: DB model and schema Support service for data transfer Moving to cloud computing IBP General Overview

Public-Private partnerships  VSNi Lead the awareness campaign for the Platform Develop and update our GoToMarket effort Business Plan Partner niche and collaboration with other commercial partners Commercial team IBP General Overview

Public-Private partnerships  Benefits Flexibility to adjust size and shape, based on demand Very reliable and clear M&E process Product and impact mindset and orientation IBP General Overview

IBP Solutions Software tools Breeding services and products Professional support

GIS Centralised Crop DB (CGIAR) Crop Ontology Crop info Local Pheno DB Breeding Services Geno/Pheno Genotyping DB BMS Predictive markers Crop Simple traits Generation Atlas Capacity Building eLearning Communities of Practice Social Network Forums: mutual problem solving Professional and Technical Support Service: Central team and Regional Hubs Protocols Access to Germplasm and Genetic resources IBP Core business Manuals Tutorials DM good practice policy DBBreeding informationServicesInfo/Knowledge Courses IBP: Components and Products

Breeding tools All available in one comprehensive package: the Breeding Management System (BMS)

Breeding Management System A suite of interconnected software tools and applications specifically designed to help breeders manage their day-to-day activities: Programme management Customise preferences and monitor programme activities from the Workbench, a dashboard application with integrated tools to manage and query crop information across the system Marker-assisted breeding Select germplasm and design crosses by complementing phenotypic selection with marker technology, for integrated breeding decisions Breeding activities Prepare trials and nurseries, manage seed inventories and keep continuous genealogy records season after season Statistical analysis Analyse field and lab data with powerful statistics and mixed model comparisons of locations and genotypes

BMS product concept  Simple and easy-to-use application containing all informatics tools needed by a breeder  Seamless flow of data between mutually-compatible applications  Accumulation, sharing and re-use of breeding data As at November 2014 twelve crop-specific databases with historical data: bean, cassava, chickpea, cowpea, groundnut, lentil, maize, pearl millet, rice, sorghum, soya bean and wheat Up next will be: barley, potato and sweet potato Empty DB available for all crops Phenotyping DB schema: Chado Natural Diversity Module  Targets routine breeding activities and will not replace research tools IBP General Overview

BMS product concept:  Will allow integration of users’ own tools into the system through a publicly accessible API  Implementable as a standalone system Access central and local DB, as well as the BMS on a local PC  Will also be implementable as a cloud-based system via iPlant Collaborative cyber-infrastructure For computationally intensive analyses or large data storage needs IBP General Overview Version 3.0 released in September 2014

BMS: THE core product of the IBP  Version 3 released September 31 st 2014  The production version for individual users IBP General Overview The Breeding Management System (BMS) Breeding Activities Parental selection Crossing Population development Germplasm Management Open Project Specify objectives Identify team Data resources Define strategy Project Planning Experimental Design Fieldbook production Data collection Data loading Germplasm Evaluation Marker selection Fingerprinting Genotyping Data loading Molecular Analysis Quality Assurance Trait analysis Genetic Analysis QTL Analysis Index Analysis Data Analysis Selected lines Recombines Recombination plans Breeding Decisions

Core applications IBP General Overview Programme & information management WorkBench (dashboard view) Study Browser Breeder Queries Ontology Manager (9 crops) Germplasm import tool Data import tool Breeding activities Germplasm List Manager Crossing Manager Nursery Manager, with Seed Inventory Trial Manager Integrated Breeding FieldBook Statistical analysis – Breeding View: Single-Site Analysis Multi-Site Analysis Multi-Year Multi-Site Analysis; Breeding View Standalone for QTL Quality assurance Marker-assisted breeding Integrated Breeding Planner Genotypic Data Management System (GDMS) QTL Analysis Tools Molecular Breeding Design Tool (MBDT) OptiMAS ​

Integrated Breeding Database  Genealogy Management System (GMS) Germplasm nomenclature, chronology, IP and passport data Pedigrees and breeding history  Phenotyping Data Management System (DMS) Germplasm characterization and evaluation data Annotated with Crop Research and Crop Trait Ontologies  Genotypic Data Management System (GDMS) Medium density fingerprinting data Genotyping data for MAS and MABC Genotyping data for Marker-trait association analysis Inter-operable API to link with other DB IBP General Overview

To be successful in enhancing plant-breeding efficiency in developing countries, we need to deliver much more than a simple analytical pipeline! IBP General Overview

Breeding services & products

 Services: The IBP website provides access to a network of partners and providers of quality breeding services at concessionary rates, including: Genotyping services at renowned laboratories; Trait and metabolite, drought phenotyping and other phenotyping services; Location analysis and climate resources online IBP General Overview

Breeding services & products  Services: Marker-assisted selection (MAS) can greatly shorten the time for developing and releasing new varieties. SNP markers have become the preferred markers for marker-assisted breeding but the access to them by developing-country breeders is very limited. Genotyping Support Service (GSS, established in 2007) supports first time users from developing country breeding programmes. IBP General Overview

Breeding services & products  Products: the IBP website provides knowledge, specialised information and genetic resources: Crop databases (phenotypic and genotypic) and query tools that can be linked to other specialised data sources, with standardised trait dictionaries for nine crops; A repertoire of publications by prominent scientists, researchers and breeders from around the world; Catalogue of diagnostic markers linked to target traits, and access to publicly available germplasm IBP General Overview

Communities and support

 The technology development part is the easiest part  Need for: Good support strategy that combines a centralised team for overall coordination, and a network of local hubs for daily operations Clear procedure: whom do I call or contact for what? Reliable, quick, local and adapted service to the user profile  Different users, different services: CB needs Breeding support Customisation of the tools and pipeline  Support service quality: a presentation card of the entire Platform  Poor support is a sure killer IBP General Overview

Communities and support  We believe that the dissemination of best practices in plant breeding is facilitated by bringing the right people together at the right time.  The IBP website provides access to: Educational material and educational activities to enrich the user’s professional development; Initial deployment assistance and continued technical support to help take on the Breeding Management System; Online communities to connect with peers, find assistance and share experiences. IBP General Overview

IBP General Overview IBP Delivery Regional hubs User tiers and pricing Change management

Delivery model  Regional hubs: champion IBP tools and services in their respective regions facilitate adoption by new users foster strong regional networks interact directly with local users to get feedback and inform them of new BMS functionalities consistent with their needs. IBP General Overview

Delivery model

Considering the nature of IBP and the very diverse potential users of the BMS, it is critical to provide a top-quality support services to ensure sustainable adoption. Regional hubs are designed to provide:  3 areas of Professional Support: 1.Client-oriented breeding support primarily targeting developing-country breeders 2.Capacity building support to provide professional and comprehensive training in orientation to, and using, the tools 3.Interaction with peers through social networks and CoPs  2 levels of Technical Support for all users: 1.Level 1 – installation technical support: to overcome any difficulties in downloading, installing and getting started with the BMS and related tools 2.Level 2 – operational technical support: for users that might encounter problems in day-to-day use of the BMS and related tools IBP General Overview

Central Support Team: Managers plus ad hoc specialists Promotion and commercialisation Team Users from Tier 2 C&S America African Asia (Europe, North America) DB/DM BMS CB Breeding Coordinate and facilitate access to IBP tools and services User Feedback to impact on BMS development and implementation

User tiers and pricing  The IBP initiative has a clear humanitarian purpose  But to offer a free analytical product without the corresponding support serves nobody  Different user tiers will access the BMS at different prices, with a customised support package, based on needs and resources  A basic package including the BMS and appropriate technical support will be offered to all customers Top tier: private sector in developed countries will pay full price Lower tiers: institutions in developing countries will access the BMS for free IBP General Overview

User tiers and pricing  The BMS will be offered under free licensing until December 2014  The objective is not to make the IBP entirely self- sustaining but the core business part may be sustainable by 2019  Key partner institutions will become stakeholders of the Platform IBP General Overview

Mission Priority Social Network CoPs BMS + Tech Support Courses Crop Support Crop Support Commercial Priority BMS Customisation BMS Customisation Professional Support Free for users from the public sector in developing counties Full price for users from the private sector Introduction /Functionalities Field Management Data Management Phenotyping Breeding Discount for users from the public sector in developed counties User tiers and pricing Price for private sector will be scalable in 4 dimensions: Economic: level of net income Activities: Usage of the different IBWS components Diversity: number of crops Size: number of people

Change management  Adoption Developing tools and technologies the easiest part Not-so-easy part: Users – it is about mind-sets, trust and cultural change Requires professional technical support But even more importantly, needs top-level buy-in to provide the means and Institutional support necessary for adoption  Data quality control New technology/DB alone not a silver bullet for data quality issues But… electronic data capture and good documentation will help QC/QA starts at the individual level IBP General Overview

Change management  Focus To serve the needs of a single breeder to those of a large breeding programme Providing for simple to very sophisticated breeding approaches  Defining appropriate business model for a public-good effort Managing perceptions and expectations (free not good….) Shift from participatory approach to PPP (service providers)  Perception What will happen after December 2014? Sustainable plan under development (donors/stakeholders) IBP General Overview

Change management  Changing behaviour is a real challenge: Most people are reluctant or resistant to change Even clear benefits from change are not sufficient incentive Most change can be implemented only by: Strong bottom-up demand Mandatory top-down decision Need to be ready to: Change the way you do business Dedicate time to learn new things Dedicate time to things that might not benefit your work directly Share results/methods in an open manner Adopt a corporative spirit Enforcement and implementation: big difference between the private and public sector IBP General Overview

IBP General Overview IBP Perspectives Looking ahead

 Access to suitable tools and analytical pipeline is not a key limitation anymore  Capacity in most target countries is increasing significantly Human capacity: fast progress Infrastructure: still slow  Major challenge remains in the area of adoption and support We must have the buy-in of upper management of user institutions Must apply a proactive promotion with kick-off meeting at user institutions Stepwise approach starting by populating the DB Support must be: reliable, quick, local and adapted to the user profile One size doesn’t fit all! IBP General Overview

Looking ahead  Time is right (and ripe!) to make a change: Major public investments The technology is ready Solid international networking (e.g. CRPs, Gates’ Initiatives, GCP) Open access policy adopted and implemented IBP General Overview

The BMS going forward…  Single user production version Version 3 of BMS released in September 2014, a single user application (central and local database model)  Multiple users production version Version 4 of BMS a LAN version (Q1 2015) for small group of breeders in one location with enhanced functionality (a single database model implementation)  Commercial version Version 5 of BMS (Q3 2015) full data synchronization and offline working capabilities. Roles and permissions implemented. Marker support targeted More details of functionality to come, clear user requirement mechanism in place, regular updates on our new IBP website IBP General Overview